From 0b1009641deea7a81a82794a029a666917cc8589 Mon Sep 17 00:00:00 2001 From: James Gilbert Date: Fri, 15 Nov 2024 19:28:53 +0000 Subject: [PATCH] Changed test files for updated output format --- .../bChlMac1_3-pretext-to-tpf.chr_report.csv | 79 + ..._3-pretext-to-tpf.hap1.chromsomes.list.csv | 38 + ..._3-pretext-to-tpf.hap2.chromsomes.list.csv | 36 + ...tpf => bChlMac1_3-pretext-to-tpf.hap2.tpf} | 240 +- ...> bChlMac1_3-pretext-to-tpf.haplotigs.tpf} | 0 .../bChlMac1_3/bChlMac1_3-pretext-to-tpf.log | 18 +- ...tpf => bchlmac1_3-pretext-to-tpf.hap1.tpf} | 280 +- tests/data/bChlMac1_3/chrs_Hap1.csv | 38 - tests/data/bChlMac1_3/chrs_Hap2.csv | 36 - tests/data/csSphGirg1_1_hr/chrs.csv | 21 - ...phGirg1_1_hr-pretext-to-tpf.chr_report.csv | 22 + ...g1_1_hr-pretext-to-tpf.chromsomes.list.csv | 21 + ...irg1_1_hr-pretext-to-tpf.contaminants.tpf} | 0 .../csSphGirg1_1_hr-pretext-to-tpf.log | 6 +- .../csSphGirg1_1_hr-pretext-to-tpf.tpf | 822 +- tests/data/eaAstIrre1/chrs.csv | 22 - .../eaAstIrre1-pretext-to-tpf.chr_report.csv | 23 + ...stIrre1-pretext-to-tpf.chromsomes.list.csv | 22 + ...aAstIrre1-pretext-to-tpf.contaminants.tpf} | 0 ...> eaAstIrre1-pretext-to-tpf.haplotigs.tpf} | 0 .../eaAstIrre1/eaAstIrre1-pretext-to-tpf.log | 8 +- .../eaAstIrre1/eaAstIrre1-pretext-to-tpf.tpf | 1580 ++-- tests/data/idDilFebr1/chrs.csv | 6 - .../idDilFebr1-pretext-to-tpf.chr_report.csv | 7 + ...ilFebr1-pretext-to-tpf.chromsomes.list.csv | 6 + ...> idDilFebr1-pretext-to-tpf.haplotigs.tpf} | 0 .../idDilFebr1/idDilFebr1-pretext-to-tpf.log | 8 +- .../idDilFebr1/idDilFebr1-pretext-to-tpf.tpf | 714 +- tests/data/idSyrVitr1/chrs.csv | 5 - .../idSyrVitr1-pretext-to-tpf.chr_report.csv | 6 + ...yrVitr1-pretext-to-tpf.chromsomes.list.csv | 5 + ...> idSyrVitr1-pretext-to-tpf.haplotigs.tpf} | 0 .../idSyrVitr1/idSyrVitr1-pretext-to-tpf.log | 12 +- .../idSyrVitr1/idSyrVitr1-pretext-to-tpf.tpf | 962 +-- tests/data/ilIthSala1_1/chrs_HAP1.csv | 40 - tests/data/ilIthSala1_1/chrs_HAP2.csv | 38 - ...ilIthSala1_1-pretext-to-tpf.chr_report.csv | 79 + ..._1-pretext-to-tpf.hap1.chromsomes.list.csv | 40 + ...f => ilIthSala1_1-pretext-to-tpf.hap1.tpf} | 346 +- ..._1-pretext-to-tpf.hap2.chromsomes.list.csv | 38 + ...f => ilIthSala1_1-pretext-to-tpf.hap2.tpf} | 416 +- ...ilIthSala1_1-pretext-to-tpf.haplotigs.tpf} | 0 .../ilIthSala1_1-pretext-to-tpf.log | 18 +- tests/data/iyExeIsch1/chrs.csv | 12 - .../iyExeIsch1-pretext-to-tpf.chr_report.csv | 13 + ...xeIsch1-pretext-to-tpf.chromsomes.list.csv | 12 + .../iyExeIsch1/iyExeIsch1-pretext-to-tpf.log | 4 +- .../iyExeIsch1/iyExeIsch1-pretext-to-tpf.tpf | 940 +-- tests/data/ngHelPoly1_1/chrs.csv | 6 - ...ngHelPoly1_1-pretext-to-tpf.chr_report.csv | 69 + ...Poly1_1-pretext-to-tpf.chromsomes.list.csv | 6 + ...ngHelPoly1_1-pretext-to-tpf.haplotigs.tpf} | 0 .../ngHelPoly1_1-pretext-to-tpf.log | 8 +- .../ngHelPoly1_1-pretext-to-tpf.tpf | 7058 ++++++++--------- tests/data/nxCaeSini1_1/chrs.csv | 6 - ...nxCaeSini1_1-pretext-to-tpf.chr_report.csv | 8 + ...Sini1_1-pretext-to-tpf.chromsomes.list.csv | 6 + ...nxCaeSini1_1-pretext-to-tpf.haplotigs.tpf} | 0 .../nxCaeSini1_1-pretext-to-tpf.log | 6 +- .../nxCaeSini1_1-pretext-to-tpf.tpf | 76 +- tests/data/nxCaeSpej1/chrs.csv | 6 - .../nxCaeSpej1-pretext-to-tpf.chr_report.csv | 7 + ...aeSpej1-pretext-to-tpf.chromsomes.list.csv | 6 + ...> nxCaeSpej1-pretext-to-tpf.haplotigs.tpf} | 0 .../nxCaeSpej1/nxCaeSpej1-pretext-to-tpf.log | 14 +- .../nxCaeSpej1/nxCaeSpej1-pretext-to-tpf.tpf | 42 +- 66 files changed, 7338 insertions(+), 7025 deletions(-) create mode 100644 tests/data/bChlMac1_3/bChlMac1_3-pretext-to-tpf.chr_report.csv create mode 100644 tests/data/bChlMac1_3/bChlMac1_3-pretext-to-tpf.hap1.chromsomes.list.csv create mode 100644 tests/data/bChlMac1_3/bChlMac1_3-pretext-to-tpf.hap2.chromsomes.list.csv rename tests/data/bChlMac1_3/{bChlMac1_3-pretext-to-tpf_Hap2.tpf => bChlMac1_3-pretext-to-tpf.hap2.tpf} (74%) rename tests/data/bChlMac1_3/{bChlMac1_3-pretext-to-tpf_Haplotigs.tpf => bChlMac1_3-pretext-to-tpf.haplotigs.tpf} (100%) rename tests/data/bChlMac1_3/{bChlMac1_3-pretext-to-tpf_Hap1.tpf => bchlmac1_3-pretext-to-tpf.hap1.tpf} (70%) delete mode 100644 tests/data/bChlMac1_3/chrs_Hap1.csv delete mode 100644 tests/data/bChlMac1_3/chrs_Hap2.csv delete mode 100644 tests/data/csSphGirg1_1_hr/chrs.csv create mode 100644 tests/data/csSphGirg1_1_hr/csSphGirg1_1_hr-pretext-to-tpf.chr_report.csv create mode 100644 tests/data/csSphGirg1_1_hr/csSphGirg1_1_hr-pretext-to-tpf.chromsomes.list.csv rename tests/data/csSphGirg1_1_hr/{csSphGirg1_1_hr-pretext-to-tpf_Contaminants.tpf => csSphGirg1_1_hr-pretext-to-tpf.contaminants.tpf} (100%) delete mode 100644 tests/data/eaAstIrre1/chrs.csv create mode 100644 tests/data/eaAstIrre1/eaAstIrre1-pretext-to-tpf.chr_report.csv create mode 100644 tests/data/eaAstIrre1/eaAstIrre1-pretext-to-tpf.chromsomes.list.csv rename tests/data/eaAstIrre1/{eaAstIrre1-pretext-to-tpf_Contaminants.tpf => eaAstIrre1-pretext-to-tpf.contaminants.tpf} (100%) rename tests/data/eaAstIrre1/{eaAstIrre1-pretext-to-tpf_Haplotigs.tpf => eaAstIrre1-pretext-to-tpf.haplotigs.tpf} (100%) delete mode 100644 tests/data/idDilFebr1/chrs.csv create mode 100644 tests/data/idDilFebr1/idDilFebr1-pretext-to-tpf.chr_report.csv create mode 100644 tests/data/idDilFebr1/idDilFebr1-pretext-to-tpf.chromsomes.list.csv rename tests/data/idDilFebr1/{idDilFebr1-pretext-to-tpf_Haplotigs.tpf => idDilFebr1-pretext-to-tpf.haplotigs.tpf} (100%) delete mode 100644 tests/data/idSyrVitr1/chrs.csv create mode 100644 tests/data/idSyrVitr1/idSyrVitr1-pretext-to-tpf.chr_report.csv create mode 100644 tests/data/idSyrVitr1/idSyrVitr1-pretext-to-tpf.chromsomes.list.csv rename tests/data/idSyrVitr1/{idSyrVitr1-pretext-to-tpf_Haplotigs.tpf => idSyrVitr1-pretext-to-tpf.haplotigs.tpf} (100%) delete mode 100644 tests/data/ilIthSala1_1/chrs_HAP1.csv delete mode 100644 tests/data/ilIthSala1_1/chrs_HAP2.csv create mode 100644 tests/data/ilIthSala1_1/ilIthSala1_1-pretext-to-tpf.chr_report.csv create mode 100644 tests/data/ilIthSala1_1/ilIthSala1_1-pretext-to-tpf.hap1.chromsomes.list.csv rename tests/data/ilIthSala1_1/{ilIthSala1_1-pretext-to-tpf_HAP1.tpf => ilIthSala1_1-pretext-to-tpf.hap1.tpf} (84%) create mode 100644 tests/data/ilIthSala1_1/ilIthSala1_1-pretext-to-tpf.hap2.chromsomes.list.csv rename tests/data/ilIthSala1_1/{ilIthSala1_1-pretext-to-tpf_HAP2.tpf => ilIthSala1_1-pretext-to-tpf.hap2.tpf} (85%) rename tests/data/ilIthSala1_1/{ilIthSala1_1-pretext-to-tpf_Haplotigs.tpf => ilIthSala1_1-pretext-to-tpf.haplotigs.tpf} (100%) delete mode 100644 tests/data/iyExeIsch1/chrs.csv create mode 100644 tests/data/iyExeIsch1/iyExeIsch1-pretext-to-tpf.chr_report.csv create mode 100644 tests/data/iyExeIsch1/iyExeIsch1-pretext-to-tpf.chromsomes.list.csv delete mode 100644 tests/data/ngHelPoly1_1/chrs.csv create mode 100644 tests/data/ngHelPoly1_1/ngHelPoly1_1-pretext-to-tpf.chr_report.csv create mode 100644 tests/data/ngHelPoly1_1/ngHelPoly1_1-pretext-to-tpf.chromsomes.list.csv rename tests/data/ngHelPoly1_1/{ngHelPoly1_1-pretext-to-tpf_Haplotigs.tpf => ngHelPoly1_1-pretext-to-tpf.haplotigs.tpf} (100%) delete mode 100644 tests/data/nxCaeSini1_1/chrs.csv create mode 100644 tests/data/nxCaeSini1_1/nxCaeSini1_1-pretext-to-tpf.chr_report.csv create mode 100644 tests/data/nxCaeSini1_1/nxCaeSini1_1-pretext-to-tpf.chromsomes.list.csv rename tests/data/nxCaeSini1_1/{nxCaeSini1_1-pretext-to-tpf_Haplotigs.tpf => nxCaeSini1_1-pretext-to-tpf.haplotigs.tpf} (100%) delete mode 100644 tests/data/nxCaeSpej1/chrs.csv create mode 100644 tests/data/nxCaeSpej1/nxCaeSpej1-pretext-to-tpf.chr_report.csv create mode 100644 tests/data/nxCaeSpej1/nxCaeSpej1-pretext-to-tpf.chromsomes.list.csv rename tests/data/nxCaeSpej1/{nxCaeSpej1-pretext-to-tpf_Haplotigs.tpf => nxCaeSpej1-pretext-to-tpf.haplotigs.tpf} (100%) diff --git a/tests/data/bChlMac1_3/bChlMac1_3-pretext-to-tpf.chr_report.csv b/tests/data/bChlMac1_3/bChlMac1_3-pretext-to-tpf.chr_report.csv new file mode 100644 index 0000000..577da75 --- /dev/null +++ b/tests/data/bChlMac1_3/bChlMac1_3-pretext-to-tpf.chr_report.csv @@ -0,0 +1,79 @@ +assembly,seq_name,chr_name,localised,pretext_scaffold,length,length_minus_gaps +Hap1,SUPER_1,1,true,Scaffold_1,215693158,215692358 +Hap1,SUPER_2,2,true,Scaffold_3,164294231,164293231 +Hap1,SUPER_3,3,true,Scaffold_5,128056697,128055897 +Hap1,SUPER_4,4,true,Scaffold_9,84623986,84623186 +Hap1,SUPER_5,5,true,Scaffold_11,72825560,72824760 +Hap1,SUPER_6,6,true,Scaffold_13,45742398,45741398 +Hap1,SUPER_7,7,true,Scaffold_15,40665136,40664736 +Hap1,SUPER_8,8,true,Scaffold_17,38754472,38754272 +Hap1,SUPER_9,9,true,Scaffold_19,28029218,28028818 +Hap1,SUPER_9_unloc_1,9,false,Scaffold_19,153243,153243 +Hap1,SUPER_9_unloc_2,9,false,Scaffold_19,144510,144510 +Hap1,SUPER_10,10,true,Scaffold_21,23764681,23764681 +Hap1,SUPER_11,11,true,Scaffold_25,23436253,23436253 +Hap1,SUPER_12,12,true,Scaffold_23,23395923,23395923 +Hap1,SUPER_13,13,true,Scaffold_27,22304326,22304326 +Hap1,SUPER_14,14,true,Scaffold_29,20896716,20896716 +Hap1,SUPER_15,15,true,Scaffold_31,18299171,18299171 +Hap1,SUPER_16,16,true,Scaffold_33,16860029,16859829 +Hap1,SUPER_17,17,true,Scaffold_35,16261461,16261461 +Hap1,SUPER_18,18,true,Scaffold_37,14078390,14077990 +Hap1,SUPER_19,19,true,Scaffold_39,12962427,12962027 +Hap1,SUPER_20,20,true,Scaffold_41,12646375,12645975 +Hap1,SUPER_21,21,true,Scaffold_43,9813053,9812653 +Hap1,SUPER_22,22,true,Scaffold_57,8409327,8408927 +Hap1,SUPER_23,23,true,Scaffold_47,7515650,7515250 +Hap1,SUPER_24,24,true,Scaffold_45,7396006,7396006 +Hap1,SUPER_25,25,true,Scaffold_49,6865239,6865039 +Hap1,SUPER_26,26,true,Scaffold_59,6446260,6446060 +Hap1,SUPER_27,27,true,Scaffold_51,6239360,6238360 +Hap1,SUPER_28,28,true,Scaffold_53,3290335,3289335 +Hap1,SUPER_29,29,true,Scaffold_55,2992603,2991203 +Hap1,SUPER_30,30,true,Scaffold_61,990997,990197 +Hap1,SUPER_31,31,true,Scaffold_69,629270,628670 +Hap1,SUPER_32,32,true,Scaffold_65,434314,434314 +Hap1,SUPER_33,33,true,Scaffold_63,383818,383418 +Hap1,SUPER_34,34,true,Scaffold_73,303736,303536 +Hap1,SUPER_35,35,true,Scaffold_71,294221,293821 +Hap1,SUPER_36,36,true,Scaffold_67,292585,292585 +Hap1,SUPER_W,W,true,Scaffold_8,54811411,54806811 +Hap1,SUPER_Z,Z,true,Scaffold_7,84787522,84787122 +Hap2,SUPER_1,1,true,Scaffold_2,214589255,214587655 +Hap2,SUPER_2,2,true,Scaffold_4,165124570,165123770 +Hap2,SUPER_3,3,true,Scaffold_6,112879342,112878342 +Hap2,SUPER_4,4,true,Scaffold_10,84298225,84297625 +Hap2,SUPER_5,5,true,Scaffold_12,73172226,73171626 +Hap2,SUPER_6,6,true,Scaffold_14,47945211,47945011 +Hap2,SUPER_7,7,true,Scaffold_16,40868638,40868438 +Hap2,SUPER_8,8,true,Scaffold_18,39015622,39015022 +Hap2,SUPER_9,9,true,Scaffold_20,28481021,28480621 +Hap2,SUPER_9_unloc_1,9,false,Scaffold_20,222322,222322 +Hap2,SUPER_9_unloc_2,9,false,Scaffold_20,111597,111597 +Hap2,SUPER_10,10,true,Scaffold_22,21279146,21278746 +Hap2,SUPER_11,11,true,Scaffold_26,21552742,21552542 +Hap2,SUPER_12,12,true,Scaffold_24,23436807,23436807 +Hap2,SUPER_13,13,true,Scaffold_28,21315647,21315447 +Hap2,SUPER_14,14,true,Scaffold_30,20945612,20945612 +Hap2,SUPER_15,15,true,Scaffold_32,18271594,18271194 +Hap2,SUPER_16,16,true,Scaffold_34,16898778,16898578 +Hap2,SUPER_17,17,true,Scaffold_36,16235962,16235962 +Hap2,SUPER_18,18,true,Scaffold_38,10366566,10366366 +Hap2,SUPER_19,19,true,Scaffold_40,10650489,10650089 +Hap2,SUPER_20,20,true,Scaffold_42,10710084,10709684 +Hap2,SUPER_21,21,true,Scaffold_44,8199818,8199218 +Hap2,SUPER_22,22,true,Scaffold_58,3792372,3791972 +Hap2,SUPER_23,23,true,Scaffold_48,7492395,7492195 +Hap2,SUPER_24,24,true,Scaffold_46,7700939,7700939 +Hap2,SUPER_25,25,true,Scaffold_50,6839605,6839405 +Hap2,SUPER_26,26,true,Scaffold_60,6141571,6140971 +Hap2,SUPER_27,27,true,Scaffold_52,5928255,5927255 +Hap2,SUPER_28,28,true,Scaffold_54,3315814,3314814 +Hap2,SUPER_29,29,true,Scaffold_56,2810891,2809291 +Hap2,SUPER_30,30,true,Scaffold_62,997064,996064 +Hap2,SUPER_31,31,true,Scaffold_70,707255,706255 +Hap2,SUPER_32,32,true,Scaffold_66,419859,419859 +Hap2,SUPER_33,33,true,Scaffold_64,301782,301782 +Hap2,SUPER_34,34,true,Scaffold_74,188044,188044 +Hap2,SUPER_35,35,true,Scaffold_72,386587,386387 +Hap2,SUPER_36,36,true,Scaffold_68,304097,303897 diff --git a/tests/data/bChlMac1_3/bChlMac1_3-pretext-to-tpf.hap1.chromsomes.list.csv b/tests/data/bChlMac1_3/bChlMac1_3-pretext-to-tpf.hap1.chromsomes.list.csv new file mode 100644 index 0000000..4ce4445 --- /dev/null +++ b/tests/data/bChlMac1_3/bChlMac1_3-pretext-to-tpf.hap1.chromsomes.list.csv @@ -0,0 +1,38 @@ +SUPER_1 +SUPER_2 +SUPER_3 +SUPER_4 +SUPER_5 +SUPER_6 +SUPER_7 +SUPER_8 +SUPER_9,SUPER_9_unloc_1,SUPER_9_unloc_2 +SUPER_10 +SUPER_11 +SUPER_12 +SUPER_13 +SUPER_14 +SUPER_15 +SUPER_16 +SUPER_17 +SUPER_18 +SUPER_19 +SUPER_20 +SUPER_21 +SUPER_22 +SUPER_23 +SUPER_24 +SUPER_25 +SUPER_26 +SUPER_27 +SUPER_28 +SUPER_29 +SUPER_30 +SUPER_31 +SUPER_32 +SUPER_33 +SUPER_34 +SUPER_35 +SUPER_36 +SUPER_W +SUPER_Z diff --git a/tests/data/bChlMac1_3/bChlMac1_3-pretext-to-tpf.hap2.chromsomes.list.csv b/tests/data/bChlMac1_3/bChlMac1_3-pretext-to-tpf.hap2.chromsomes.list.csv new file mode 100644 index 0000000..31f026e --- /dev/null +++ b/tests/data/bChlMac1_3/bChlMac1_3-pretext-to-tpf.hap2.chromsomes.list.csv @@ -0,0 +1,36 @@ +SUPER_1 +SUPER_2 +SUPER_3 +SUPER_4 +SUPER_5 +SUPER_6 +SUPER_7 +SUPER_8 +SUPER_9,SUPER_9_unloc_1,SUPER_9_unloc_2 +SUPER_10 +SUPER_11 +SUPER_12 +SUPER_13 +SUPER_14 +SUPER_15 +SUPER_16 +SUPER_17 +SUPER_18 +SUPER_19 +SUPER_20 +SUPER_21 +SUPER_22 +SUPER_23 +SUPER_24 +SUPER_25 +SUPER_26 +SUPER_27 +SUPER_28 +SUPER_29 +SUPER_30 +SUPER_31 +SUPER_32 +SUPER_33 +SUPER_34 +SUPER_35 +SUPER_36 diff --git a/tests/data/bChlMac1_3/bChlMac1_3-pretext-to-tpf_Hap2.tpf b/tests/data/bChlMac1_3/bChlMac1_3-pretext-to-tpf.hap2.tpf similarity index 74% rename from tests/data/bChlMac1_3/bChlMac1_3-pretext-to-tpf_Hap2.tpf rename to tests/data/bChlMac1_3/bChlMac1_3-pretext-to-tpf.hap2.tpf index 026462c..08792e5 100644 --- a/tests/data/bChlMac1_3/bChlMac1_3-pretext-to-tpf_Hap2.tpf +++ b/tests/data/bChlMac1_3/bChlMac1_3-pretext-to-tpf.hap2.tpf @@ -1,205 +1,205 @@ -? HAP2_SCAFFOLD_342:1-972266 RL_2 PLUS +? HAP2_SCAFFOLD_342:1-972266 SUPER_1 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_342:972467-48535341 RL_2 PLUS +? HAP2_SCAFFOLD_342:972467-48535341 SUPER_1 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_342:48535542-57617924 RL_2 PLUS +? HAP2_SCAFFOLD_342:48535542-57617924 SUPER_1 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_342:57618125-82836822 RL_2 PLUS +? HAP2_SCAFFOLD_342:57618125-82836822 SUPER_1 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_342:82837023-197897256 RL_2 PLUS +? HAP2_SCAFFOLD_342:82837023-197897256 SUPER_1 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_342:197897457-212435454 RL_2 PLUS +? HAP2_SCAFFOLD_342:197897457-212435454 SUPER_1 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_342:212435655-212973692 RL_2 PLUS +? HAP2_SCAFFOLD_342:212435655-212973692 SUPER_1 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_342:212973893-213938046 RL_2 PLUS +? HAP2_SCAFFOLD_342:212973893-213938046 SUPER_1 PLUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_183:1-651009 RL_2 PLUS -? HAP2_SCAFFOLD_242:163363399-164170947 RL_4 MINUS +? HAP1_SCAFFOLD_183:1-651009 SUPER_1 PLUS +? HAP2_SCAFFOLD_242:163363399-164170947 SUPER_2 MINUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_242:1-163363198 RL_4 MINUS +? HAP2_SCAFFOLD_242:1-163363198 SUPER_2 MINUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_253:1-303979 RL_4 PLUS +? HAP2_SCAFFOLD_253:1-303979 SUPER_2 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_253:304180-876025 RL_4 PLUS +? HAP2_SCAFFOLD_253:304180-876025 SUPER_2 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_253:876226-953423 RL_4 PLUS -? HAP2_SCAFFOLD_241:111683547-112928050 RL_6 MINUS +? HAP2_SCAFFOLD_253:876226-953423 SUPER_2 PLUS +? HAP2_SCAFFOLD_241:111683547-112928050 SUPER_3 MINUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_241:111172258-111683346 RL_6 MINUS +? HAP2_SCAFFOLD_241:111172258-111683346 SUPER_3 MINUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_241:20404326-111172057 RL_6 MINUS +? HAP2_SCAFFOLD_241:20404326-111172057 SUPER_3 MINUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_241:11938377-20404125 RL_6 PLUS +? HAP2_SCAFFOLD_241:11938377-20404125 SUPER_3 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_241:1-2352127 RL_6 PLUS +? HAP2_SCAFFOLD_241:1-2352127 SUPER_3 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_241:2352328-11889468 RL_6 MINUS -? HAP2_SCAFFOLD_239:1-58030883 RL_10 PLUS +? HAP2_SCAFFOLD_241:2352328-11889468 SUPER_3 MINUS +? HAP2_SCAFFOLD_239:1-58030883 SUPER_4 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_239:58031084-83579430 RL_10 PLUS +? HAP2_SCAFFOLD_239:58031084-83579430 SUPER_4 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_246:1-299280 RL_10 PLUS +? HAP2_SCAFFOLD_246:1-299280 SUPER_4 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_246:299481-718595 RL_10 PLUS -? HAP2_SCAFFOLD_238:13904811-73172226 RL_12 MINUS +? HAP2_SCAFFOLD_246:299481-718595 SUPER_4 PLUS +? HAP2_SCAFFOLD_238:13904811-73172226 SUPER_5 MINUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_238:2292545-13904610 RL_12 MINUS +? HAP2_SCAFFOLD_238:2292545-13904610 SUPER_5 MINUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_238:2139240-2292344 RL_12 MINUS +? HAP2_SCAFFOLD_238:2139240-2292344 SUPER_5 MINUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_238:1-2139039 RL_12 MINUS -? HAP2_SCAFFOLD_237:18860975-47945211 RL_14 MINUS +? HAP2_SCAFFOLD_238:1-2139039 SUPER_5 MINUS +? HAP2_SCAFFOLD_237:18860975-47945211 SUPER_6 MINUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_237:1-18860774 RL_14 MINUS -? HAP2_SCAFFOLD_236:1-17663398 RL_16 PLUS +? HAP2_SCAFFOLD_237:1-18860774 SUPER_6 MINUS +? HAP2_SCAFFOLD_236:1-17663398 SUPER_7 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_236:17663599-40868638 RL_16 PLUS -? HAP2_SCAFFOLD_235:1-22587767 RL_18 PLUS +? HAP2_SCAFFOLD_236:17663599-40868638 SUPER_7 PLUS +? HAP2_SCAFFOLD_235:1-22587767 SUPER_8 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_235:22587968-34578638 RL_18 PLUS +? HAP2_SCAFFOLD_235:22587968-34578638 SUPER_8 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_235:34578839-34992858 RL_18 PLUS +? HAP2_SCAFFOLD_235:34578839-34992858 SUPER_8 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_235:34993059-39015622 RL_18 PLUS -? HAP2_SCAFFOLD_234:25446100-28481021 RL_20 MINUS +? HAP2_SCAFFOLD_235:34993059-39015622 SUPER_8 PLUS +? HAP2_SCAFFOLD_234:25446100-28481021 SUPER_9 MINUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_234:19492443-25445899 RL_20 MINUS +? HAP2_SCAFFOLD_234:19492443-25445899 SUPER_9 MINUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_234:1-19492242 RL_20 MINUS -? HAP2_SCAFFOLD_323:1-222322 RL_20_unloc_1 MINUS -? HAP2_SCAFFOLD_71:1-111597 RL_20_unloc_2 MINUS -? HAP2_SCAFFOLD_231:16669716-21279146 RL_22 PLUS +? HAP2_SCAFFOLD_234:1-19492242 SUPER_9 MINUS +? HAP2_SCAFFOLD_323:1-222322 SUPER_9_unloc_1 MINUS +? HAP2_SCAFFOLD_71:1-111597 SUPER_9_unloc_2 MINUS +? HAP2_SCAFFOLD_231:16669716-21279146 SUPER_10 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_231:13243127-16669515 RL_22 MINUS +? HAP2_SCAFFOLD_231:13243127-16669515 SUPER_10 MINUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_231:1-13242926 RL_22 MINUS -? HAP2_SCAFFOLD_233:1-23436807 RL_24 MINUS -? HAP2_SCAFFOLD_229:1-20194798 RL_26 PLUS +? HAP2_SCAFFOLD_231:1-13242926 SUPER_10 MINUS +? HAP2_SCAFFOLD_229:1-20194798 SUPER_11 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_257:1-1357744 RL_26 PLUS -? HAP2_SCAFFOLD_221:20130048-21315647 RL_28 MINUS +? HAP2_SCAFFOLD_257:1-1357744 SUPER_11 PLUS +? HAP2_SCAFFOLD_233:1-23436807 SUPER_12 MINUS +? HAP2_SCAFFOLD_221:20130048-21315647 SUPER_13 MINUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_221:1-20129847 RL_28 MINUS -? HAP2_SCAFFOLD_230:1-20945612 RL_30 PLUS -? HAP1_SCAFFOLD_217:1-11760085 RL_32 PLUS +? HAP2_SCAFFOLD_221:1-20129847 SUPER_13 MINUS +? HAP2_SCAFFOLD_230:1-20945612 SUPER_14 PLUS +? HAP1_SCAFFOLD_217:1-11760085 SUPER_15 PLUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_217:11760286-13340281 RL_32 PLUS +? HAP1_SCAFFOLD_217:11760286-13340281 SUPER_15 PLUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_217:13340482-18271594 RL_32 PLUS -? HAP2_SCAFFOLD_227:1-1495688 RL_34 PLUS +? HAP1_SCAFFOLD_217:13340482-18271594 SUPER_15 PLUS +? HAP2_SCAFFOLD_227:1-1495688 SUPER_16 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_227:1495889-16898778 RL_34 PLUS -? HAP2_SCAFFOLD_226:1-16235962 RL_36 MINUS -? HAP2_SCAFFOLD_222:683436-10366566 RL_38 MINUS +? HAP2_SCAFFOLD_227:1495889-16898778 SUPER_16 PLUS +? HAP2_SCAFFOLD_226:1-16235962 SUPER_17 MINUS +? HAP2_SCAFFOLD_222:683436-10366566 SUPER_18 MINUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_222:1-683235 RL_38 MINUS -? HAP2_SCAFFOLD_223:1-5312328 RL_40 PLUS +? HAP2_SCAFFOLD_222:1-683235 SUPER_18 MINUS +? HAP2_SCAFFOLD_223:1-5312328 SUPER_19 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_223:5312529-7076579 RL_40 PLUS +? HAP2_SCAFFOLD_223:5312529-7076579 SUPER_19 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_223:7076780-10650489 RL_40 PLUS -? HAP2_SCAFFOLD_224:1-595419 RL_42 PLUS +? HAP2_SCAFFOLD_223:7076780-10650489 SUPER_19 PLUS +? HAP2_SCAFFOLD_224:1-595419 SUPER_20 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_224:595620-9916590 RL_42 PLUS +? HAP2_SCAFFOLD_224:595620-9916590 SUPER_20 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_224:9916791-10710084 RL_42 PLUS -? HAP2_SCAFFOLD_232:4082936-8199818 RL_44 MINUS +? HAP2_SCAFFOLD_224:9916791-10710084 SUPER_20 PLUS +? HAP2_SCAFFOLD_232:4082936-8199818 SUPER_21 MINUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_232:1866049-4082735 RL_44 MINUS +? HAP2_SCAFFOLD_232:1866049-4082735 SUPER_21 MINUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_232:937848-1865848 RL_44 MINUS +? HAP2_SCAFFOLD_232:937848-1865848 SUPER_21 MINUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_232:1-937647 RL_44 MINUS -? HAP2_SCAFFOLD_264:1-7700939 RL_46 PLUS -? HAP2_SCAFFOLD_263:6462850-7492395 RL_48 MINUS +? HAP2_SCAFFOLD_232:1-937647 SUPER_21 MINUS +? HAP2_SCAFFOLD_259:1-515230 SUPER_22 MINUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_263:1-6462649 RL_48 MINUS -? HAP2_SCAFFOLD_262:5760615-6839605 RL_50 MINUS +? HAP2_SCAFFOLD_259:515431-1782634 SUPER_22 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_262:1-5760414 RL_50 MINUS -? HAP2_SCAFFOLD_225:1-4498636 RL_52 PLUS +? HAP2_SCAFFOLD_259:1782835-3792372 SUPER_22 PLUS +? HAP2_SCAFFOLD_263:6462850-7492395 SUPER_23 MINUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_225:4498837-4742499 RL_52 PLUS +? HAP2_SCAFFOLD_263:1-6462649 SUPER_23 MINUS +? HAP2_SCAFFOLD_264:1-7700939 SUPER_24 PLUS +? HAP2_SCAFFOLD_262:5760615-6839605 SUPER_25 MINUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_225:4742700-5016211 RL_52 PLUS +? HAP2_SCAFFOLD_262:1-5760414 SUPER_25 MINUS +? HAP2_SCAFFOLD_260:1-949231 SUPER_26 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_225:5016412-5215731 RL_52 PLUS +? HAP2_SCAFFOLD_260:949432-5478110 SUPER_26 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_225:5215932-5382760 RL_52 PLUS +? HAP2_SCAFFOLD_260:5478311-6074542 SUPER_26 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_225:5382961-5928255 RL_52 PLUS -? HAP2_SCAFFOLD_225:5928456-6525115 RL_54 PLUS +? HAP2_SCAFFOLD_260:6074743-6141571 SUPER_26 PLUS +? HAP2_SCAFFOLD_225:1-4498636 SUPER_27 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_225:6525316-7609970 RL_54 PLUS +? HAP2_SCAFFOLD_225:4498837-4742499 SUPER_27 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_225:7610171-7655236 RL_54 PLUS +? HAP2_SCAFFOLD_225:4742700-5016211 SUPER_27 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_225:7655437-7898796 RL_54 PLUS +? HAP2_SCAFFOLD_225:5016412-5215731 SUPER_27 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_225:7898997-8129467 RL_54 PLUS +? HAP2_SCAFFOLD_225:5215932-5382760 SUPER_27 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_225:8129668-9244269 RL_54 PLUS -? HAP2_SCAFFOLD_225:11281872-12055360 RL_56 MINUS +? HAP2_SCAFFOLD_225:5382961-5928255 SUPER_27 PLUS +? HAP2_SCAFFOLD_225:5928456-6525115 SUPER_28 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_225:11160053-11281671 RL_56 MINUS +? HAP2_SCAFFOLD_225:6525316-7609970 SUPER_28 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_225:10942965-11159852 RL_56 MINUS +? HAP2_SCAFFOLD_225:7610171-7655236 SUPER_28 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_225:10175645-10942764 RL_56 MINUS +? HAP2_SCAFFOLD_225:7655437-7898796 SUPER_28 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_225:10042991-10175444 RL_56 MINUS +? HAP2_SCAFFOLD_225:7898997-8129467 SUPER_28 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_225:9857957-10042790 RL_56 MINUS +? HAP2_SCAFFOLD_225:8129668-9244269 SUPER_28 PLUS +? HAP2_SCAFFOLD_225:11281872-12055360 SUPER_29 MINUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_225:9741965-9857756 RL_56 MINUS +? HAP2_SCAFFOLD_225:11160053-11281671 SUPER_29 MINUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_225:9659272-9741764 RL_56 MINUS +? HAP2_SCAFFOLD_225:10942965-11159852 SUPER_29 MINUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_225:9244470-9659071 RL_56 MINUS -? HAP2_SCAFFOLD_259:1-515230 RL_58 MINUS +? HAP2_SCAFFOLD_225:10175645-10942764 SUPER_29 MINUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_259:515431-1782634 RL_58 PLUS +? HAP2_SCAFFOLD_225:10042991-10175444 SUPER_29 MINUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_259:1782835-3792372 RL_58 PLUS -? HAP2_SCAFFOLD_260:1-949231 RL_60 PLUS +? HAP2_SCAFFOLD_225:9857957-10042790 SUPER_29 MINUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_260:949432-5478110 RL_60 PLUS +? HAP2_SCAFFOLD_225:9741965-9857756 SUPER_29 MINUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_260:5478311-6074542 RL_60 PLUS +? HAP2_SCAFFOLD_225:9659272-9741764 SUPER_29 MINUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_260:6074743-6141571 RL_60 PLUS -? HAP2_SCAFFOLD_196:338193-525955 RL_62 MINUS +? HAP2_SCAFFOLD_225:9244470-9659071 SUPER_29 MINUS +? HAP2_SCAFFOLD_196:338193-525955 SUPER_30 MINUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_196:1-337992 RL_62 MINUS +? HAP2_SCAFFOLD_196:1-337992 SUPER_30 MINUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_177:345565-392745 RL_62 MINUS +? HAP2_SCAFFOLD_177:345565-392745 SUPER_30 MINUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_177:238939-345364 RL_62 MINUS +? HAP2_SCAFFOLD_177:238939-345364 SUPER_30 MINUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_177:1-238738 RL_62 MINUS +? HAP2_SCAFFOLD_177:1-238738 SUPER_30 MINUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_33:1-77964 RL_62 PLUS -? HAP2_SCAFFOLD_188:1-301782 RL_64 MINUS -? HAP2_SCAFFOLD_247:304298-724156 RL_66 MINUS -? HAP2_SCAFFOLD_247:1-274960 RL_68 PLUS +? HAP2_SCAFFOLD_33:1-77964 SUPER_30 PLUS +? HAP2_SCAFFOLD_351:1-201934 SUPER_31 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_247:275161-304097 RL_68 PLUS -? HAP2_SCAFFOLD_351:1-201934 RL_70 PLUS +? HAP2_SCAFFOLD_321:1-156027 SUPER_31 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_321:1-156027 RL_70 PLUS +? HAP2_SCAFFOLD_321:156228-221232 SUPER_31 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_321:156228-221232 RL_70 PLUS +? HAP2_SCAFFOLD_9:1-46078 SUPER_31 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_9:1-46078 RL_70 PLUS +? HAP2_SCAFFOLD_9:46279-92793 SUPER_31 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_9:46279-92793 RL_70 PLUS +? HAP2_SCAFFOLD_338:1-190696 SUPER_31 MINUS +? HAP2_SCAFFOLD_247:304298-724156 SUPER_32 MINUS +? HAP2_SCAFFOLD_188:1-301782 SUPER_33 MINUS +? HAP2_SCAFFOLD_336:1-188044 SUPER_34 PLUS +? HAP2_SCAFFOLD_294:1-150790 SUPER_35 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_338:1-190696 RL_70 MINUS -? HAP2_SCAFFOLD_294:1-150790 RL_72 PLUS +? HAP2_SCAFFOLD_330:1-235597 SUPER_35 PLUS +? HAP2_SCAFFOLD_247:1-274960 SUPER_36 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_330:1-235597 RL_72 PLUS -? HAP2_SCAFFOLD_336:1-188044 RL_74 PLUS +? HAP2_SCAFFOLD_247:275161-304097 SUPER_36 PLUS ? HAP2_SCAFFOLD_1:1-95628 HAP2_SCAFFOLD_1 PLUS ? HAP2_SCAFFOLD_2:1-86959 HAP2_SCAFFOLD_2 PLUS ? HAP2_SCAFFOLD_3:1-88319 HAP2_SCAFFOLD_3 PLUS diff --git a/tests/data/bChlMac1_3/bChlMac1_3-pretext-to-tpf_Haplotigs.tpf b/tests/data/bChlMac1_3/bChlMac1_3-pretext-to-tpf.haplotigs.tpf similarity index 100% rename from tests/data/bChlMac1_3/bChlMac1_3-pretext-to-tpf_Haplotigs.tpf rename to tests/data/bChlMac1_3/bChlMac1_3-pretext-to-tpf.haplotigs.tpf diff --git a/tests/data/bChlMac1_3/bChlMac1_3-pretext-to-tpf.log b/tests/data/bChlMac1_3/bChlMac1_3-pretext-to-tpf.log index 2031432..f41fc48 100644 --- a/tests/data/bChlMac1_3/bChlMac1_3-pretext-to-tpf.log +++ b/tests/data/bChlMac1_3/bChlMac1_3-pretext-to-tpf.log @@ -7,18 +7,18 @@ cut into: 8,465,749 HAP2_SCAFFOLD_241:11938377-20404125(+) Cut -bChlMac1_3-pretext-to-tpf_Hap1 +bChlMac1_3-pretext-to-tpf.hap1 1,275,074,175 bp sequence (minus gaps) Autosomes: n = 36 - 215,692,358 RL_1 + 215,692,358 SUPER_1 ... ... - 292,585 RL_67 + 292,585 SUPER_36 1,086,170,135 bp total Named: n = 2 - 54,806,811 W - 84,787,122 Z + 54,806,811 SUPER_W + 84,787,122 SUPER_Z 139,593,933 bp total Unplaced: n = 289 @@ -27,13 +27,13 @@ bChlMac1_3-pretext-to-tpf_Hap1 24,798 HAP1_SCAFFOLD_108 49,310,107 bp total -bChlMac1_3-pretext-to-tpf_Hap2 +bChlMac1_3-pretext-to-tpf.hap2 1,105,677,449 bp sequence (minus gaps) Autosomes: n = 36 - 214,587,655 RL_2 + 214,587,655 SUPER_1 ... ... - 188,044 RL_74 + 188,044 SUPER_34 1,053,881,404 bp total Unplaced: n = 305 @@ -42,7 +42,7 @@ bChlMac1_3-pretext-to-tpf_Hap2 13,916 HAP2_SCAFFOLD_112 51,796,045 bp total -bChlMac1_3-pretext-to-tpf_Haplotigs +bChlMac1_3-pretext-to-tpf.haplotigs 4,560,100 bp sequence (minus gaps) n = 1 4,560,100 H_1 diff --git a/tests/data/bChlMac1_3/bChlMac1_3-pretext-to-tpf_Hap1.tpf b/tests/data/bChlMac1_3/bchlmac1_3-pretext-to-tpf.hap1.tpf similarity index 70% rename from tests/data/bChlMac1_3/bChlMac1_3-pretext-to-tpf_Hap1.tpf rename to tests/data/bChlMac1_3/bchlmac1_3-pretext-to-tpf.hap1.tpf index 6637921..9d8dd8c 100644 --- a/tests/data/bChlMac1_3/bChlMac1_3-pretext-to-tpf_Hap1.tpf +++ b/tests/data/bChlMac1_3/bchlmac1_3-pretext-to-tpf.hap1.tpf @@ -1,243 +1,243 @@ -? HAP1_SCAFFOLD_326:1-1161036 RL_1 PLUS +? HAP1_SCAFFOLD_326:1-1161036 SUPER_1 PLUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_326:1161237-58521028 RL_1 PLUS +? HAP1_SCAFFOLD_326:1161237-58521028 SUPER_1 PLUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_326:58521229-83856695 RL_1 PLUS +? HAP1_SCAFFOLD_326:58521229-83856695 SUPER_1 PLUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_326:83856896-153488468 RL_1 PLUS +? HAP1_SCAFFOLD_326:83856896-153488468 SUPER_1 PLUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_326:153488669-215693158 RL_1 PLUS -? HAP1_SCAFFOLD_231:1-122418308 RL_3 PLUS +? HAP1_SCAFFOLD_326:153488669-215693158 SUPER_1 PLUS +? HAP1_SCAFFOLD_231:1-122418308 SUPER_2 PLUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_231:122418509-132038786 RL_3 PLUS +? HAP1_SCAFFOLD_231:122418509-132038786 SUPER_2 PLUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_231:132038987-146030187 RL_3 PLUS +? HAP1_SCAFFOLD_231:132038987-146030187 SUPER_2 PLUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_231:146030388-163414438 RL_3 PLUS +? HAP1_SCAFFOLD_231:146030388-163414438 SUPER_2 PLUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_234:665248-879593 RL_3 MINUS +? HAP1_SCAFFOLD_234:665248-879593 SUPER_2 MINUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_234:1-665047 RL_3 MINUS -? HAP1_SCAFFOLD_230:1-1176710 RL_5 PLUS +? HAP1_SCAFFOLD_234:1-665047 SUPER_2 MINUS +? HAP1_SCAFFOLD_230:1-1176710 SUPER_3 PLUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_230:1176911-1669094 RL_5 PLUS +? HAP1_SCAFFOLD_230:1176911-1669094 SUPER_3 PLUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_230:1669295-23717868 RL_5 PLUS +? HAP1_SCAFFOLD_230:1669295-23717868 SUPER_3 PLUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_230:23718069-118680724 RL_5 PLUS +? HAP1_SCAFFOLD_230:23718069-118680724 SUPER_3 PLUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_230:118680925-128056697 RL_5 PLUS -? HAP1_SCAFFOLD_229:1-16298107 RL_9 PLUS +? HAP1_SCAFFOLD_230:118680925-128056697 SUPER_3 PLUS +? HAP1_SCAFFOLD_229:1-16298107 SUPER_4 PLUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_229:16298308-84151616 RL_9 PLUS +? HAP1_SCAFFOLD_229:16298308-84151616 SUPER_4 PLUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_177:418682-472170 RL_9 MINUS +? HAP1_SCAFFOLD_177:418682-472170 SUPER_4 MINUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_177:279968-418481 RL_9 MINUS +? HAP1_SCAFFOLD_177:279968-418481 SUPER_4 MINUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_177:1-279767 RL_9 MINUS -? HAP1_SCAFFOLD_228:1-27891694 RL_11 PLUS +? HAP1_SCAFFOLD_177:1-279767 SUPER_4 MINUS +? HAP1_SCAFFOLD_228:1-27891694 SUPER_5 PLUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_228:27891895-59082128 RL_11 PLUS +? HAP1_SCAFFOLD_228:27891895-59082128 SUPER_5 PLUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_228:59082329-70571806 RL_11 PLUS +? HAP1_SCAFFOLD_228:59082329-70571806 SUPER_5 PLUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_228:70572007-71019442 RL_11 PLUS +? HAP1_SCAFFOLD_228:70572007-71019442 SUPER_5 PLUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_228:71019643-72825560 RL_11 PLUS -? HAP1_SCAFFOLD_227:1-25100583 RL_13 PLUS +? HAP1_SCAFFOLD_228:71019643-72825560 SUPER_5 PLUS +? HAP1_SCAFFOLD_227:1-25100583 SUPER_6 PLUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_227:25100784-28890953 RL_13 PLUS +? HAP1_SCAFFOLD_227:25100784-28890953 SUPER_6 PLUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_227:28891154-32010291 RL_13 PLUS +? HAP1_SCAFFOLD_227:28891154-32010291 SUPER_6 PLUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_227:32010492-40727740 RL_13 PLUS +? HAP1_SCAFFOLD_227:32010492-40727740 SUPER_6 PLUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_227:40727941-43971045 RL_13 PLUS +? HAP1_SCAFFOLD_227:40727941-43971045 SUPER_6 PLUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_242:1-1771153 RL_13 PLUS -? HAP1_SCAFFOLD_226:1-17742748 RL_15 MINUS +? HAP1_SCAFFOLD_242:1-1771153 SUPER_6 PLUS +? HAP1_SCAFFOLD_226:1-17742748 SUPER_7 MINUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_226:17742949-18790034 RL_15 PLUS +? HAP1_SCAFFOLD_226:17742949-18790034 SUPER_7 PLUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_226:18790235-40665136 RL_15 PLUS -? HAP1_SCAFFOLD_225:1-22324801 RL_17 PLUS +? HAP1_SCAFFOLD_226:18790235-40665136 SUPER_7 PLUS +? HAP1_SCAFFOLD_225:1-22324801 SUPER_8 PLUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_225:22325002-38754472 RL_17 PLUS -? HAP1_SCAFFOLD_224:1-2887854 RL_19 PLUS +? HAP1_SCAFFOLD_225:22325002-38754472 SUPER_8 PLUS +? HAP1_SCAFFOLD_224:1-2887854 SUPER_9 PLUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_224:2888055-8592260 RL_19 PLUS +? HAP1_SCAFFOLD_224:2888055-8592260 SUPER_9 PLUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_224:8592461-28029218 RL_19 PLUS -? HAP1_SCAFFOLD_274:1-153243 RL_19_unloc_1 MINUS -? HAP1_SCAFFOLD_278:1-144510 RL_19_unloc_2 PLUS -? HAP1_SCAFFOLD_211:1-23764681 RL_21 PLUS -? HAP1_SCAFFOLD_220:1-23395923 RL_23 PLUS -? HAP1_SCAFFOLD_221:1-23436253 RL_25 PLUS -? HAP1_SCAFFOLD_219:1-22304326 RL_27 PLUS -? HAP1_SCAFFOLD_218:1-20896716 RL_29 PLUS -? HAP2_SCAFFOLD_228:1-18299171 RL_31 PLUS -? HAP1_SCAFFOLD_216:1-1489557 RL_33 PLUS +? HAP1_SCAFFOLD_224:8592461-28029218 SUPER_9 PLUS +? HAP1_SCAFFOLD_274:1-153243 SUPER_9_unloc_1 MINUS +? HAP1_SCAFFOLD_278:1-144510 SUPER_9_unloc_2 PLUS +? HAP1_SCAFFOLD_211:1-23764681 SUPER_10 PLUS +? HAP1_SCAFFOLD_221:1-23436253 SUPER_11 PLUS +? HAP1_SCAFFOLD_220:1-23395923 SUPER_12 PLUS +? HAP1_SCAFFOLD_219:1-22304326 SUPER_13 PLUS +? HAP1_SCAFFOLD_218:1-20896716 SUPER_14 PLUS +? HAP2_SCAFFOLD_228:1-18299171 SUPER_15 PLUS +? HAP1_SCAFFOLD_216:1-1489557 SUPER_16 PLUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_216:1489758-16860029 RL_33 PLUS -? HAP1_SCAFFOLD_215:1-16261461 RL_35 PLUS -? HAP1_SCAFFOLD_213:1-3224616 RL_37 PLUS +? HAP1_SCAFFOLD_216:1489758-16860029 SUPER_16 PLUS +? HAP1_SCAFFOLD_215:1-16261461 SUPER_17 PLUS +? HAP1_SCAFFOLD_213:1-3224616 SUPER_18 PLUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_213:3224817-9695875 RL_37 PLUS +? HAP1_SCAFFOLD_213:3224817-9695875 SUPER_18 PLUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_213:9696076-14078390 RL_37 PLUS -? HAP1_SCAFFOLD_212:1-2238905 RL_39 PLUS +? HAP1_SCAFFOLD_213:9696076-14078390 SUPER_18 PLUS +? HAP1_SCAFFOLD_212:1-2238905 SUPER_19 PLUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_212:2239106-9513986 RL_39 PLUS +? HAP1_SCAFFOLD_212:2239106-9513986 SUPER_19 PLUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_212:9514187-12962427 RL_39 PLUS -? HAP1_SCAFFOLD_222:1-9912929 RL_41 PLUS +? HAP1_SCAFFOLD_212:9514187-12962427 SUPER_19 PLUS +? HAP1_SCAFFOLD_222:1-9912929 SUPER_20 PLUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_222:9913130-10601839 RL_41 PLUS +? HAP1_SCAFFOLD_222:9913130-10601839 SUPER_20 PLUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_222:10602040-12646375 RL_41 PLUS -? HAP1_SCAFFOLD_252:1-8027349 RL_43 PLUS +? HAP1_SCAFFOLD_222:10602040-12646375 SUPER_20 PLUS +? HAP1_SCAFFOLD_252:1-8027349 SUPER_21 PLUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_252:8027550-8979135 RL_43 PLUS +? HAP1_SCAFFOLD_252:8027550-8979135 SUPER_21 PLUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_252:8979336-9813053 RL_43 PLUS -? HAP1_SCAFFOLD_248:1-7396006 RL_45 PLUS -? HAP1_SCAFFOLD_249:1-1070098 RL_47 PLUS +? HAP1_SCAFFOLD_252:8979336-9813053 SUPER_21 PLUS +? HAP1_SCAFFOLD_250:1-372906 SUPER_22 PLUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_249:1070299-1359791 RL_47 PLUS +? HAP1_SCAFFOLD_250:373107-1514044 SUPER_22 PLUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_249:1359992-7515650 RL_47 PLUS -? HAP1_SCAFFOLD_247:1-1104625 RL_49 PLUS +? HAP1_SCAFFOLD_250:1514245-8409327 SUPER_22 PLUS +? HAP1_SCAFFOLD_249:1-1070098 SUPER_23 PLUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_247:1104826-6865239 RL_49 PLUS -? HAP1_SCAFFOLD_245:1-4703149 RL_51 PLUS +? HAP1_SCAFFOLD_249:1070299-1359791 SUPER_23 PLUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_245:5836569-6239360 RL_51 MINUS +? HAP1_SCAFFOLD_249:1359992-7515650 SUPER_23 PLUS +? HAP1_SCAFFOLD_248:1-7396006 SUPER_24 PLUS +? HAP1_SCAFFOLD_247:1-1104625 SUPER_25 PLUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_245:5557168-5836368 RL_51 MINUS +? HAP1_SCAFFOLD_247:1104826-6865239 SUPER_25 PLUS +? HAP1_SCAFFOLD_246:1-5712456 SUPER_26 PLUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_245:5370363-5556967 RL_51 MINUS +? HAP1_SCAFFOLD_246:5712657-6446260 SUPER_26 PLUS +? HAP1_SCAFFOLD_245:1-4703149 SUPER_27 PLUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_245:5216682-5370162 RL_51 MINUS +? HAP1_SCAFFOLD_245:5836569-6239360 SUPER_27 MINUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_245:4703350-5216481 RL_51 MINUS -? HAP1_SCAFFOLD_244:1-682142 RL_53 PLUS +? HAP1_SCAFFOLD_245:5557168-5836368 SUPER_27 MINUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_244:682343-1386537 RL_53 PLUS +? HAP1_SCAFFOLD_245:5370363-5556967 SUPER_27 MINUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_244:1386738-1780920 RL_53 PLUS +? HAP1_SCAFFOLD_245:5216682-5370162 SUPER_27 MINUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_244:1781121-2006566 RL_53 PLUS +? HAP1_SCAFFOLD_245:4703350-5216481 SUPER_27 MINUS +? HAP1_SCAFFOLD_244:1-682142 SUPER_28 PLUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_244:2006767-2260907 RL_53 PLUS +? HAP1_SCAFFOLD_244:682343-1386537 SUPER_28 PLUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_244:2261108-3290335 RL_53 PLUS -? HAP1_SCAFFOLD_232:1-622382 RL_55 PLUS +? HAP1_SCAFFOLD_244:1386738-1780920 SUPER_28 PLUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_232:622583-749813 RL_55 PLUS +? HAP1_SCAFFOLD_244:1781121-2006566 SUPER_28 PLUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_232:750014-1112612 RL_55 PLUS +? HAP1_SCAFFOLD_244:2006767-2260907 SUPER_28 PLUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_232:1112813-2006287 RL_55 PLUS +? HAP1_SCAFFOLD_244:2261108-3290335 SUPER_28 PLUS +? HAP1_SCAFFOLD_232:1-622382 SUPER_29 PLUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_232:2006488-2321846 RL_55 PLUS +? HAP1_SCAFFOLD_232:622583-749813 SUPER_29 PLUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_232:2322047-2445195 RL_55 PLUS +? HAP1_SCAFFOLD_232:750014-1112612 SUPER_29 PLUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_232:2445396-2515494 RL_55 PLUS +? HAP1_SCAFFOLD_232:1112813-2006287 SUPER_29 PLUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_232:2515695-2992603 RL_55 PLUS -? HAP1_SCAFFOLD_250:1-372906 RL_57 PLUS +? HAP1_SCAFFOLD_232:2006488-2321846 SUPER_29 PLUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_250:373107-1514044 RL_57 PLUS +? HAP1_SCAFFOLD_232:2322047-2445195 SUPER_29 PLUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_250:1514245-8409327 RL_57 PLUS -? HAP1_SCAFFOLD_246:1-5712456 RL_59 PLUS +? HAP1_SCAFFOLD_232:2445396-2515494 SUPER_29 PLUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_246:5712657-6446260 RL_59 PLUS -? HAP1_SCAFFOLD_236:1-224651 RL_61 PLUS +? HAP1_SCAFFOLD_232:2515695-2992603 SUPER_29 PLUS +? HAP1_SCAFFOLD_236:1-224651 SUPER_30 PLUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_236:224852-544297 RL_61 PLUS +? HAP1_SCAFFOLD_236:224852-544297 SUPER_30 PLUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_236:544498-600098 RL_61 PLUS +? HAP1_SCAFFOLD_236:544498-600098 SUPER_30 PLUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_236:600299-752059 RL_61 PLUS +? HAP1_SCAFFOLD_236:600299-752059 SUPER_30 PLUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_236:752260-990997 RL_61 PLUS -? HAP1_SCAFFOLD_180:122436-383818 RL_63 MINUS +? HAP1_SCAFFOLD_236:752260-990997 SUPER_30 PLUS +? HAP1_SCAFFOLD_182:1-197531 SUPER_31 PLUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_180:66198-122235 RL_63 MINUS +? HAP1_SCAFFOLD_182:197732-250227 SUPER_31 PLUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_180:1-65997 RL_63 MINUS -? HAP1_SCAFFOLD_188:1-434314 RL_65 PLUS -? HAP1_SCAFFOLD_188:434515-727099 RL_67 MINUS -? HAP1_SCAFFOLD_182:1-197531 RL_69 PLUS +? HAP1_SCAFFOLD_182:250428-388057 SUPER_31 PLUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_182:197732-250227 RL_69 PLUS +? HAP1_SCAFFOLD_182:388258-629270 SUPER_31 PLUS +? HAP1_SCAFFOLD_188:1-434314 SUPER_32 PLUS +? HAP1_SCAFFOLD_180:122436-383818 SUPER_33 MINUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_182:250428-388057 RL_69 PLUS +? HAP1_SCAFFOLD_180:66198-122235 SUPER_33 MINUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_182:388258-629270 RL_69 PLUS -? HAP1_SCAFFOLD_192:1-47745 RL_71 PLUS +? HAP1_SCAFFOLD_180:1-65997 SUPER_33 MINUS +? HAP1_SCAFFOLD_196:89281-303736 SUPER_34 MINUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_192:47946-93454 RL_71 PLUS +? HAP1_SCAFFOLD_196:1-89080 SUPER_34 MINUS +? HAP1_SCAFFOLD_192:1-47745 SUPER_35 PLUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_192:93655-294221 RL_71 PLUS -? HAP1_SCAFFOLD_196:89281-303736 RL_73 MINUS +? HAP1_SCAFFOLD_192:47946-93454 SUPER_35 PLUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_196:1-89080 RL_73 MINUS -? HAP1_SCAFFOLD_251:2367532-4742550 W MINUS +? HAP1_SCAFFOLD_192:93655-294221 SUPER_35 PLUS +? HAP1_SCAFFOLD_188:434515-727099 SUPER_36 MINUS +? HAP1_SCAFFOLD_251:2367532-4742550 SUPER_W MINUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_251:1-2367331 W MINUS +? HAP1_SCAFFOLD_251:1-2367331 SUPER_W MINUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_237:1-1024191 W MINUS +? HAP1_SCAFFOLD_237:1-1024191 SUPER_W MINUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_235:1-832503 W PLUS +? HAP1_SCAFFOLD_235:1-832503 SUPER_W PLUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_235:832704-979667 W PLUS +? HAP1_SCAFFOLD_235:832704-979667 SUPER_W PLUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_223:14361934-26027000 W MINUS +? HAP1_SCAFFOLD_223:14361934-26027000 SUPER_W MINUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_261:1-6583587 W MINUS +? HAP2_SCAFFOLD_261:1-6583587 SUPER_W MINUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_223:1-8451738 W PLUS +? HAP1_SCAFFOLD_223:1-8451738 SUPER_W PLUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_223:8451939-9853930 W PLUS +? HAP1_SCAFFOLD_223:8451939-9853930 SUPER_W PLUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_223:12933960-14361733 W MINUS +? HAP1_SCAFFOLD_223:12933960-14361733 SUPER_W MINUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_223:11287126-12933759 W MINUS +? HAP1_SCAFFOLD_223:11287126-12933759 SUPER_W MINUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_223:9854131-11286925 W MINUS +? HAP1_SCAFFOLD_223:9854131-11286925 SUPER_W MINUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_214:14778130-15453416 W MINUS +? HAP1_SCAFFOLD_214:14778130-15453416 SUPER_W MINUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_214:11097608-14777929 W MINUS +? HAP1_SCAFFOLD_214:11097608-14777929 SUPER_W MINUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_214:9348459-11097407 W MINUS +? HAP1_SCAFFOLD_214:9348459-11097407 SUPER_W MINUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_214:8836554-9348258 W MINUS +? HAP1_SCAFFOLD_214:8836554-9348258 SUPER_W MINUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_214:7313630-8836353 W MINUS +? HAP1_SCAFFOLD_214:7313630-8836353 SUPER_W MINUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_214:6141117-7313429 W MINUS +? HAP1_SCAFFOLD_214:6141117-7313429 SUPER_W MINUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_214:5971883-6140916 W MINUS +? HAP1_SCAFFOLD_214:5971883-6140916 SUPER_W MINUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_214:5466501-5971682 W MINUS +? HAP1_SCAFFOLD_214:5466501-5971682 SUPER_W MINUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_214:4069243-5466300 W MINUS +? HAP1_SCAFFOLD_214:4069243-5466300 SUPER_W MINUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_214:3003515-4069042 W MINUS +? HAP1_SCAFFOLD_214:3003515-4069042 SUPER_W MINUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_214:1003122-3003314 W MINUS +? HAP1_SCAFFOLD_214:1003122-3003314 SUPER_W MINUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_214:1-1002921 W MINUS -? HAP1_SCAFFOLD_251:4742751-9302850 Z PLUS +? HAP1_SCAFFOLD_214:1-1002921 SUPER_W MINUS +? HAP1_SCAFFOLD_251:4742751-9302850 SUPER_Z PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_240:1-80178314 Z MINUS +? HAP2_SCAFFOLD_240:1-80178314 SUPER_Z MINUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_241:11889669-11938376 Z PLUS +? HAP2_SCAFFOLD_241:11889669-11938376 SUPER_Z PLUS ? HAP1_SCAFFOLD_1:1-86080 HAP1_SCAFFOLD_1 PLUS ? HAP1_SCAFFOLD_2:1-74004 HAP1_SCAFFOLD_2 PLUS ? HAP1_SCAFFOLD_3:1-76480 HAP1_SCAFFOLD_3 PLUS diff --git a/tests/data/bChlMac1_3/chrs_Hap1.csv b/tests/data/bChlMac1_3/chrs_Hap1.csv deleted file mode 100644 index c20229d..0000000 --- a/tests/data/bChlMac1_3/chrs_Hap1.csv +++ /dev/null @@ -1,38 +0,0 @@ -RL_1 -RL_3 -RL_5 -RL_9 -RL_11 -RL_13 -RL_15 -RL_17 -RL_19,RL_19_unloc_1,RL_19_unloc_2 -RL_21 -RL_23 -RL_25 -RL_27 -RL_29 -RL_31 -RL_33 -RL_35 -RL_37 -RL_39 -RL_41 -RL_43 -RL_45 -RL_47 -RL_49 -RL_51 -RL_53 -RL_55 -RL_57 -RL_59 -RL_61 -RL_63 -RL_65 -RL_67 -RL_69 -RL_71 -RL_73 -W -Z diff --git a/tests/data/bChlMac1_3/chrs_Hap2.csv b/tests/data/bChlMac1_3/chrs_Hap2.csv deleted file mode 100644 index 6bf7942..0000000 --- a/tests/data/bChlMac1_3/chrs_Hap2.csv +++ /dev/null @@ -1,36 +0,0 @@ -RL_2 -RL_4 -RL_6 -RL_10 -RL_12 -RL_14 -RL_16 -RL_18 -RL_20,RL_20_unloc_1,RL_20_unloc_2 -RL_22 -RL_24 -RL_26 -RL_28 -RL_30 -RL_32 -RL_34 -RL_36 -RL_38 -RL_40 -RL_42 -RL_44 -RL_46 -RL_48 -RL_50 -RL_52 -RL_54 -RL_56 -RL_58 -RL_60 -RL_62 -RL_64 -RL_66 -RL_68 -RL_70 -RL_72 -RL_74 diff --git a/tests/data/csSphGirg1_1_hr/chrs.csv b/tests/data/csSphGirg1_1_hr/chrs.csv deleted file mode 100644 index e8193c6..0000000 --- a/tests/data/csSphGirg1_1_hr/chrs.csv +++ /dev/null @@ -1,21 +0,0 @@ -RL_1 -RL_2 -RL_3 -RL_4 -RL_5 -RL_6 -RL_7 -RL_8 -RL_9 -RL_10 -RL_11 -RL_12 -RL_13 -RL_14 -RL_15 -RL_16 -RL_17 -RL_18 -RL_19 -RL_20 -RL_21 diff --git a/tests/data/csSphGirg1_1_hr/csSphGirg1_1_hr-pretext-to-tpf.chr_report.csv b/tests/data/csSphGirg1_1_hr/csSphGirg1_1_hr-pretext-to-tpf.chr_report.csv new file mode 100644 index 0000000..6ebda56 --- /dev/null +++ b/tests/data/csSphGirg1_1_hr/csSphGirg1_1_hr-pretext-to-tpf.chr_report.csv @@ -0,0 +1,22 @@ +assembly,seq_name,chr_name,localised,pretext_scaffold,length,length_minus_gaps +Primary,SUPER_1,1,true,Scaffold_1,35523924,35515324 +Primary,SUPER_2,2,true,Scaffold_2,33126581,33120981 +Primary,SUPER_3,3,true,Scaffold_3,26723202,26717802 +Primary,SUPER_4,4,true,Scaffold_4,25662992,25656192 +Primary,SUPER_5,5,true,Scaffold_5,25230262,25225262 +Primary,SUPER_6,6,true,Scaffold_6,24968750,24966350 +Primary,SUPER_7,7,true,Scaffold_7,24781397,24778197 +Primary,SUPER_8,8,true,Scaffold_8,23017309,23014109 +Primary,SUPER_9,9,true,Scaffold_9,20232413,20229013 +Primary,SUPER_10,10,true,Scaffold_11,20110816,20107216 +Primary,SUPER_11,11,true,Scaffold_10,20044415,20039615 +Primary,SUPER_12,12,true,Scaffold_12,19709499,19707099 +Primary,SUPER_13,13,true,Scaffold_13,19572699,19568699 +Primary,SUPER_14,14,true,Scaffold_14,18914180,18910780 +Primary,SUPER_15,15,true,Scaffold_15,18046598,18042998 +Primary,SUPER_16,16,true,Scaffold_16,17999561,17995561 +Primary,SUPER_17,17,true,Scaffold_17,17338928,17335728 +Primary,SUPER_18,18,true,Scaffold_18,17010705,17008705 +Primary,SUPER_19,19,true,Scaffold_19,16957264,16954264 +Primary,SUPER_20,20,true,Scaffold_20,5348773,5348373 +Primary,SUPER_21,21,true,Scaffold_21,1588691,1588691 diff --git a/tests/data/csSphGirg1_1_hr/csSphGirg1_1_hr-pretext-to-tpf.chromsomes.list.csv b/tests/data/csSphGirg1_1_hr/csSphGirg1_1_hr-pretext-to-tpf.chromsomes.list.csv new file mode 100644 index 0000000..2e709a8 --- /dev/null +++ b/tests/data/csSphGirg1_1_hr/csSphGirg1_1_hr-pretext-to-tpf.chromsomes.list.csv @@ -0,0 +1,21 @@ +SUPER_1 +SUPER_2 +SUPER_3 +SUPER_4 +SUPER_5 +SUPER_6 +SUPER_7 +SUPER_8 +SUPER_9 +SUPER_10 +SUPER_11 +SUPER_12 +SUPER_13 +SUPER_14 +SUPER_15 +SUPER_16 +SUPER_17 +SUPER_18 +SUPER_19 +SUPER_20 +SUPER_21 diff --git a/tests/data/csSphGirg1_1_hr/csSphGirg1_1_hr-pretext-to-tpf_Contaminants.tpf b/tests/data/csSphGirg1_1_hr/csSphGirg1_1_hr-pretext-to-tpf.contaminants.tpf similarity index 100% rename from tests/data/csSphGirg1_1_hr/csSphGirg1_1_hr-pretext-to-tpf_Contaminants.tpf rename to tests/data/csSphGirg1_1_hr/csSphGirg1_1_hr-pretext-to-tpf.contaminants.tpf diff --git a/tests/data/csSphGirg1_1_hr/csSphGirg1_1_hr-pretext-to-tpf.log b/tests/data/csSphGirg1_1_hr/csSphGirg1_1_hr-pretext-to-tpf.log index cd9648b..5a2f5b1 100644 --- a/tests/data/csSphGirg1_1_hr/csSphGirg1_1_hr-pretext-to-tpf.log +++ b/tests/data/csSphGirg1_1_hr/csSphGirg1_1_hr-pretext-to-tpf.log @@ -5,9 +5,9 @@ csSphGirg1_1_hr-pretext-to-tpf 431,990,959 bp sequence (minus gaps) Autosomes: n = 21 - 35,515,324 RL_1 + 35,515,324 SUPER_1 ... ... - 1,588,691 RL_21 + 1,588,691 SUPER_21 431,830,959 bp total Unplaced: n = 137 @@ -16,7 +16,7 @@ csSphGirg1_1_hr-pretext-to-tpf 1,000 SCAFFOLD_5395 160,000 bp total -csSphGirg1_1_hr-pretext-to-tpf_Contaminants +csSphGirg1_1_hr-pretext-to-tpf.contaminants 15,253,452 bp sequence (minus gaps) n = 502 269,705 SCAFFOLD_62 diff --git a/tests/data/csSphGirg1_1_hr/csSphGirg1_1_hr-pretext-to-tpf.tpf b/tests/data/csSphGirg1_1_hr/csSphGirg1_1_hr-pretext-to-tpf.tpf index fc9d15d..2896afe 100644 --- a/tests/data/csSphGirg1_1_hr/csSphGirg1_1_hr-pretext-to-tpf.tpf +++ b/tests/data/csSphGirg1_1_hr/csSphGirg1_1_hr-pretext-to-tpf.tpf @@ -1,804 +1,804 @@ -? SCAFFOLD_1:1-518904 RL_1 PLUS +? SCAFFOLD_1:1-518904 SUPER_1 PLUS GAP TYPE-2 200 -? SCAFFOLD_1:519105-740285 RL_1 PLUS +? SCAFFOLD_1:519105-740285 SUPER_1 PLUS GAP TYPE-2 200 -? SCAFFOLD_1:740486-2315345 RL_1 PLUS +? SCAFFOLD_1:740486-2315345 SUPER_1 PLUS GAP TYPE-2 200 -? SCAFFOLD_1:2315546-2721925 RL_1 PLUS +? SCAFFOLD_1:2315546-2721925 SUPER_1 PLUS GAP TYPE-2 200 -? SCAFFOLD_1:2722126-3456187 RL_1 PLUS +? SCAFFOLD_1:2722126-3456187 SUPER_1 PLUS GAP TYPE-2 200 -? SCAFFOLD_1:3456388-4188086 RL_1 PLUS +? SCAFFOLD_1:3456388-4188086 SUPER_1 PLUS GAP TYPE-2 200 -? SCAFFOLD_1:4188287-7586084 RL_1 PLUS +? SCAFFOLD_1:4188287-7586084 SUPER_1 PLUS GAP TYPE-2 200 -? SCAFFOLD_1:7586285-8310240 RL_1 PLUS +? SCAFFOLD_1:7586285-8310240 SUPER_1 PLUS GAP TYPE-2 200 -? SCAFFOLD_1:8310441-8418960 RL_1 PLUS +? SCAFFOLD_1:8310441-8418960 SUPER_1 PLUS GAP TYPE-2 200 -? SCAFFOLD_1:8419161-8572943 RL_1 PLUS +? SCAFFOLD_1:8419161-8572943 SUPER_1 PLUS GAP TYPE-2 200 -? SCAFFOLD_1:8573144-8910809 RL_1 PLUS +? SCAFFOLD_1:8573144-8910809 SUPER_1 PLUS GAP TYPE-2 200 -? SCAFFOLD_1:8911010-10083009 RL_1 PLUS +? SCAFFOLD_1:8911010-10083009 SUPER_1 PLUS GAP TYPE-2 200 -? SCAFFOLD_1:10083210-11507771 RL_1 PLUS +? SCAFFOLD_1:10083210-11507771 SUPER_1 PLUS GAP TYPE-2 200 -? SCAFFOLD_1:11507972-11923917 RL_1 PLUS +? SCAFFOLD_1:11507972-11923917 SUPER_1 PLUS GAP TYPE-2 200 -? SCAFFOLD_1:11924118-12942993 RL_1 PLUS +? SCAFFOLD_1:11924118-12942993 SUPER_1 PLUS GAP TYPE-2 200 -? SCAFFOLD_1:12943194-16187025 RL_1 PLUS +? SCAFFOLD_1:12943194-16187025 SUPER_1 PLUS GAP TYPE-2 200 -? SCAFFOLD_1:16187226-17113979 RL_1 PLUS +? SCAFFOLD_1:16187226-17113979 SUPER_1 PLUS GAP TYPE-2 200 -? SCAFFOLD_1:17114180-17450009 RL_1 PLUS +? SCAFFOLD_1:17114180-17450009 SUPER_1 PLUS GAP TYPE-2 200 -? SCAFFOLD_1:17450210-18197459 RL_1 PLUS +? SCAFFOLD_1:17450210-18197459 SUPER_1 PLUS GAP TYPE-2 200 -? SCAFFOLD_1:18197660-18976499 RL_1 PLUS +? SCAFFOLD_1:18197660-18976499 SUPER_1 PLUS GAP TYPE-2 200 -? SCAFFOLD_1:18976700-21390235 RL_1 PLUS +? SCAFFOLD_1:18976700-21390235 SUPER_1 PLUS GAP TYPE-2 200 -? SCAFFOLD_1:21390436-21893476 RL_1 PLUS +? SCAFFOLD_1:21390436-21893476 SUPER_1 PLUS GAP TYPE-2 200 -? SCAFFOLD_1:21893677-23382386 RL_1 PLUS +? SCAFFOLD_1:21893677-23382386 SUPER_1 PLUS GAP TYPE-2 200 -? SCAFFOLD_1:23382587-26399796 RL_1 PLUS +? SCAFFOLD_1:23382587-26399796 SUPER_1 PLUS GAP TYPE-2 200 -? SCAFFOLD_1:26399997-26431961 RL_1 PLUS +? SCAFFOLD_1:26399997-26431961 SUPER_1 PLUS GAP TYPE-2 200 -? SCAFFOLD_1:26432162-26795179 RL_1 PLUS +? SCAFFOLD_1:26432162-26795179 SUPER_1 PLUS GAP TYPE-2 200 -? SCAFFOLD_1:26795380-26897854 RL_1 PLUS +? SCAFFOLD_1:26795380-26897854 SUPER_1 PLUS GAP TYPE-2 200 -? SCAFFOLD_1:26898055-26992275 RL_1 PLUS +? SCAFFOLD_1:26898055-26992275 SUPER_1 PLUS GAP TYPE-2 200 -? SCAFFOLD_1:26992476-27979856 RL_1 PLUS +? SCAFFOLD_1:26992476-27979856 SUPER_1 PLUS GAP TYPE-2 200 -? SCAFFOLD_1:27980057-28557346 RL_1 PLUS +? SCAFFOLD_1:27980057-28557346 SUPER_1 PLUS GAP TYPE-2 200 -? SCAFFOLD_1:28557547-29748069 RL_1 PLUS +? SCAFFOLD_1:28557547-29748069 SUPER_1 PLUS GAP TYPE-2 200 -? SCAFFOLD_1:29748270-29861474 RL_1 PLUS +? SCAFFOLD_1:29748270-29861474 SUPER_1 PLUS GAP TYPE-2 200 -? SCAFFOLD_1:29861675-30138223 RL_1 PLUS +? SCAFFOLD_1:29861675-30138223 SUPER_1 PLUS GAP TYPE-2 200 -? SCAFFOLD_1:30138424-30539805 RL_1 PLUS +? SCAFFOLD_1:30138424-30539805 SUPER_1 PLUS GAP TYPE-2 200 -? SCAFFOLD_1:30540006-30666461 RL_1 PLUS +? SCAFFOLD_1:30540006-30666461 SUPER_1 PLUS GAP TYPE-2 200 -? SCAFFOLD_1:30666662-30871618 RL_1 PLUS +? SCAFFOLD_1:30666662-30871618 SUPER_1 PLUS GAP TYPE-2 200 -? SCAFFOLD_1:30871819-31449347 RL_1 PLUS +? SCAFFOLD_1:30871819-31449347 SUPER_1 PLUS GAP TYPE-2 200 -? SCAFFOLD_1:31449548-33001212 RL_1 PLUS +? SCAFFOLD_1:31449548-33001212 SUPER_1 PLUS GAP TYPE-2 200 -? SCAFFOLD_1:33001413-33200399 RL_1 PLUS +? SCAFFOLD_1:33001413-33200399 SUPER_1 PLUS GAP TYPE-2 200 -? SCAFFOLD_1:33200600-33342471 RL_1 PLUS +? SCAFFOLD_1:33200600-33342471 SUPER_1 PLUS GAP TYPE-2 200 -? SCAFFOLD_1:33342672-34008675 RL_1 PLUS +? SCAFFOLD_1:33342672-34008675 SUPER_1 PLUS GAP TYPE-2 200 -? SCAFFOLD_1:34008876-34373625 RL_1 PLUS +? SCAFFOLD_1:34008876-34373625 SUPER_1 PLUS GAP TYPE-2 200 -? SCAFFOLD_1:34373826-35355913 RL_1 PLUS +? SCAFFOLD_1:34373826-35355913 SUPER_1 PLUS GAP TYPE-2 200 -? SCAFFOLD_1:35356114-35523924 RL_1 PLUS -? SCAFFOLD_2:1-3795133 RL_2 PLUS +? SCAFFOLD_1:35356114-35523924 SUPER_1 PLUS +? SCAFFOLD_2:1-3795133 SUPER_2 PLUS GAP TYPE-2 200 -? SCAFFOLD_2:3795334-4348991 RL_2 PLUS +? SCAFFOLD_2:3795334-4348991 SUPER_2 PLUS GAP TYPE-2 200 -? SCAFFOLD_2:4349192-5028514 RL_2 PLUS +? SCAFFOLD_2:4349192-5028514 SUPER_2 PLUS GAP TYPE-2 200 -? SCAFFOLD_2:5028715-5683875 RL_2 PLUS +? SCAFFOLD_2:5028715-5683875 SUPER_2 PLUS GAP TYPE-2 200 -? SCAFFOLD_2:5684076-7442787 RL_2 PLUS +? SCAFFOLD_2:5684076-7442787 SUPER_2 PLUS GAP TYPE-2 200 -? SCAFFOLD_2:7442988-8139345 RL_2 PLUS +? SCAFFOLD_2:7442988-8139345 SUPER_2 PLUS GAP TYPE-2 200 -? SCAFFOLD_2:8139546-8337318 RL_2 PLUS +? SCAFFOLD_2:8139546-8337318 SUPER_2 PLUS GAP TYPE-2 200 -? SCAFFOLD_2:8337519-8446205 RL_2 PLUS +? SCAFFOLD_2:8337519-8446205 SUPER_2 PLUS GAP TYPE-2 200 -? SCAFFOLD_2:8446406-12056727 RL_2 PLUS +? SCAFFOLD_2:8446406-12056727 SUPER_2 PLUS GAP TYPE-2 200 -? SCAFFOLD_2:12056928-12578212 RL_2 PLUS +? SCAFFOLD_2:12056928-12578212 SUPER_2 PLUS GAP TYPE-2 200 -? SCAFFOLD_2:12578413-12967969 RL_2 PLUS +? SCAFFOLD_2:12578413-12967969 SUPER_2 PLUS GAP TYPE-2 200 -? SCAFFOLD_2:12968170-13042068 RL_2 PLUS +? SCAFFOLD_2:12968170-13042068 SUPER_2 PLUS GAP TYPE-2 200 -? SCAFFOLD_2:13042269-15772466 RL_2 PLUS +? SCAFFOLD_2:13042269-15772466 SUPER_2 PLUS GAP TYPE-2 200 -? SCAFFOLD_2:15772667-16935328 RL_2 PLUS +? SCAFFOLD_2:15772667-16935328 SUPER_2 PLUS GAP TYPE-2 200 -? SCAFFOLD_2:16935529-18248158 RL_2 PLUS +? 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SCAFFOLD_15:16256608-16652117 SUPER_15 PLUS GAP TYPE-2 200 -? SCAFFOLD_15:16652318-17965197 RL_15 PLUS +? SCAFFOLD_15:16652318-17965197 SUPER_15 PLUS GAP TYPE-2 200 -? SCAFFOLD_15:17965398-18046598 RL_15 PLUS -? SCAFFOLD_16:1-1762736 RL_16 PLUS +? SCAFFOLD_15:17965398-18046598 SUPER_15 PLUS +? SCAFFOLD_16:1-1762736 SUPER_16 PLUS GAP TYPE-2 200 -? SCAFFOLD_16:1762937-2350077 RL_16 PLUS +? SCAFFOLD_16:1762937-2350077 SUPER_16 PLUS GAP TYPE-2 200 -? SCAFFOLD_16:2350278-2426247 RL_16 PLUS +? SCAFFOLD_16:2350278-2426247 SUPER_16 PLUS GAP TYPE-2 200 -? SCAFFOLD_16:2426448-2885110 RL_16 PLUS +? SCAFFOLD_16:2426448-2885110 SUPER_16 PLUS GAP TYPE-2 200 -? SCAFFOLD_16:2885311-3131583 RL_16 PLUS +? SCAFFOLD_16:2885311-3131583 SUPER_16 PLUS GAP TYPE-2 200 -? SCAFFOLD_16:3131784-3221124 RL_16 PLUS +? SCAFFOLD_16:3131784-3221124 SUPER_16 PLUS GAP TYPE-2 200 -? SCAFFOLD_16:3221325-4003873 RL_16 PLUS +? SCAFFOLD_16:3221325-4003873 SUPER_16 PLUS GAP TYPE-2 200 -? SCAFFOLD_16:4004074-4038459 RL_16 PLUS +? SCAFFOLD_16:4004074-4038459 SUPER_16 PLUS GAP TYPE-2 200 -? SCAFFOLD_16:4038660-4217425 RL_16 PLUS +? SCAFFOLD_16:4038660-4217425 SUPER_16 PLUS GAP TYPE-2 200 -? SCAFFOLD_16:4217626-9540656 RL_16 PLUS +? SCAFFOLD_16:4217626-9540656 SUPER_16 PLUS GAP TYPE-2 200 -? SCAFFOLD_16:9540857-10324489 RL_16 PLUS +? SCAFFOLD_16:9540857-10324489 SUPER_16 PLUS GAP TYPE-2 200 -? SCAFFOLD_16:10324690-10747382 RL_16 PLUS +? SCAFFOLD_16:10324690-10747382 SUPER_16 PLUS GAP TYPE-2 200 -? SCAFFOLD_16:10747583-10966872 RL_16 PLUS +? SCAFFOLD_16:10747583-10966872 SUPER_16 PLUS GAP TYPE-2 200 -? SCAFFOLD_16:10967073-11722235 RL_16 PLUS +? SCAFFOLD_16:10967073-11722235 SUPER_16 PLUS GAP TYPE-2 200 -? SCAFFOLD_16:11722436-12008368 RL_16 PLUS +? SCAFFOLD_16:11722436-12008368 SUPER_16 PLUS GAP TYPE-2 200 -? SCAFFOLD_16:12008569-12108281 RL_16 PLUS +? SCAFFOLD_16:12008569-12108281 SUPER_16 PLUS GAP TYPE-2 200 -? SCAFFOLD_16:12108482-12169362 RL_16 PLUS +? SCAFFOLD_16:12108482-12169362 SUPER_16 PLUS GAP TYPE-2 200 -? SCAFFOLD_16:12169563-12727703 RL_16 PLUS +? SCAFFOLD_16:12169563-12727703 SUPER_16 PLUS GAP TYPE-2 200 -? SCAFFOLD_16:12727904-13268191 RL_16 PLUS +? SCAFFOLD_16:12727904-13268191 SUPER_16 PLUS GAP TYPE-2 200 -? SCAFFOLD_16:13268392-15556999 RL_16 PLUS +? SCAFFOLD_16:13268392-15556999 SUPER_16 PLUS GAP TYPE-2 200 -? SCAFFOLD_16:15557200-17999561 RL_16 PLUS -? SCAFFOLD_17:1-197229 RL_17 PLUS +? SCAFFOLD_16:15557200-17999561 SUPER_16 PLUS +? SCAFFOLD_17:1-197229 SUPER_17 PLUS GAP TYPE-2 200 -? SCAFFOLD_17:197430-606516 RL_17 PLUS +? SCAFFOLD_17:197430-606516 SUPER_17 PLUS GAP TYPE-2 200 -? SCAFFOLD_17:606717-3544060 RL_17 PLUS +? SCAFFOLD_17:606717-3544060 SUPER_17 PLUS GAP TYPE-2 200 -? SCAFFOLD_17:3544261-3574528 RL_17 PLUS +? SCAFFOLD_17:3544261-3574528 SUPER_17 PLUS GAP TYPE-2 200 -? SCAFFOLD_17:3574729-3974511 RL_17 PLUS +? SCAFFOLD_17:3574729-3974511 SUPER_17 PLUS GAP TYPE-2 200 -? SCAFFOLD_17:3974712-4353062 RL_17 PLUS +? SCAFFOLD_17:3974712-4353062 SUPER_17 PLUS GAP TYPE-2 200 -? SCAFFOLD_17:4353263-5129263 RL_17 PLUS +? SCAFFOLD_17:4353263-5129263 SUPER_17 PLUS GAP TYPE-2 200 -? SCAFFOLD_17:5129464-5331592 RL_17 PLUS +? SCAFFOLD_17:5129464-5331592 SUPER_17 PLUS GAP TYPE-2 200 -? SCAFFOLD_17:5331793-6450757 RL_17 PLUS +? SCAFFOLD_17:5331793-6450757 SUPER_17 PLUS GAP TYPE-2 200 -? SCAFFOLD_17:6450958-8119086 RL_17 PLUS +? SCAFFOLD_17:6450958-8119086 SUPER_17 PLUS GAP TYPE-2 200 -? SCAFFOLD_17:8119287-9216034 RL_17 PLUS +? SCAFFOLD_17:8119287-9216034 SUPER_17 PLUS GAP TYPE-2 200 -? SCAFFOLD_17:9216235-10505766 RL_17 PLUS +? SCAFFOLD_17:9216235-10505766 SUPER_17 PLUS GAP TYPE-2 200 -? SCAFFOLD_17:10505967-14090588 RL_17 PLUS +? SCAFFOLD_17:10505967-14090588 SUPER_17 PLUS GAP TYPE-2 200 -? SCAFFOLD_17:14090789-14655262 RL_17 PLUS +? SCAFFOLD_17:14090789-14655262 SUPER_17 PLUS GAP TYPE-2 200 -? SCAFFOLD_17:14655463-14843422 RL_17 PLUS +? SCAFFOLD_17:14655463-14843422 SUPER_17 PLUS GAP TYPE-2 200 -? SCAFFOLD_17:14843623-15316867 RL_17 PLUS +? SCAFFOLD_17:14843623-15316867 SUPER_17 PLUS GAP TYPE-2 200 -? SCAFFOLD_17:15317068-17338928 RL_17 PLUS -? SCAFFOLD_18:1-494770 RL_18 PLUS +? SCAFFOLD_17:15317068-17338928 SUPER_17 PLUS +? SCAFFOLD_18:1-494770 SUPER_18 PLUS GAP TYPE-2 200 -? SCAFFOLD_18:494971-2380937 RL_18 PLUS +? SCAFFOLD_18:494971-2380937 SUPER_18 PLUS GAP TYPE-2 200 -? SCAFFOLD_18:2381138-4720596 RL_18 PLUS +? SCAFFOLD_18:2381138-4720596 SUPER_18 PLUS GAP TYPE-2 200 -? SCAFFOLD_18:4720797-5099725 RL_18 PLUS +? SCAFFOLD_18:4720797-5099725 SUPER_18 PLUS GAP TYPE-2 200 -? SCAFFOLD_18:5099926-6469350 RL_18 PLUS +? SCAFFOLD_18:5099926-6469350 SUPER_18 PLUS GAP TYPE-2 200 -? SCAFFOLD_18:6469551-9351491 RL_18 PLUS +? SCAFFOLD_18:6469551-9351491 SUPER_18 PLUS GAP TYPE-2 200 -? SCAFFOLD_18:9351692-10513412 RL_18 PLUS +? SCAFFOLD_18:9351692-10513412 SUPER_18 PLUS GAP TYPE-2 200 -? SCAFFOLD_18:10513613-12140835 RL_18 PLUS +? SCAFFOLD_18:10513613-12140835 SUPER_18 PLUS GAP TYPE-2 200 -? SCAFFOLD_18:12141036-15120279 RL_18 PLUS +? SCAFFOLD_18:12141036-15120279 SUPER_18 PLUS GAP TYPE-2 200 -? SCAFFOLD_18:15120480-16489260 RL_18 PLUS +? SCAFFOLD_18:15120480-16489260 SUPER_18 PLUS GAP TYPE-2 200 -? SCAFFOLD_18:16489461-17010705 RL_18 PLUS -? SCAFFOLD_19:1-1784109 RL_19 PLUS +? SCAFFOLD_18:16489461-17010705 SUPER_18 PLUS +? SCAFFOLD_19:1-1784109 SUPER_19 PLUS GAP TYPE-2 200 -? SCAFFOLD_19:1784310-2502512 RL_19 PLUS +? SCAFFOLD_19:1784310-2502512 SUPER_19 PLUS GAP TYPE-2 200 -? SCAFFOLD_19:2502713-2871705 RL_19 PLUS +? SCAFFOLD_19:2502713-2871705 SUPER_19 PLUS GAP TYPE-2 200 -? SCAFFOLD_19:2871906-2948939 RL_19 PLUS +? SCAFFOLD_19:2871906-2948939 SUPER_19 PLUS GAP TYPE-2 200 -? SCAFFOLD_19:2949140-3169564 RL_19 PLUS +? SCAFFOLD_19:2949140-3169564 SUPER_19 PLUS GAP TYPE-2 200 -? SCAFFOLD_19:3169765-3419785 RL_19 PLUS +? SCAFFOLD_19:3169765-3419785 SUPER_19 PLUS GAP TYPE-2 200 -? SCAFFOLD_19:3419986-4898600 RL_19 PLUS +? SCAFFOLD_19:3419986-4898600 SUPER_19 PLUS GAP TYPE-2 200 -? SCAFFOLD_19:4898801-5921511 RL_19 PLUS +? SCAFFOLD_19:4898801-5921511 SUPER_19 PLUS GAP TYPE-2 200 -? SCAFFOLD_19:5921712-6377608 RL_19 PLUS +? SCAFFOLD_19:5921712-6377608 SUPER_19 PLUS GAP TYPE-2 200 -? SCAFFOLD_19:6377809-8208733 RL_19 PLUS +? SCAFFOLD_19:6377809-8208733 SUPER_19 PLUS GAP TYPE-2 200 -? SCAFFOLD_19:8208934-10284715 RL_19 PLUS +? SCAFFOLD_19:8208934-10284715 SUPER_19 PLUS GAP TYPE-2 200 -? SCAFFOLD_19:10284916-10848696 RL_19 PLUS +? SCAFFOLD_19:10284916-10848696 SUPER_19 PLUS GAP TYPE-2 200 -? SCAFFOLD_19:10848897-11055258 RL_19 PLUS +? SCAFFOLD_19:10848897-11055258 SUPER_19 PLUS GAP TYPE-2 200 -? SCAFFOLD_19:11055459-11425540 RL_19 PLUS +? SCAFFOLD_19:11055459-11425540 SUPER_19 PLUS GAP TYPE-2 200 -? SCAFFOLD_19:11425741-15072688 RL_19 PLUS +? SCAFFOLD_19:11425741-15072688 SUPER_19 PLUS GAP TYPE-2 200 -? SCAFFOLD_19:15072889-16957264 RL_19 PLUS -? SCAFFOLD_23:1-625640 RL_20 PLUS +? SCAFFOLD_19:15072889-16957264 SUPER_19 PLUS +? SCAFFOLD_23:1-625640 SUPER_20 PLUS GAP TYPE-2 200 -? SCAFFOLD_23:625841-2678377 RL_20 PLUS +? SCAFFOLD_23:625841-2678377 SUPER_20 PLUS GAP TYPE-2 200 -? SCAFFOLD_23:2678578-5348773 RL_20 PLUS -? SCAFFOLD_23:5348974-6937664 RL_21 PLUS +? SCAFFOLD_23:2678578-5348773 SUPER_20 PLUS +? SCAFFOLD_23:5348974-6937664 SUPER_21 PLUS ? SCAFFOLD_5064:1-3000 SCAFFOLD_5064 PLUS ? SCAFFOLD_5085:1-3000 SCAFFOLD_5085 PLUS ? SCAFFOLD_5096:1-2000 SCAFFOLD_5096 PLUS diff --git a/tests/data/eaAstIrre1/chrs.csv b/tests/data/eaAstIrre1/chrs.csv deleted file mode 100644 index 41fa280..0000000 --- a/tests/data/eaAstIrre1/chrs.csv +++ /dev/null @@ -1,22 +0,0 @@ -RL_1 -RL_2 -RL_3 -RL_4 -RL_5 -RL_6 -RL_7 -RL_8 -RL_9 -RL_10 -RL_11 -RL_12 -RL_13 -RL_14 -RL_15 -RL_16 -RL_17 -RL_18 -RL_19 -RL_20 -RL_21 -RL_22 diff --git a/tests/data/eaAstIrre1/eaAstIrre1-pretext-to-tpf.chr_report.csv b/tests/data/eaAstIrre1/eaAstIrre1-pretext-to-tpf.chr_report.csv new file mode 100644 index 0000000..cc6bdac --- /dev/null +++ b/tests/data/eaAstIrre1/eaAstIrre1-pretext-to-tpf.chr_report.csv @@ -0,0 +1,23 @@ +assembly,seq_name,chr_name,localised,pretext_scaffold,length,length_minus_gaps +Primary,SUPER_1,1,true,Scaffold_2,38710804,38696204 +Primary,SUPER_2,2,true,Scaffold_1,38350819,38337819 +Primary,SUPER_3,3,true,Scaffold_3,28656373,28646573 +Primary,SUPER_4,4,true,Scaffold_5,28153658,28144058 +Primary,SUPER_5,5,true,Scaffold_4,27239987,27230187 +Primary,SUPER_6,6,true,Scaffold_21,23316102,23308502 +Primary,SUPER_7,7,true,Scaffold_6,23149544,23142344 +Primary,SUPER_8,8,true,Scaffold_7,22732073,22724273 +Primary,SUPER_9,9,true,Scaffold_11,21341990,21336190 +Primary,SUPER_10,10,true,Scaffold_8,20880861,20875461 +Primary,SUPER_11,11,true,Scaffold_9,20386141,20378941 +Primary,SUPER_12,12,true,Scaffold_20,19666115,19659715 +Primary,SUPER_13,13,true,Scaffold_10,18848580,18844580 +Primary,SUPER_14,14,true,Scaffold_12,18438656,18433856 +Primary,SUPER_15,15,true,Scaffold_13,16693320,16689520 +Primary,SUPER_16,16,true,Scaffold_15,15362158,15357758 +Primary,SUPER_17,17,true,Scaffold_14,15263469,15257669 +Primary,SUPER_18,18,true,Scaffold_16,14753411,14747611 +Primary,SUPER_19,19,true,Scaffold_22,14698662,14694062 +Primary,SUPER_20,20,true,Scaffold_18,14015683,14011083 +Primary,SUPER_21,21,true,Scaffold_17,13698639,13692639 +Primary,SUPER_22,22,true,Scaffold_19,12138321,12132721 diff --git a/tests/data/eaAstIrre1/eaAstIrre1-pretext-to-tpf.chromsomes.list.csv b/tests/data/eaAstIrre1/eaAstIrre1-pretext-to-tpf.chromsomes.list.csv new file mode 100644 index 0000000..9ea642c --- /dev/null +++ b/tests/data/eaAstIrre1/eaAstIrre1-pretext-to-tpf.chromsomes.list.csv @@ -0,0 +1,22 @@ +SUPER_1 +SUPER_2 +SUPER_3 +SUPER_4 +SUPER_5 +SUPER_6 +SUPER_7 +SUPER_8 +SUPER_9 +SUPER_10 +SUPER_11 +SUPER_12 +SUPER_13 +SUPER_14 +SUPER_15 +SUPER_16 +SUPER_17 +SUPER_18 +SUPER_19 +SUPER_20 +SUPER_21 +SUPER_22 diff --git a/tests/data/eaAstIrre1/eaAstIrre1-pretext-to-tpf_Contaminants.tpf b/tests/data/eaAstIrre1/eaAstIrre1-pretext-to-tpf.contaminants.tpf similarity index 100% rename from tests/data/eaAstIrre1/eaAstIrre1-pretext-to-tpf_Contaminants.tpf rename to tests/data/eaAstIrre1/eaAstIrre1-pretext-to-tpf.contaminants.tpf diff --git a/tests/data/eaAstIrre1/eaAstIrre1-pretext-to-tpf_Haplotigs.tpf b/tests/data/eaAstIrre1/eaAstIrre1-pretext-to-tpf.haplotigs.tpf similarity index 100% rename from tests/data/eaAstIrre1/eaAstIrre1-pretext-to-tpf_Haplotigs.tpf rename to tests/data/eaAstIrre1/eaAstIrre1-pretext-to-tpf.haplotigs.tpf diff --git a/tests/data/eaAstIrre1/eaAstIrre1-pretext-to-tpf.log b/tests/data/eaAstIrre1/eaAstIrre1-pretext-to-tpf.log index fe28335..efc4a07 100644 --- a/tests/data/eaAstIrre1/eaAstIrre1-pretext-to-tpf.log +++ b/tests/data/eaAstIrre1/eaAstIrre1-pretext-to-tpf.log @@ -120,9 +120,9 @@ eaAstIrre1-pretext-to-tpf 476,369,490 bp sequence (minus gaps) Autosomes: n = 22 - 38,696,204 RL_2 + 38,696,204 SUPER_1 ... ... - 12,132,721 RL_19 + 12,132,721 SUPER_22 466,341,766 bp total Unplaced: n = 164 @@ -131,7 +131,7 @@ eaAstIrre1-pretext-to-tpf 1,000 SCAFFOLD_273 10,027,724 bp total -eaAstIrre1-pretext-to-tpf_Haplotigs +eaAstIrre1-pretext-to-tpf.haplotigs 20,154,414 bp sequence (minus gaps) n = 44 3,717,954 H_1 @@ -139,7 +139,7 @@ eaAstIrre1-pretext-to-tpf_Haplotigs 79,837 H_44 20,154,414 bp total -eaAstIrre1-pretext-to-tpf_Contaminants +eaAstIrre1-pretext-to-tpf.contaminants 2,742,977 bp sequence (minus gaps) n = 34 280,776 SCAFFOLD_64 diff --git a/tests/data/eaAstIrre1/eaAstIrre1-pretext-to-tpf.tpf b/tests/data/eaAstIrre1/eaAstIrre1-pretext-to-tpf.tpf index becc226..0d34fc9 100644 --- a/tests/data/eaAstIrre1/eaAstIrre1-pretext-to-tpf.tpf +++ b/tests/data/eaAstIrre1/eaAstIrre1-pretext-to-tpf.tpf @@ -1,1561 +1,1561 @@ -? SCAFFOLD_1:1-291000 RL_1 PLUS +? SCAFFOLD_50:398055-467395 SUPER_1 MINUS GAP TYPE-2 200 -? SCAFFOLD_1:291201-511307 RL_1 PLUS +? SCAFFOLD_50:1-397854 SUPER_1 MINUS GAP TYPE-2 200 -? SCAFFOLD_1:511508-576249 RL_1 PLUS +? SCAFFOLD_75:1-198325 SUPER_1 MINUS GAP TYPE-2 200 -? SCAFFOLD_1:576450-741859 RL_1 PLUS +? SCAFFOLD_84:1-161967 SUPER_1 MINUS GAP TYPE-2 200 -? SCAFFOLD_1:742060-1371998 RL_1 PLUS +? SCAFFOLD_22:9991277-10272339 SUPER_1 MINUS GAP TYPE-2 200 -? SCAFFOLD_1:1372199-1447321 RL_1 PLUS +? SCAFFOLD_22:9888054-9991076 SUPER_1 MINUS GAP TYPE-2 200 -? SCAFFOLD_1:1447522-2214521 RL_1 PLUS +? SCAFFOLD_22:9824050-9887853 SUPER_1 MINUS GAP TYPE-2 200 -? SCAFFOLD_1:2214722-4108731 RL_1 PLUS +? SCAFFOLD_22:9396183-9823849 SUPER_1 MINUS GAP TYPE-2 200 -? SCAFFOLD_1:4108932-5235674 RL_1 PLUS +? SCAFFOLD_22:9162025-9395982 SUPER_1 MINUS GAP TYPE-2 200 -? SCAFFOLD_1:5235875-6174559 RL_1 PLUS +? SCAFFOLD_22:8942418-9161824 SUPER_1 MINUS GAP TYPE-2 200 -? SCAFFOLD_1:6174760-6550787 RL_1 PLUS +? SCAFFOLD_22:8789391-8942217 SUPER_1 MINUS GAP TYPE-2 200 -? SCAFFOLD_1:6550988-6904980 RL_1 PLUS +? SCAFFOLD_22:8025764-8789190 SUPER_1 MINUS GAP TYPE-2 200 -? SCAFFOLD_1:6905181-7112013 RL_1 PLUS +? SCAFFOLD_22:7687452-8025563 SUPER_1 MINUS GAP TYPE-2 200 -? SCAFFOLD_1:7112214-7648227 RL_1 PLUS +? SCAFFOLD_22:7540209-7687251 SUPER_1 MINUS GAP TYPE-2 200 -? SCAFFOLD_1:7648428-8840612 RL_1 PLUS +? SCAFFOLD_22:6601943-7540008 SUPER_1 MINUS GAP TYPE-2 200 -? SCAFFOLD_1:8840813-9421367 RL_1 PLUS +? SCAFFOLD_36:1-710756 SUPER_1 MINUS GAP TYPE-2 200 -? SCAFFOLD_1:9421568-9753705 RL_1 PLUS +? SCAFFOLD_22:4671406-6601742 SUPER_1 MINUS GAP TYPE-2 200 -? SCAFFOLD_1:9753906-10172948 RL_1 PLUS +? SCAFFOLD_22:4349201-4413864 SUPER_1 MINUS GAP TYPE-2 200 -? SCAFFOLD_1:10173149-11503208 RL_1 PLUS +? SCAFFOLD_22:4212155-4349000 SUPER_1 MINUS GAP TYPE-2 200 -? SCAFFOLD_1:11503409-11967822 RL_1 PLUS +? SCAFFOLD_22:3720955-4211954 SUPER_1 MINUS GAP TYPE-2 200 -? SCAFFOLD_1:11968023-12046008 RL_1 PLUS +? SCAFFOLD_86:1-156938 SUPER_1 PLUS GAP TYPE-2 200 -? SCAFFOLD_1:12046209-12090469 RL_1 PLUS +? SCAFFOLD_60:1-310000 SUPER_1 MINUS GAP TYPE-2 200 -? SCAFFOLD_44:1-500958 RL_1 PLUS +? SCAFFOLD_22:4414065-4671405 SUPER_1 MINUS GAP TYPE-2 200 -? SCAFFOLD_1:12223385-13876055 RL_1 PLUS +? SCAFFOLD_63:1-289187 SUPER_1 MINUS GAP TYPE-2 200 -? SCAFFOLD_1:13876256-14646755 RL_1 PLUS +? SCAFFOLD_2:3375910-3810281 SUPER_1 MINUS GAP TYPE-2 200 -? SCAFFOLD_1:14646956-15921159 RL_1 PLUS +? SCAFFOLD_2:3202558-3291418 SUPER_1 MINUS GAP TYPE-2 200 -? SCAFFOLD_1:15921360-16553359 RL_1 PLUS +? SCAFFOLD_2:3087219-3202357 SUPER_1 MINUS GAP TYPE-2 200 -? SCAFFOLD_1:16553560-17376505 RL_1 PLUS +? SCAFFOLD_2:2231019-3087018 SUPER_1 MINUS GAP TYPE-2 200 -? SCAFFOLD_1:17376706-18229857 RL_1 PLUS +? SCAFFOLD_2:800160-1091555 SUPER_1 MINUS GAP TYPE-2 200 -? SCAFFOLD_1:18230058-18415808 RL_1 PLUS +? SCAFFOLD_2:1402184-2230818 SUPER_1 PLUS GAP TYPE-2 200 -? SCAFFOLD_1:18416009-18777008 RL_1 PLUS +? SCAFFOLD_2:4510029-4997371 SUPER_1 MINUS GAP TYPE-2 200 -? SCAFFOLD_1:18777209-20523756 RL_1 PLUS +? SCAFFOLD_2:4136547-4509828 SUPER_1 MINUS GAP TYPE-2 200 -? SCAFFOLD_1:20523957-21292438 RL_1 PLUS +? SCAFFOLD_2:3810282-4136346 SUPER_1 MINUS GAP TYPE-2 200 -? SCAFFOLD_1:21292639-22097242 RL_1 PLUS +? SCAFFOLD_2:4997572-5106209 SUPER_1 PLUS GAP TYPE-2 200 -? SCAFFOLD_1:22097443-22412405 RL_1 PLUS +? SCAFFOLD_2:5106410-5256792 SUPER_1 PLUS GAP TYPE-2 200 -? SCAFFOLD_1:22412606-23016264 RL_1 PLUS +? SCAFFOLD_2:5256993-5351992 SUPER_1 PLUS GAP TYPE-2 200 -? SCAFFOLD_1:23016465-24056245 RL_1 PLUS +? SCAFFOLD_2:5352193-5660616 SUPER_1 PLUS GAP TYPE-2 200 -? SCAFFOLD_1:24056446-25460472 RL_1 PLUS +? SCAFFOLD_2:5660817-5985343 SUPER_1 PLUS GAP TYPE-2 200 -? SCAFFOLD_1:25460673-25978502 RL_1 PLUS +? SCAFFOLD_2:5985544-6458571 SUPER_1 PLUS GAP TYPE-2 200 -? SCAFFOLD_1:26112824-27042845 RL_1 PLUS +? SCAFFOLD_2:6458772-7251552 SUPER_1 PLUS GAP TYPE-2 200 -? SCAFFOLD_1:27043046-27258568 RL_1 PLUS +? SCAFFOLD_2:7251753-7447883 SUPER_1 PLUS GAP TYPE-2 200 -? SCAFFOLD_1:27258769-27396238 RL_1 PLUS +? SCAFFOLD_2:7643426-9394209 SUPER_1 PLUS GAP TYPE-2 200 -? SCAFFOLD_1:27396439-28135201 RL_1 PLUS +? SCAFFOLD_2:9394410-9655469 SUPER_1 PLUS GAP TYPE-2 200 -? SCAFFOLD_1:28135402-28343088 RL_1 PLUS +? SCAFFOLD_2:9655670-10645490 SUPER_1 PLUS GAP TYPE-2 200 -? SCAFFOLD_1:28343289-28522679 RL_1 PLUS +? SCAFFOLD_2:10645691-11938981 SUPER_1 PLUS GAP TYPE-2 200 -? SCAFFOLD_1:28522880-28898877 RL_1 PLUS +? SCAFFOLD_2:11939182-12509422 SUPER_1 PLUS GAP TYPE-2 200 -? SCAFFOLD_1:28899078-29103275 RL_1 PLUS +? SCAFFOLD_2:12509623-12765304 SUPER_1 PLUS GAP TYPE-2 200 -? SCAFFOLD_1:29103476-29159344 RL_1 PLUS +? SCAFFOLD_2:12765505-14104107 SUPER_1 PLUS GAP TYPE-2 200 -? SCAFFOLD_1:29159545-29392775 RL_1 PLUS +? SCAFFOLD_2:14104308-14224050 SUPER_1 PLUS GAP TYPE-2 200 -? 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SCAFFOLD_26:5756564-6200142 RL_21 MINUS +? SCAFFOLD_18:10618207-11014112 SUPER_20 PLUS GAP TYPE-2 200 -? SCAFFOLD_26:5690387-5756363 RL_21 MINUS +? SCAFFOLD_18:11014313-11723312 SUPER_20 PLUS GAP TYPE-2 200 -? SCAFFOLD_26:5570047-5690186 RL_21 MINUS +? SCAFFOLD_18:11723513-12086540 SUPER_20 PLUS GAP TYPE-2 200 -? SCAFFOLD_26:5347644-5569846 RL_21 MINUS +? SCAFFOLD_18:12086741-13096105 SUPER_20 PLUS +? SCAFFOLD_17:1-976330 SUPER_21 PLUS GAP TYPE-2 200 -? SCAFFOLD_26:5147583-5347443 RL_21 MINUS +? SCAFFOLD_17:1150706-2401527 SUPER_21 PLUS GAP TYPE-2 200 -? SCAFFOLD_26:5087069-5147382 RL_21 MINUS +? SCAFFOLD_17:2401728-2994736 SUPER_21 PLUS GAP TYPE-2 200 -? SCAFFOLD_26:4863892-5086868 RL_21 MINUS +? SCAFFOLD_17:2994937-3134936 SUPER_21 PLUS GAP TYPE-2 200 -? SCAFFOLD_26:4818313-4863691 RL_21 MINUS +? SCAFFOLD_17:3135137-3485828 SUPER_21 PLUS GAP TYPE-2 200 -? SCAFFOLD_26:4660295-4818112 RL_21 MINUS +? SCAFFOLD_17:3486029-3519499 SUPER_21 PLUS GAP TYPE-2 200 -? SCAFFOLD_26:3701347-4660094 RL_21 MINUS +? SCAFFOLD_17:3519700-3567535 SUPER_21 PLUS GAP TYPE-2 200 -? SCAFFOLD_26:3135719-3701146 RL_21 MINUS +? SCAFFOLD_17:3567736-3932234 SUPER_21 PLUS GAP TYPE-2 200 -? SCAFFOLD_26:2986840-3135518 RL_21 MINUS +? SCAFFOLD_17:3932435-4210317 SUPER_21 PLUS GAP TYPE-2 200 -? SCAFFOLD_26:2770035-2986639 RL_21 MINUS +? SCAFFOLD_17:4210518-4432861 SUPER_21 PLUS GAP TYPE-2 200 -? SCAFFOLD_26:2716784-2769834 RL_21 MINUS +? SCAFFOLD_17:4433062-4500930 SUPER_21 PLUS GAP TYPE-2 200 -? SCAFFOLD_68:1-266000 RL_21 PLUS +? SCAFFOLD_17:4501131-4568659 SUPER_21 PLUS GAP TYPE-2 200 -? SCAFFOLD_26:1889402-2716583 RL_21 MINUS +? SCAFFOLD_17:4568860-4919564 SUPER_21 PLUS GAP TYPE-2 200 -? SCAFFOLD_26:795282-1889201 RL_21 MINUS +? SCAFFOLD_17:4919765-5381850 SUPER_21 PLUS GAP TYPE-2 200 -? SCAFFOLD_26:1-795081 RL_21 MINUS +? SCAFFOLD_17:5382051-5612105 SUPER_21 PLUS GAP TYPE-2 200 -? SCAFFOLD_21:1-905967 RL_21 PLUS +? SCAFFOLD_17:5612306-6624329 SUPER_21 PLUS GAP TYPE-2 200 -? SCAFFOLD_21:906168-1574362 RL_21 PLUS +? SCAFFOLD_17:6624530-7124710 SUPER_21 PLUS GAP TYPE-2 200 -? SCAFFOLD_21:1574563-2190926 RL_21 PLUS +? SCAFFOLD_17:7124911-7277027 SUPER_21 PLUS GAP TYPE-2 200 -? SCAFFOLD_21:2191127-2974728 RL_21 PLUS +? SCAFFOLD_17:7277228-7424206 SUPER_21 PLUS GAP TYPE-2 200 -? SCAFFOLD_27:2831871-3527354 RL_21 MINUS +? SCAFFOLD_17:7424407-7764491 SUPER_21 PLUS GAP TYPE-2 200 -? SCAFFOLD_27:2764096-2831670 RL_21 MINUS +? SCAFFOLD_17:7764692-8469878 SUPER_21 PLUS GAP TYPE-2 200 -? SCAFFOLD_27:1788586-2763895 RL_21 MINUS +? SCAFFOLD_17:8470079-8661602 SUPER_21 PLUS GAP TYPE-2 200 -? SCAFFOLD_27:1333498-1788385 RL_21 MINUS +? SCAFFOLD_17:8661803-8772450 SUPER_21 PLUS GAP TYPE-2 200 -? SCAFFOLD_27:1-1333297 RL_21 MINUS +? SCAFFOLD_17:8772651-9179835 SUPER_21 PLUS GAP TYPE-2 200 -? SCAFFOLD_55:1-400413 RL_21 MINUS +? SCAFFOLD_17:9180036-9887400 SUPER_21 PLUS GAP TYPE-2 200 -? SCAFFOLD_21:8787732-12921393 RL_21 MINUS +? SCAFFOLD_17:9887601-10461066 SUPER_21 PLUS GAP TYPE-2 200 -? SCAFFOLD_21:7951431-8787531 RL_21 MINUS +? SCAFFOLD_17:10461267-10813266 SUPER_21 PLUS GAP TYPE-2 200 -? SCAFFOLD_21:7617282-7951230 RL_21 MINUS +? SCAFFOLD_17:10813467-12369466 SUPER_21 PLUS GAP TYPE-2 200 -? SCAFFOLD_21:6394404-7617081 RL_21 MINUS +? SCAFFOLD_17:12369667-13108038 SUPER_21 PLUS GAP TYPE-2 200 -? SCAFFOLD_21:6358988-6394203 RL_21 MINUS +? SCAFFOLD_17:13108239-13760125 SUPER_21 PLUS GAP TYPE-2 200 -? SCAFFOLD_21:5914021-6358787 RL_21 MINUS +? SCAFFOLD_17:13760326-13872814 SUPER_21 PLUS +? SCAFFOLD_19:1-627649 SUPER_22 PLUS GAP TYPE-2 200 -? SCAFFOLD_21:5549387-5913820 RL_21 MINUS +? SCAFFOLD_19:627850-2095610 SUPER_22 PLUS GAP TYPE-2 200 -? SCAFFOLD_21:5415146-5549186 RL_21 MINUS +? SCAFFOLD_19:2095811-2295388 SUPER_22 PLUS GAP TYPE-2 200 -? SCAFFOLD_21:4361509-5414945 RL_21 MINUS +? SCAFFOLD_19:2295589-2325015 SUPER_22 PLUS GAP TYPE-2 200 -? SCAFFOLD_21:3985114-4361308 RL_21 MINUS +? SCAFFOLD_19:2325216-2366211 SUPER_22 PLUS GAP TYPE-2 200 -? SCAFFOLD_21:2974929-3984913 RL_21 MINUS -? SCAFFOLD_25:1-2329745 RL_22 PLUS +? SCAFFOLD_19:2366412-2733958 SUPER_22 PLUS GAP TYPE-2 200 -? SCAFFOLD_25:2329946-3743464 RL_22 PLUS +? SCAFFOLD_19:2734159-2863538 SUPER_22 PLUS GAP TYPE-2 200 -? SCAFFOLD_25:3743665-4071220 RL_22 PLUS +? SCAFFOLD_19:2863739-2975263 SUPER_22 PLUS GAP TYPE-2 200 -? SCAFFOLD_25:4071421-5151935 RL_22 PLUS +? SCAFFOLD_19:2975464-4287534 SUPER_22 PLUS GAP TYPE-2 200 -? SCAFFOLD_25:5152136-5978455 RL_22 PLUS +? SCAFFOLD_19:4287735-4395207 SUPER_22 PLUS GAP TYPE-2 200 -? SCAFFOLD_25:5978656-6401358 RL_22 PLUS +? SCAFFOLD_19:4395408-4497597 SUPER_22 PLUS GAP TYPE-2 200 -? SCAFFOLD_23:116830-224150 RL_22 PLUS +? SCAFFOLD_19:4497798-4777758 SUPER_22 PLUS GAP TYPE-2 200 -? SCAFFOLD_23:224351-308875 RL_22 PLUS +? SCAFFOLD_19:5572412-5860210 SUPER_22 PLUS GAP TYPE-2 200 -? SCAFFOLD_23:309076-935194 RL_22 PLUS +? SCAFFOLD_19:5860411-6619247 SUPER_22 PLUS GAP TYPE-2 200 -? SCAFFOLD_23:935395-1218526 RL_22 PLUS +? SCAFFOLD_19:6619448-6827315 SUPER_22 PLUS GAP TYPE-2 200 -? SCAFFOLD_23:1218727-1402600 RL_22 PLUS +? SCAFFOLD_19:6827516-6927855 SUPER_22 PLUS GAP TYPE-2 200 -? SCAFFOLD_23:1402801-1623034 RL_22 PLUS +? SCAFFOLD_19:6928056-7346055 SUPER_22 PLUS GAP TYPE-2 200 -? SCAFFOLD_23:1623235-2518401 RL_22 PLUS +? SCAFFOLD_19:7346256-7481186 SUPER_22 PLUS GAP TYPE-2 200 -? SCAFFOLD_23:2518602-2664689 RL_22 PLUS +? SCAFFOLD_19:7481387-8535924 SUPER_22 PLUS GAP TYPE-2 200 -? SCAFFOLD_23:2664890-2902852 RL_22 PLUS +? SCAFFOLD_19:8536125-8606868 SUPER_22 PLUS GAP TYPE-2 200 -? SCAFFOLD_23:2903053-2988749 RL_22 PLUS +? SCAFFOLD_19:8607069-8734801 SUPER_22 PLUS GAP TYPE-2 200 -? SCAFFOLD_23:2988950-3039413 RL_22 PLUS +? SCAFFOLD_19:8735002-9126302 SUPER_22 PLUS GAP TYPE-2 200 -? SCAFFOLD_23:3039614-3381199 RL_22 PLUS +? SCAFFOLD_19:9126503-9848563 SUPER_22 PLUS GAP TYPE-2 200 -? SCAFFOLD_23:3381400-3524341 RL_22 PLUS +? SCAFFOLD_19:9848764-10003558 SUPER_22 PLUS GAP TYPE-2 200 -? SCAFFOLD_23:3524542-4067791 RL_22 PLUS +? SCAFFOLD_19:10003759-10272087 SUPER_22 PLUS GAP TYPE-2 200 -? SCAFFOLD_23:4067992-6408469 RL_22 PLUS +? SCAFFOLD_19:10272288-10720382 SUPER_22 PLUS GAP TYPE-2 200 -? SCAFFOLD_23:6408670-7892048 RL_22 PLUS +? SCAFFOLD_19:10849370-11984033 SUPER_22 PLUS GAP TYPE-2 200 -? SCAFFOLD_23:7892249-8115527 RL_22 PLUS +? SCAFFOLD_19:11984234-12669979 SUPER_22 PLUS GAP TYPE-2 200 -? SCAFFOLD_23:8115728-8413933 RL_22 PLUS +? SCAFFOLD_19:12670180-13061561 SUPER_22 PLUS ? SCAFFOLD_47:1-482541 SCAFFOLD_47 PLUS ? SCAFFOLD_49:1-468513 SCAFFOLD_49 PLUS ? SCAFFOLD_51:1-463377 SCAFFOLD_51 PLUS diff --git a/tests/data/idDilFebr1/chrs.csv b/tests/data/idDilFebr1/chrs.csv deleted file mode 100644 index d7a165c..0000000 --- a/tests/data/idDilFebr1/chrs.csv +++ /dev/null @@ -1,6 +0,0 @@ -RL_1 -RL_2 -RL_3 -RL_4 -RL_5 -X diff --git a/tests/data/idDilFebr1/idDilFebr1-pretext-to-tpf.chr_report.csv b/tests/data/idDilFebr1/idDilFebr1-pretext-to-tpf.chr_report.csv new file mode 100644 index 0000000..11f3da4 --- /dev/null +++ b/tests/data/idDilFebr1/idDilFebr1-pretext-to-tpf.chr_report.csv @@ -0,0 +1,7 @@ +assembly,seq_name,chr_name,localised,pretext_scaffold,length,length_minus_gaps +Primary,SUPER_1,1,true,Scaffold_1,70722326,70706926 +Primary,SUPER_2,2,true,Scaffold_2,60202627,60189227 +Primary,SUPER_3,3,true,Scaffold_3,48912965,48901365 +Primary,SUPER_4,4,true,Scaffold_4,46956897,46946897 +Primary,SUPER_5,5,true,Scaffold_5,41264860,41257060 +Primary,SUPER_X,X,true,Scaffold_6,24678171,24666171 diff --git a/tests/data/idDilFebr1/idDilFebr1-pretext-to-tpf.chromsomes.list.csv b/tests/data/idDilFebr1/idDilFebr1-pretext-to-tpf.chromsomes.list.csv new file mode 100644 index 0000000..3f61023 --- /dev/null +++ b/tests/data/idDilFebr1/idDilFebr1-pretext-to-tpf.chromsomes.list.csv @@ -0,0 +1,6 @@ +SUPER_1 +SUPER_2 +SUPER_3 +SUPER_4 +SUPER_5 +SUPER_X diff --git a/tests/data/idDilFebr1/idDilFebr1-pretext-to-tpf_Haplotigs.tpf b/tests/data/idDilFebr1/idDilFebr1-pretext-to-tpf.haplotigs.tpf similarity index 100% rename from tests/data/idDilFebr1/idDilFebr1-pretext-to-tpf_Haplotigs.tpf rename to tests/data/idDilFebr1/idDilFebr1-pretext-to-tpf.haplotigs.tpf diff --git a/tests/data/idDilFebr1/idDilFebr1-pretext-to-tpf.log b/tests/data/idDilFebr1/idDilFebr1-pretext-to-tpf.log index f6e6b7e..b2c90e1 100644 --- a/tests/data/idDilFebr1/idDilFebr1-pretext-to-tpf.log +++ b/tests/data/idDilFebr1/idDilFebr1-pretext-to-tpf.log @@ -5,13 +5,13 @@ idDilFebr1-pretext-to-tpf 308,817,177 bp sequence (minus gaps) Autosomes: n = 5 - 70,706,926 RL_1 + 70,706,926 SUPER_1 ... ... - 41,257,060 RL_5 + 41,257,060 SUPER_5 268,001,475 bp total Named: n = 1 - 24,666,171 X + 24,666,171 SUPER_X Unplaced: n = 120 1,535,000 scaffold_8 @@ -19,7 +19,7 @@ idDilFebr1-pretext-to-tpf 1,000 scaffold_162 16,149,531 bp total -idDilFebr1-pretext-to-tpf_Haplotigs +idDilFebr1-pretext-to-tpf.haplotigs 3,119,814 bp sequence (minus gaps) n = 7 950,000 H_1 diff --git a/tests/data/idDilFebr1/idDilFebr1-pretext-to-tpf.tpf b/tests/data/idDilFebr1/idDilFebr1-pretext-to-tpf.tpf index aff22f7..0e26df8 100644 --- a/tests/data/idDilFebr1/idDilFebr1-pretext-to-tpf.tpf +++ b/tests/data/idDilFebr1/idDilFebr1-pretext-to-tpf.tpf @@ -1,711 +1,711 @@ -? scaffold_1:1-1260473 RL_1 PLUS +? scaffold_1:1-1260473 SUPER_1 PLUS GAP TYPE-2 200 -? scaffold_1:1260674-1297323 RL_1 PLUS +? scaffold_1:1260674-1297323 SUPER_1 PLUS GAP TYPE-2 200 -? scaffold_1:1297524-1686753 RL_1 PLUS +? scaffold_1:1297524-1686753 SUPER_1 PLUS GAP TYPE-2 200 -? scaffold_1:1686954-3871914 RL_1 PLUS +? scaffold_1:1686954-3871914 SUPER_1 PLUS GAP TYPE-2 200 -? scaffold_1:3872115-4491480 RL_1 PLUS +? scaffold_1:3872115-4491480 SUPER_1 PLUS GAP TYPE-2 200 -? scaffold_1:4491681-6945990 RL_1 PLUS +? scaffold_1:4491681-6945990 SUPER_1 PLUS GAP TYPE-2 200 -? scaffold_1:6946191-7727539 RL_1 PLUS +? scaffold_1:6946191-7727539 SUPER_1 PLUS GAP TYPE-2 200 -? scaffold_1:7727740-7883825 RL_1 PLUS +? scaffold_1:7727740-7883825 SUPER_1 PLUS GAP TYPE-2 200 -? scaffold_1:7883826-8600631 RL_1 PLUS +? scaffold_1:7883826-8600631 SUPER_1 PLUS GAP TYPE-2 200 -? scaffold_1:8600832-8717058 RL_1 PLUS +? scaffold_1:8600832-8717058 SUPER_1 PLUS GAP TYPE-2 200 -? scaffold_1:8717259-8753098 RL_1 PLUS +? scaffold_1:8717259-8753098 SUPER_1 PLUS GAP TYPE-2 200 -? scaffold_1:8753299-8873522 RL_1 PLUS +? scaffold_1:8753299-8873522 SUPER_1 PLUS GAP TYPE-2 200 -? scaffold_1:8873723-9158679 RL_1 PLUS +? scaffold_1:8873723-9158679 SUPER_1 PLUS GAP TYPE-2 200 -? scaffold_1:9158880-9412450 RL_1 PLUS +? scaffold_1:9158880-9412450 SUPER_1 PLUS GAP TYPE-2 200 -? scaffold_1:10362851-11847104 RL_1 PLUS +? scaffold_1:10362851-11847104 SUPER_1 PLUS GAP TYPE-2 200 -? scaffold_1:12168513-13458090 RL_1 PLUS +? scaffold_1:12168513-13458090 SUPER_1 PLUS GAP TYPE-2 200 -? scaffold_1:13458291-14690529 RL_1 PLUS +? scaffold_1:13458291-14690529 SUPER_1 PLUS GAP TYPE-2 200 -? scaffold_1:14690730-15027649 RL_1 PLUS +? scaffold_1:14690730-15027649 SUPER_1 PLUS GAP TYPE-2 200 -? scaffold_1:15027850-15573440 RL_1 PLUS +? scaffold_1:15027850-15573440 SUPER_1 PLUS GAP TYPE-2 200 -? scaffold_1:15573641-16000438 RL_1 PLUS +? scaffold_1:15573641-16000438 SUPER_1 PLUS GAP TYPE-2 200 -? scaffold_23:1-438823 RL_1 PLUS +? scaffold_23:1-438823 SUPER_1 PLUS GAP TYPE-2 200 -? scaffold_1:16000639-16716659 RL_1 PLUS +? scaffold_1:16000639-16716659 SUPER_1 PLUS GAP TYPE-2 200 -? scaffold_1:16716860-17614477 RL_1 PLUS +? scaffold_1:16716860-17614477 SUPER_1 PLUS GAP TYPE-2 200 -? scaffold_1:17614678-18457106 RL_1 PLUS +? scaffold_1:17614678-18457106 SUPER_1 PLUS GAP TYPE-2 200 -? scaffold_1:18457307-22063306 RL_1 PLUS +? scaffold_1:18457307-22063306 SUPER_1 PLUS GAP TYPE-2 200 -? scaffold_1:22063507-23396974 RL_1 PLUS +? scaffold_1:22063507-23396974 SUPER_1 PLUS GAP TYPE-2 200 -? scaffold_1:23397175-24599054 RL_1 PLUS +? scaffold_1:23397175-24599054 SUPER_1 PLUS GAP TYPE-2 200 -? scaffold_1:24599255-27743129 RL_1 PLUS +? scaffold_1:24599255-27743129 SUPER_1 PLUS GAP TYPE-2 200 -? scaffold_1:27743330-28709329 RL_1 PLUS +? scaffold_1:27743330-28709329 SUPER_1 PLUS GAP TYPE-2 200 -? scaffold_1:28709530-28798215 RL_1 PLUS +? scaffold_1:28709530-28798215 SUPER_1 PLUS GAP TYPE-2 200 -? scaffold_1:28798416-28974830 RL_1 PLUS +? scaffold_1:28798416-28974830 SUPER_1 PLUS GAP TYPE-2 200 -? scaffold_1:28975031-29116832 RL_1 PLUS +? scaffold_1:28975031-29116832 SUPER_1 PLUS GAP TYPE-2 200 -? scaffold_1:29116833-31692834 RL_1 PLUS +? scaffold_1:29116833-31692834 SUPER_1 PLUS GAP TYPE-2 200 -? scaffold_1:31693035-32117456 RL_1 PLUS +? scaffold_1:31693035-32117456 SUPER_1 PLUS GAP TYPE-2 200 -? scaffold_1:32117657-33567908 RL_1 PLUS +? scaffold_1:32117657-33567908 SUPER_1 PLUS GAP TYPE-2 200 -? scaffold_1:33568109-34770027 RL_1 PLUS +? scaffold_1:33568109-34770027 SUPER_1 PLUS GAP TYPE-2 200 -? scaffold_1:34770228-34982094 RL_1 PLUS +? scaffold_1:34770228-34982094 SUPER_1 PLUS GAP TYPE-2 200 -? scaffold_1:34982095-36732227 RL_1 PLUS +? scaffold_1:34982095-36732227 SUPER_1 PLUS GAP TYPE-2 200 -? scaffold_1:36732428-37215960 RL_1 PLUS +? scaffold_1:36732428-37215960 SUPER_1 PLUS GAP TYPE-2 200 -? scaffold_1:37216161-37262837 RL_1 PLUS +? scaffold_1:37216161-37262837 SUPER_1 PLUS GAP TYPE-2 200 -? scaffold_1:37263038-37595871 RL_1 PLUS +? scaffold_1:37263038-37595871 SUPER_1 PLUS GAP TYPE-2 200 -? scaffold_1:37596072-39243443 RL_1 PLUS +? scaffold_1:37596072-39243443 SUPER_1 PLUS GAP TYPE-2 200 -? scaffold_1:39243644-40333145 RL_1 PLUS +? scaffold_1:39243644-40333145 SUPER_1 PLUS GAP TYPE-2 200 -? scaffold_1:40333346-41230858 RL_1 PLUS +? scaffold_1:40333346-41230858 SUPER_1 PLUS GAP TYPE-2 200 -? scaffold_1:41231059-42974633 RL_1 PLUS +? scaffold_1:41231059-42974633 SUPER_1 PLUS GAP TYPE-2 200 -? scaffold_1:42974834-43512129 RL_1 PLUS +? scaffold_1:42974834-43512129 SUPER_1 PLUS GAP TYPE-2 200 -? scaffold_1:43512330-44763075 RL_1 PLUS +? scaffold_1:43512330-44763075 SUPER_1 PLUS GAP TYPE-2 200 -? scaffold_1:44763276-45620498 RL_1 PLUS +? scaffold_1:44763276-45620498 SUPER_1 PLUS GAP TYPE-2 200 -? scaffold_1:45620699-45783829 RL_1 PLUS +? scaffold_1:45620699-45783829 SUPER_1 PLUS GAP TYPE-2 200 -? scaffold_1:45784030-47597029 RL_1 PLUS +? scaffold_1:45784030-47597029 SUPER_1 PLUS GAP TYPE-2 200 -? scaffold_1:47597230-47679963 RL_1 PLUS +? scaffold_1:47597230-47679963 SUPER_1 PLUS GAP TYPE-2 200 -? scaffold_1:47680164-48702761 RL_1 PLUS +? scaffold_1:47680164-48702761 SUPER_1 PLUS GAP TYPE-2 200 -? scaffold_1:48702962-48948442 RL_1 PLUS +? scaffold_1:48702962-48948442 SUPER_1 PLUS GAP TYPE-2 200 -? scaffold_1:48948643-49360020 RL_1 PLUS +? scaffold_1:48948643-49360020 SUPER_1 PLUS GAP TYPE-2 200 -? scaffold_1:49360221-50312142 RL_1 PLUS +? scaffold_1:49360221-50312142 SUPER_1 PLUS GAP TYPE-2 200 -? scaffold_1:50312343-50527489 RL_1 PLUS +? scaffold_1:50312343-50527489 SUPER_1 PLUS GAP TYPE-2 200 -? scaffold_1:50527690-51052586 RL_1 PLUS +? scaffold_1:50527690-51052586 SUPER_1 PLUS GAP TYPE-2 200 -? scaffold_1:51052787-51376529 RL_1 PLUS +? scaffold_1:51052787-51376529 SUPER_1 PLUS GAP TYPE-2 200 -? scaffold_1:51376730-51830729 RL_1 PLUS +? scaffold_1:51376730-51830729 SUPER_1 PLUS GAP TYPE-2 200 -? scaffold_1:51830930-52100470 RL_1 PLUS +? scaffold_1:51830930-52100470 SUPER_1 PLUS GAP TYPE-2 200 -? scaffold_1:52100671-53969495 RL_1 PLUS +? scaffold_1:52100671-53969495 SUPER_1 PLUS GAP TYPE-2 200 -? scaffold_1:53969696-54582370 RL_1 PLUS +? scaffold_1:53969696-54582370 SUPER_1 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scaffold_6:11591213-11798596 SUPER_X PLUS GAP TYPE-2 200 -? scaffold_6:11798797-11869716 X PLUS +? scaffold_6:11798797-11869716 SUPER_X PLUS GAP TYPE-2 200 -? scaffold_6:11869917-12183605 X PLUS +? scaffold_6:11869917-12183605 SUPER_X PLUS GAP TYPE-2 200 -? scaffold_6:12183806-12797333 X PLUS +? scaffold_6:12183806-12797333 SUPER_X PLUS GAP TYPE-2 200 -? scaffold_6:12797534-12834989 X PLUS +? scaffold_6:12797534-12834989 SUPER_X PLUS GAP TYPE-2 200 -? scaffold_6:12835190-13644629 X PLUS +? scaffold_6:12835190-13644629 SUPER_X PLUS ? scaffold_8:1-1535000 scaffold_8 PLUS ? scaffold_11:1-1150633 scaffold_11 PLUS ? scaffold_13:1-941880 scaffold_13 PLUS diff --git a/tests/data/idSyrVitr1/chrs.csv b/tests/data/idSyrVitr1/chrs.csv deleted file mode 100644 index 879a7fb..0000000 --- a/tests/data/idSyrVitr1/chrs.csv +++ /dev/null @@ -1,5 +0,0 @@ -RL_1 -RL_2 -RL_3 -X -Y diff --git a/tests/data/idSyrVitr1/idSyrVitr1-pretext-to-tpf.chr_report.csv b/tests/data/idSyrVitr1/idSyrVitr1-pretext-to-tpf.chr_report.csv new file mode 100644 index 0000000..13b3733 --- /dev/null +++ b/tests/data/idSyrVitr1/idSyrVitr1-pretext-to-tpf.chr_report.csv @@ -0,0 +1,6 @@ +assembly,seq_name,chr_name,localised,pretext_scaffold,length,length_minus_gaps +Primary,SUPER_1,1,true,Scaffold_1,148792233,148767433 +Primary,SUPER_2,2,true,Scaffold_3,110905286,110870686 +Primary,SUPER_3,3,true,Scaffold_2,110522704,110494704 +Primary,SUPER_X,X,true,Scaffold_4,8861054,8853854 +Primary,SUPER_Y,Y,true,Scaffold_5,889347,888747 diff --git a/tests/data/idSyrVitr1/idSyrVitr1-pretext-to-tpf.chromsomes.list.csv b/tests/data/idSyrVitr1/idSyrVitr1-pretext-to-tpf.chromsomes.list.csv new file mode 100644 index 0000000..822f517 --- /dev/null +++ b/tests/data/idSyrVitr1/idSyrVitr1-pretext-to-tpf.chromsomes.list.csv @@ -0,0 +1,5 @@ +SUPER_1 +SUPER_2 +SUPER_3 +SUPER_X +SUPER_Y diff --git a/tests/data/idSyrVitr1/idSyrVitr1-pretext-to-tpf_Haplotigs.tpf b/tests/data/idSyrVitr1/idSyrVitr1-pretext-to-tpf.haplotigs.tpf similarity index 100% rename from tests/data/idSyrVitr1/idSyrVitr1-pretext-to-tpf_Haplotigs.tpf rename to tests/data/idSyrVitr1/idSyrVitr1-pretext-to-tpf.haplotigs.tpf diff --git a/tests/data/idSyrVitr1/idSyrVitr1-pretext-to-tpf.log b/tests/data/idSyrVitr1/idSyrVitr1-pretext-to-tpf.log index 526b3f3..2605947 100644 --- a/tests/data/idSyrVitr1/idSyrVitr1-pretext-to-tpf.log +++ b/tests/data/idSyrVitr1/idSyrVitr1-pretext-to-tpf.log @@ -5,14 +5,14 @@ idSyrVitr1-pretext-to-tpf 388,720,741 bp sequence (minus gaps) Autosomes: n = 3 - 148,767,433 RL_1 - 110,870,686 RL_3 - 110,494,704 RL_2 + 148,767,433 SUPER_1 + 110,870,686 SUPER_2 + 110,494,704 SUPER_3 370,132,823 bp total Named: n = 2 - 8,853,854 X - 888,747 Y + 8,853,854 SUPER_X + 888,747 SUPER_Y 9,742,601 bp total Unplaced: n = 394 @@ -21,7 +21,7 @@ idSyrVitr1-pretext-to-tpf 1,000 scaffold_492 8,845,317 bp total -idSyrVitr1-pretext-to-tpf_Haplotigs +idSyrVitr1-pretext-to-tpf.haplotigs 812,954 bp sequence (minus gaps) n = 1 812,954 H_1 diff --git a/tests/data/idSyrVitr1/idSyrVitr1-pretext-to-tpf.tpf b/tests/data/idSyrVitr1/idSyrVitr1-pretext-to-tpf.tpf index c87570a..2102d99 100644 --- a/tests/data/idSyrVitr1/idSyrVitr1-pretext-to-tpf.tpf +++ b/tests/data/idSyrVitr1/idSyrVitr1-pretext-to-tpf.tpf @@ -1,960 +1,960 @@ -? scaffold_1:1-2795873 RL_1 PLUS +? scaffold_1:1-2795873 SUPER_1 PLUS GAP TYPE-2 200 -? scaffold_1:2796074-5816795 RL_1 PLUS +? scaffold_1:2796074-5816795 SUPER_1 PLUS GAP TYPE-2 200 -? scaffold_1:5816996-6609255 RL_1 PLUS +? scaffold_1:5816996-6609255 SUPER_1 PLUS GAP TYPE-2 200 -? scaffold_1:6609456-7809381 RL_1 PLUS +? scaffold_1:6609456-7809381 SUPER_1 PLUS GAP TYPE-2 200 -? scaffold_1:7809582-8605664 RL_1 PLUS +? scaffold_1:7809582-8605664 SUPER_1 PLUS GAP TYPE-2 200 -? scaffold_1:8605865-9486617 RL_1 PLUS +? scaffold_1:8605865-9486617 SUPER_1 PLUS GAP TYPE-2 200 -? scaffold_1:9486818-12108918 RL_1 PLUS +? 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scaffold_67:1-103476 SUPER_X MINUS +? scaffold_17:1-682345 SUPER_Y MINUS GAP TYPE-2 200 -? scaffold_202:1-24479 Y PLUS +? scaffold_202:1-24479 SUPER_Y PLUS GAP TYPE-2 200 -? scaffold_99:1-57860 Y PLUS +? scaffold_99:1-57860 SUPER_Y PLUS GAP TYPE-2 200 -? scaffold_60:1-124063 Y MINUS +? scaffold_60:1-124063 SUPER_Y MINUS ? scaffold_59:1-124136 scaffold_59 PLUS ? scaffold_80:1-90673 scaffold_80 PLUS ? scaffold_81:1-83613 scaffold_81 PLUS diff --git a/tests/data/ilIthSala1_1/chrs_HAP1.csv b/tests/data/ilIthSala1_1/chrs_HAP1.csv deleted file mode 100644 index 41f7b7b..0000000 --- a/tests/data/ilIthSala1_1/chrs_HAP1.csv +++ /dev/null @@ -1,40 +0,0 @@ -RL_3 -RL_5 -RL_7 -RL_9 -RL_11 -RL_13 -RL_15 -RL_17 -RL_19 -RL_21 -RL_23 -RL_25 -RL_27 -RL_29 -RL_31 -RL_33 -RL_35 -RL_37 -RL_39 -RL_41 -RL_43 -RL_45 -RL_47 -RL_49 -RL_51 -RL_53 -RL_55 -RL_57 -RL_59 -RL_61 -RL_63 -RL_65 -RL_67 -RL_69 -RL_71 -RL_73 -RL_75 -RL_77 -W -Z diff --git a/tests/data/ilIthSala1_1/chrs_HAP2.csv b/tests/data/ilIthSala1_1/chrs_HAP2.csv deleted file mode 100644 index 3b1eff5..0000000 --- a/tests/data/ilIthSala1_1/chrs_HAP2.csv +++ /dev/null @@ -1,38 +0,0 @@ -RL_4 -RL_6 -RL_8 -RL_10 -RL_12 -RL_14 -RL_16 -RL_18 -RL_20 -RL_22 -RL_24 -RL_26 -RL_28 -RL_30 -RL_32 -RL_34 -RL_36 -RL_38 -RL_40 -RL_42 -RL_44 -RL_46 -RL_48 -RL_50 -RL_52 -RL_54 -RL_56 -RL_58 -RL_60 -RL_62 -RL_64 -RL_66 -RL_68 -RL_70 -RL_72 -RL_74 -RL_76 -RL_78 diff --git a/tests/data/ilIthSala1_1/ilIthSala1_1-pretext-to-tpf.chr_report.csv b/tests/data/ilIthSala1_1/ilIthSala1_1-pretext-to-tpf.chr_report.csv new file mode 100644 index 0000000..3bbe447 --- /dev/null +++ b/tests/data/ilIthSala1_1/ilIthSala1_1-pretext-to-tpf.chr_report.csv @@ -0,0 +1,79 @@ +assembly,seq_name,chr_name,localised,pretext_scaffold,length,length_minus_gaps +HAP1,SUPER_1,1,true,Scaffold_61,14313964,14311964 +HAP1,SUPER_2,2,true,Scaffold_17,13346522,13345322 +HAP1,SUPER_3,3,true,Scaffold_3,13209869,13209269 +HAP1,SUPER_4,4,true,Scaffold_5,12957954,12957754 +HAP1,SUPER_5,5,true,Scaffold_9,12829641,12828841 +HAP1,SUPER_6,6,true,Scaffold_21,12290868,12289668 +HAP1,SUPER_7,7,true,Scaffold_7,11930245,11929845 +HAP1,SUPER_8,8,true,Scaffold_33,11888852,11887452 +HAP1,SUPER_9,9,true,Scaffold_19,11562400,11561400 +HAP1,SUPER_10,10,true,Scaffold_23,11251009,11251009 +HAP1,SUPER_11,11,true,Scaffold_25,11173113,11172913 +HAP1,SUPER_12,12,true,Scaffold_11,11002767,11002167 +HAP1,SUPER_13,13,true,Scaffold_13,10983742,10983342 +HAP1,SUPER_14,14,true,Scaffold_15,10817422,10817022 +HAP1,SUPER_15,15,true,Scaffold_63,10627428,10627228 +HAP1,SUPER_16,16,true,Scaffold_27,10517711,10517311 +HAP1,SUPER_17,17,true,Scaffold_29,10009591,10008791 +HAP1,SUPER_18,18,true,Scaffold_31,9944408,9943408 +HAP1,SUPER_19,19,true,Scaffold_45,9880787,9879387 +HAP1,SUPER_20,20,true,Scaffold_35,9468859,9467859 +HAP1,SUPER_21,21,true,Scaffold_43,9292417,9291417 +HAP1,SUPER_22,22,true,Scaffold_41,9283000,9283000 +HAP1,SUPER_23,23,true,Scaffold_37,9233975,9233175 +HAP1,SUPER_24,24,true,Scaffold_39,9173466,9172866 +HAP1,SUPER_25,25,true,Scaffold_47,9128898,9128898 +HAP1,SUPER_26,26,true,Scaffold_55,9105292,9105092 +HAP1,SUPER_27,27,true,Scaffold_57,8815526,8814926 +HAP1,SUPER_28,28,true,Scaffold_51,8748231,8746831 +HAP1,SUPER_29,29,true,Scaffold_53,8655892,8655492 +HAP1,SUPER_30,30,true,Scaffold_49,8377928,8377528 +HAP1,SUPER_31,31,true,Scaffold_59,8097000,8097000 +HAP1,SUPER_32,32,true,Scaffold_69,7812980,7811980 +HAP1,SUPER_33,33,true,Scaffold_67,7258966,7258566 +HAP1,SUPER_34,34,true,Scaffold_73,6770362,6769362 +HAP1,SUPER_35,35,true,Scaffold_77,6608688,6607288 +HAP1,SUPER_36,36,true,Scaffold_65,6178352,6178152 +HAP1,SUPER_37,37,true,Scaffold_71,6142792,6142192 +HAP1,SUPER_38,38,true,Scaffold_75,5759299,5759299 +HAP1,SUPER_W,W,true,Scaffold_2,14678643,14678243 +HAP1,SUPER_Z,Z,true,Scaffold_1,22376193,22375193 +HAP2,SUPER_1,1,true,Scaffold_62,10164907,10164507 +HAP2,SUPER_2,2,true,Scaffold_18,12042094,12040094 +HAP2,SUPER_3,3,true,Scaffold_4,13186411,13185411 +HAP2,SUPER_4,4,true,Scaffold_6,12322385,12320185 +HAP2,SUPER_5,5,true,Scaffold_10,12696688,12696288 +HAP2,SUPER_6,6,true,Scaffold_22,10178198,10177398 +HAP2,SUPER_7,7,true,Scaffold_8,11778170,11777570 +HAP2,SUPER_8,8,true,Scaffold_34,10138451,10137251 +HAP2,SUPER_9,9,true,Scaffold_20,9888140,9886540 +HAP2,SUPER_10,10,true,Scaffold_24,10442365,10441965 +HAP2,SUPER_11,11,true,Scaffold_26,10311773,10311173 +HAP2,SUPER_12,12,true,Scaffold_12,12909829,12908829 +HAP2,SUPER_13,13,true,Scaffold_14,9902359,9901759 +HAP2,SUPER_14,14,true,Scaffold_16,10192743,10192143 +HAP2,SUPER_15,15,true,Scaffold_64,10044571,10043971 +HAP2,SUPER_16,16,true,Scaffold_28,9970703,9970103 +HAP2,SUPER_17,17,true,Scaffold_30,9834157,9833357 +HAP2,SUPER_18,18,true,Scaffold_32,9357679,9355279 +HAP2,SUPER_19,19,true,Scaffold_46,7968749,7967949 +HAP2,SUPER_20,20,true,Scaffold_36,8201968,8200968 +HAP2,SUPER_21,21,true,Scaffold_44,9064061,9062261 +HAP2,SUPER_22,22,true,Scaffold_42,8903320,8902320 +HAP2,SUPER_23,23,true,Scaffold_38,8654297,8653697 +HAP2,SUPER_24,24,true,Scaffold_40,9558248,9557248 +HAP2,SUPER_25,25,true,Scaffold_48,8354552,8354352 +HAP2,SUPER_26,26,true,Scaffold_56,7855413,7854813 +HAP2,SUPER_27,27,true,Scaffold_58,6746038,6745638 +HAP2,SUPER_28,28,true,Scaffold_52,8395685,8394885 +HAP2,SUPER_29,29,true,Scaffold_54,8664816,8664016 +HAP2,SUPER_30,30,true,Scaffold_50,8295645,8295045 +HAP2,SUPER_31,31,true,Scaffold_60,7166572,7165972 +HAP2,SUPER_32,32,true,Scaffold_70,7196180,7195180 +HAP2,SUPER_33,33,true,Scaffold_68,7559665,7559065 +HAP2,SUPER_34,34,true,Scaffold_74,6754590,6753790 +HAP2,SUPER_35,35,true,Scaffold_78,6107446,6106046 +HAP2,SUPER_36,36,true,Scaffold_66,5065535,5064735 +HAP2,SUPER_37,37,true,Scaffold_72,5882705,5881905 +HAP2,SUPER_38,38,true,Scaffold_76,5781102,5780502 diff --git a/tests/data/ilIthSala1_1/ilIthSala1_1-pretext-to-tpf.hap1.chromsomes.list.csv b/tests/data/ilIthSala1_1/ilIthSala1_1-pretext-to-tpf.hap1.chromsomes.list.csv new file mode 100644 index 0000000..1e98df6 --- /dev/null +++ b/tests/data/ilIthSala1_1/ilIthSala1_1-pretext-to-tpf.hap1.chromsomes.list.csv @@ -0,0 +1,40 @@ +SUPER_1 +SUPER_2 +SUPER_3 +SUPER_4 +SUPER_5 +SUPER_6 +SUPER_7 +SUPER_8 +SUPER_9 +SUPER_10 +SUPER_11 +SUPER_12 +SUPER_13 +SUPER_14 +SUPER_15 +SUPER_16 +SUPER_17 +SUPER_18 +SUPER_19 +SUPER_20 +SUPER_21 +SUPER_22 +SUPER_23 +SUPER_24 +SUPER_25 +SUPER_26 +SUPER_27 +SUPER_28 +SUPER_29 +SUPER_30 +SUPER_31 +SUPER_32 +SUPER_33 +SUPER_34 +SUPER_35 +SUPER_36 +SUPER_37 +SUPER_38 +SUPER_W +SUPER_Z diff --git a/tests/data/ilIthSala1_1/ilIthSala1_1-pretext-to-tpf_HAP1.tpf b/tests/data/ilIthSala1_1/ilIthSala1_1-pretext-to-tpf.hap1.tpf similarity index 84% rename from tests/data/ilIthSala1_1/ilIthSala1_1-pretext-to-tpf_HAP1.tpf rename to tests/data/ilIthSala1_1/ilIthSala1_1-pretext-to-tpf.hap1.tpf index 8175420..c97484a 100644 --- a/tests/data/ilIthSala1_1/ilIthSala1_1-pretext-to-tpf_HAP1.tpf +++ b/tests/data/ilIthSala1_1/ilIthSala1_1-pretext-to-tpf.hap1.tpf @@ -1,309 +1,309 @@ -? HAP1_SCAFFOLD_2:2892294-3110867 RL_3 MINUS +? HAP1_SCAFFOLD_57:1-593303 SUPER_1 PLUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_2:613987-2892093 RL_3 MINUS +? HAP2_SCAFFOLD_24:2061846-6995845 SUPER_1 MINUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_2:1-613986 RL_3 PLUS +? HAP1_SCAFFOLD_31:5280288-7962338 SUPER_1 PLUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_2:3220021-13318622 RL_3 PLUS -? HAP1_SCAFFOLD_3:1-8405754 RL_5 MINUS +? HAP1_SCAFFOLD_20:9168872-9390185 SUPER_1 PLUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_3:8405955-12957954 RL_5 MINUS -? HAP1_SCAFFOLD_4:1-5716900 RL_7 PLUS +? HAP1_SCAFFOLD_41:3984093-4433732 SUPER_1 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_5:1394211-6255802 RL_7 MINUS +? HAP1_SCAFFOLD_84:1-360079 SUPER_1 PLUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_4:11324648-12676000 RL_7 PLUS -? HAP1_SCAFFOLD_5:1-3245623 RL_9 MINUS +? HAP1_SCAFFOLD_68:1-447509 SUPER_1 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_2:8114161-9010335 RL_9 MINUS +? HAP1_SCAFFOLD_81:1-368340 SUPER_1 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_2:6615009-8113960 RL_9 MINUS +? HAP1_SCAFFOLD_86:1-357454 SUPER_1 MINUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_5:5757833-12592823 RL_9 PLUS +? HAP1_SCAFFOLD_47:1-986097 SUPER_1 PLUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_88:1-353100 RL_9 MINUS -? HAP1_SCAFFOLD_8:1-1158382 RL_11 PLUS +? HAP1_SCAFFOLD_43:1-2912177 SUPER_1 MINUS +? HAP1_SCAFFOLD_19:1-411000 SUPER_2 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_3:1012223-3573542 RL_11 PLUS +? HAP1_SCAFFOLD_19:411201-5135357 SUPER_2 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_3:3573743-3995205 RL_11 PLUS +? HAP2_SCAFFOLD_4:10514592-11619421 SUPER_2 MINUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_8:4693589-11554590 RL_11 PLUS -? HAP1_SCAFFOLD_6:1-3397394 RL_13 PLUS +? HAP1_SCAFFOLD_19:6016471-9556443 SUPER_2 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_14:3047563-6867783 RL_13 PLUS +? HAP1_SCAFFOLD_50:1-696626 SUPER_2 MINUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_6:8113201-11878927 RL_13 MINUS -? HAP1_SCAFFOLD_7:1-3660743 RL_15 PLUS +? HAP1_SCAFFOLD_44:586872-2868936 SUPER_2 MINUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_7:3660944-7535543 RL_15 PLUS +? HAP1_SCAFFOLD_44:1-586671 SUPER_2 MINUS +? HAP1_SCAFFOLD_2:2892294-3110867 SUPER_3 MINUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_12:1-3281679 RL_15 MINUS -? HAP1_SCAFFOLD_19:1-411000 RL_17 PLUS +? HAP1_SCAFFOLD_2:613987-2892093 SUPER_3 MINUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_19:411201-5135357 RL_17 PLUS +? HAP1_SCAFFOLD_2:1-613986 SUPER_3 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_4:10514592-11619421 RL_17 MINUS +? HAP1_SCAFFOLD_2:3220021-13318622 SUPER_3 PLUS +? HAP1_SCAFFOLD_3:1-8405754 SUPER_4 MINUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_19:6016471-9556443 RL_17 PLUS +? HAP1_SCAFFOLD_3:8405955-12957954 SUPER_4 MINUS +? HAP1_SCAFFOLD_5:1-3245623 SUPER_5 MINUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_50:1-696626 RL_17 MINUS +? HAP2_SCAFFOLD_2:8114161-9010335 SUPER_5 MINUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_44:586872-2868936 RL_17 MINUS +? HAP2_SCAFFOLD_2:6615009-8113960 SUPER_5 MINUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_44:1-586671 RL_17 MINUS -? HAP1_SCAFFOLD_9:5960442-6836116 RL_19 MINUS +? HAP1_SCAFFOLD_5:5757833-12592823 SUPER_5 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_8:4149659-5635377 RL_19 MINUS +? HAP1_SCAFFOLD_88:1-353100 SUPER_5 MINUS +? HAP1_SCAFFOLD_10:1-5898851 SUPER_6 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_8:4046026-4149458 RL_19 MINUS +? HAP2_SCAFFOLD_29:4230323-6391817 SUPER_6 MINUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_9:1628708-4379773 RL_19 MINUS +? HAP2_SCAFFOLD_29:2465363-4230122 SUPER_6 MINUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_9:1-1628507 RL_19 MINUS +? HAP2_SCAFFOLD_29:2225526-2465162 SUPER_6 MINUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_9:6836317-11553316 RL_19 MINUS -? HAP1_SCAFFOLD_10:1-5898851 RL_21 PLUS +? HAP2_SCAFFOLD_29:1719620-2225325 SUPER_6 MINUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_29:4230323-6391817 RL_21 MINUS +? HAP2_SCAFFOLD_29:1153085-1719419 SUPER_6 MINUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_29:2465363-4230122 RL_21 MINUS +? HAP2_SCAFFOLD_29:1-1152884 SUPER_6 MINUS +? HAP1_SCAFFOLD_4:1-5716900 SUPER_7 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_29:2225526-2465162 RL_21 MINUS +? HAP2_SCAFFOLD_5:1394211-6255802 SUPER_7 MINUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_29:1719620-2225325 RL_21 MINUS +? HAP1_SCAFFOLD_4:11324648-12676000 SUPER_7 PLUS +? HAP1_SCAFFOLD_17:1-2710000 SUPER_8 MINUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_29:1153085-1719419 RL_21 MINUS +? HAP1_SCAFFOLD_17:6330541-9814798 SUPER_8 MINUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_29:1-1152884 RL_21 MINUS -? HAP1_SCAFFOLD_11:1-11251009 RL_23 PLUS -? HAP1_SCAFFOLD_12:1-1269913 RL_25 PLUS +? HAP1_SCAFFOLD_51:1-692374 SUPER_8 PLUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_12:1270114-11173113 RL_25 PLUS -? HAP1_SCAFFOLD_14:1-4434000 RL_27 MINUS +? HAP1_SCAFFOLD_53:1-682480 SUPER_8 PLUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_14:7940898-10650127 RL_27 MINUS +? HAP1_SCAFFOLD_82:1-367888 SUPER_8 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_9:3663530-7037610 RL_27 MINUS -? HAP1_SCAFFOLD_15:1-3301885 RL_29 PLUS +? HAP1_SCAFFOLD_206:1-179955 SUPER_8 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_13:3105788-3215532 RL_29 PLUS +? HAP1_SCAFFOLD_207:1-179464 SUPER_8 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_13:3215733-4878732 RL_29 PLUS +? HAP2_SCAFFOLD_40:1-3591033 SUPER_8 MINUS +? HAP1_SCAFFOLD_9:5960442-6836116 SUPER_9 MINUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_79:1-380611 RL_29 PLUS +? HAP2_SCAFFOLD_8:4149659-5635377 SUPER_9 MINUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_15:5508391-10061940 RL_29 PLUS -? HAP1_SCAFFOLD_16:1-3046648 RL_31 PLUS +? HAP2_SCAFFOLD_8:4046026-4149458 SUPER_9 MINUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_18:2214073-2390442 RL_31 PLUS +? HAP1_SCAFFOLD_9:1628708-4379773 SUPER_9 MINUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_18:2390643-5296914 RL_31 PLUS +? HAP1_SCAFFOLD_9:1-1628507 SUPER_9 MINUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_18:5297115-6586661 RL_31 PLUS +? HAP1_SCAFFOLD_9:6836317-11553316 SUPER_9 MINUS +? HAP1_SCAFFOLD_11:1-11251009 SUPER_10 PLUS +? HAP1_SCAFFOLD_12:1-1269913 SUPER_11 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_18:6586862-6966789 RL_31 PLUS +? HAP1_SCAFFOLD_12:1270114-11173113 SUPER_11 PLUS +? HAP1_SCAFFOLD_8:1-1158382 SUPER_12 PLUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_16:7731531-9876173 RL_31 PLUS -? HAP1_SCAFFOLD_17:1-2710000 RL_33 MINUS +? HAP2_SCAFFOLD_3:1012223-3573542 SUPER_12 PLUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_17:6330541-9814798 RL_33 MINUS +? HAP2_SCAFFOLD_3:3573743-3995205 SUPER_12 PLUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_51:1-692374 RL_33 PLUS +? HAP1_SCAFFOLD_8:4693589-11554590 SUPER_12 PLUS +? HAP1_SCAFFOLD_6:1-3397394 SUPER_13 PLUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_53:1-682480 RL_33 PLUS +? HAP2_SCAFFOLD_14:3047563-6867783 SUPER_13 PLUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_82:1-367888 RL_33 PLUS +? HAP1_SCAFFOLD_6:8113201-11878927 SUPER_13 MINUS +? HAP1_SCAFFOLD_7:1-3660743 SUPER_14 PLUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_206:1-179955 RL_33 PLUS +? HAP1_SCAFFOLD_7:3660944-7535543 SUPER_14 PLUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_207:1-179464 RL_33 PLUS +? HAP2_SCAFFOLD_12:1-3281679 SUPER_14 MINUS +? HAP1_SCAFFOLD_32:1-7503991 SUPER_15 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_40:1-3591033 RL_33 MINUS -? HAP1_SCAFFOLD_18:1-781383 RL_35 PLUS +? HAP2_SCAFFOLD_42:1-3123237 SUPER_15 MINUS +? HAP1_SCAFFOLD_14:1-4434000 SUPER_16 MINUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_18:781584-5089269 RL_35 PLUS +? HAP1_SCAFFOLD_14:7940898-10650127 SUPER_16 MINUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_22:109154-1527674 RL_35 PLUS +? HAP2_SCAFFOLD_9:3663530-7037610 SUPER_16 MINUS +? HAP1_SCAFFOLD_15:1-3301885 SUPER_17 PLUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_18:6564126-7231401 RL_35 PLUS +? HAP2_SCAFFOLD_13:3105788-3215532 SUPER_17 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_22:2482390-4059263 RL_35 PLUS +? HAP2_SCAFFOLD_13:3215733-4878732 SUPER_17 PLUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_18:9087007-9803125 RL_35 PLUS -? HAP1_SCAFFOLD_20:3572858-3768985 RL_37 MINUS +? HAP1_SCAFFOLD_79:1-380611 SUPER_17 PLUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_20:409325-3572657 RL_37 MINUS +? HAP1_SCAFFOLD_15:5508391-10061940 SUPER_17 PLUS +? HAP1_SCAFFOLD_16:1-3046648 SUPER_18 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_17:3379600-3444303 RL_37 PLUS +? HAP2_SCAFFOLD_18:2214073-2390442 SUPER_18 PLUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_20:1-409324 RL_37 MINUS +? HAP2_SCAFFOLD_18:2390643-5296914 SUPER_18 PLUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_20:3769186-9168871 RL_37 MINUS -? HAP2_SCAFFOLD_11:9012543-9374297 RL_39 MINUS +? HAP2_SCAFFOLD_18:5297115-6586661 SUPER_18 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_11:7654261-9012342 RL_39 MINUS +? HAP2_SCAFFOLD_18:6586862-6966789 SUPER_18 PLUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_21:1787385-7354198 RL_39 PLUS +? HAP1_SCAFFOLD_16:7731531-9876173 SUPER_18 PLUS +? HAP1_SCAFFOLD_24:1292802-5902233 SUPER_19 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_11:1-1886215 RL_39 MINUS -? HAP1_SCAFFOLD_22:1-9283000 RL_41 PLUS -? HAP1_SCAFFOLD_23:518478-2217000 RL_43 MINUS +? HAP2_SCAFFOLD_19:4984572-5138542 SUPER_19 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_23:1-422982 RL_43 MINUS +? HAP2_SCAFFOLD_19:7993574-8304056 SUPER_19 PLUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_59:1-150085 RL_43 PLUS +? HAP2_SCAFFOLD_19:8304257-8485650 SUPER_19 PLUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_23:2217201-5348508 RL_43 PLUS +? HAP2_SCAFFOLD_66:1-227430 SUPER_19 PLUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_23:5785122-9245280 RL_43 MINUS +? HAP1_SCAFFOLD_24:753845-1292601 SUPER_19 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_23:7430544-7858903 RL_43 PLUS -? HAP1_SCAFFOLD_24:1292802-5902233 RL_45 PLUS +? HAP1_SCAFFOLD_24:6031981-9136256 SUPER_19 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_19:4984572-5138542 RL_45 PLUS +? HAP1_SCAFFOLD_24:1-753644 SUPER_19 PLUS +? HAP1_SCAFFOLD_18:1-781383 SUPER_20 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_19:7993574-8304056 RL_45 PLUS +? HAP1_SCAFFOLD_18:781584-5089269 SUPER_20 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_19:8304257-8485650 RL_45 PLUS +? HAP2_SCAFFOLD_22:109154-1527674 SUPER_20 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_66:1-227430 RL_45 PLUS +? HAP1_SCAFFOLD_18:6564126-7231401 SUPER_20 PLUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_24:753845-1292601 RL_45 PLUS +? HAP2_SCAFFOLD_22:2482390-4059263 SUPER_20 PLUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_24:6031981-9136256 RL_45 PLUS +? HAP1_SCAFFOLD_18:9087007-9803125 SUPER_20 PLUS +? HAP1_SCAFFOLD_23:518478-2217000 SUPER_21 MINUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_24:1-753644 RL_45 PLUS -? HAP1_SCAFFOLD_25:1-9128898 RL_47 PLUS -? HAP1_SCAFFOLD_65:1-476727 RL_49 MINUS +? HAP2_SCAFFOLD_23:1-422982 SUPER_21 MINUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_15:8295646-8977588 RL_49 PLUS +? HAP1_SCAFFOLD_59:1-150085 SUPER_21 PLUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_34:1-7218858 RL_49 PLUS -? HAP1_SCAFFOLD_26:1-3233664 RL_51 PLUS +? HAP1_SCAFFOLD_23:2217201-5348508 SUPER_21 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_21:5467087-5513086 RL_51 MINUS +? HAP1_SCAFFOLD_23:5785122-9245280 SUPER_21 MINUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_21:5247569-5466886 RL_51 MINUS +? HAP2_SCAFFOLD_23:7430544-7858903 SUPER_21 PLUS +? HAP1_SCAFFOLD_22:1-9283000 SUPER_22 PLUS +? HAP1_SCAFFOLD_20:3572858-3768985 SUPER_23 MINUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_26:3482354-5821926 RL_51 PLUS +? HAP1_SCAFFOLD_20:409325-3572657 SUPER_23 MINUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_21:987316-2908876 RL_51 MINUS +? HAP2_SCAFFOLD_17:3379600-3444303 SUPER_23 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_21:253493-987115 RL_51 MINUS +? HAP1_SCAFFOLD_20:1-409324 SUPER_23 MINUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_21:150998-253292 RL_51 MINUS +? HAP1_SCAFFOLD_20:3769186-9168871 SUPER_23 MINUS +? HAP2_SCAFFOLD_11:9012543-9374297 SUPER_24 MINUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_21:1-150797 RL_51 MINUS -? HAP1_SCAFFOLD_27:1-3880689 RL_53 MINUS +? HAP2_SCAFFOLD_11:7654261-9012342 SUPER_24 MINUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_68:1-209961 RL_53 PLUS +? HAP1_SCAFFOLD_21:1787385-7354198 SUPER_24 PLUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_27:3880890-8445731 RL_53 MINUS -? HAP1_SCAFFOLD_41:1-3984092 RL_55 PLUS +? HAP2_SCAFFOLD_11:1-1886215 SUPER_24 MINUS +? HAP1_SCAFFOLD_25:1-9128898 SUPER_25 PLUS +? HAP1_SCAFFOLD_41:1-3984092 SUPER_26 PLUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_28:3560471-8681470 RL_55 MINUS -? HAP1_SCAFFOLD_107:1-298000 RL_57 PLUS +? HAP1_SCAFFOLD_28:3560471-8681470 SUPER_26 MINUS +? HAP1_SCAFFOLD_107:1-298000 SUPER_27 PLUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_436:1-97000 RL_57 PLUS +? HAP1_SCAFFOLD_436:1-97000 SUPER_27 PLUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_29:1-5902748 RL_57 PLUS +? HAP1_SCAFFOLD_29:1-5902748 SUPER_27 PLUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_29:5902949-8420126 RL_57 PLUS -? HAP1_SCAFFOLD_30:1-8097000 RL_59 PLUS -? HAP1_SCAFFOLD_57:1-593303 RL_61 PLUS +? HAP1_SCAFFOLD_29:5902949-8420126 SUPER_27 PLUS +? HAP1_SCAFFOLD_26:1-3233664 SUPER_28 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_24:2061846-6995845 RL_61 MINUS +? HAP2_SCAFFOLD_21:5467087-5513086 SUPER_28 MINUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_31:5280288-7962338 RL_61 PLUS +? HAP2_SCAFFOLD_21:5247569-5466886 SUPER_28 MINUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_20:9168872-9390185 RL_61 PLUS +? HAP1_SCAFFOLD_26:3482354-5821926 SUPER_28 PLUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_41:3984093-4433732 RL_61 PLUS +? HAP2_SCAFFOLD_21:987316-2908876 SUPER_28 MINUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_84:1-360079 RL_61 PLUS +? HAP2_SCAFFOLD_21:253493-987115 SUPER_28 MINUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_68:1-447509 RL_61 PLUS +? HAP2_SCAFFOLD_21:150998-253292 SUPER_28 MINUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_81:1-368340 RL_61 PLUS +? HAP2_SCAFFOLD_21:1-150797 SUPER_28 MINUS +? HAP1_SCAFFOLD_27:1-3880689 SUPER_29 MINUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_86:1-357454 RL_61 MINUS +? HAP2_SCAFFOLD_68:1-209961 SUPER_29 PLUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_47:1-986097 RL_61 PLUS +? HAP1_SCAFFOLD_27:3880890-8445731 SUPER_29 MINUS +? HAP1_SCAFFOLD_65:1-476727 SUPER_30 MINUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_43:1-2912177 RL_61 MINUS -? HAP1_SCAFFOLD_32:1-7503991 RL_63 PLUS +? HAP2_SCAFFOLD_15:8295646-8977588 SUPER_30 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_42:1-3123237 RL_63 MINUS -? HAP1_SCAFFOLD_37:1-1386152 RL_65 PLUS +? HAP1_SCAFFOLD_34:1-7218858 SUPER_30 PLUS +? HAP1_SCAFFOLD_30:1-8097000 SUPER_31 PLUS +? HAP2_SCAFFOLD_53:1-636686 SUPER_32 PLUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_37:1386353-6178352 RL_65 PLUS -? HAP1_SCAFFOLD_33:1-1798577 RL_67 PLUS +? HAP1_SCAFFOLD_35:1-2988817 SUPER_32 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_43:1743924-2865272 RL_67 PLUS +? HAP1_SCAFFOLD_35:2989018-4338840 SUPER_32 PLUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_33:2947138-7285777 RL_67 PLUS -? HAP2_SCAFFOLD_53:1-636686 RL_69 PLUS +? HAP2_SCAFFOLD_27:3855604-4186399 SUPER_32 PLUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_35:1-2988817 RL_69 PLUS +? HAP2_SCAFFOLD_27:4186600-4961599 SUPER_32 PLUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_35:2989018-4338840 RL_69 PLUS +? HAP2_SCAFFOLD_27:4961800-6692657 SUPER_32 MINUS +? HAP1_SCAFFOLD_33:1-1798577 SUPER_33 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_27:3855604-4186399 RL_69 PLUS +? HAP2_SCAFFOLD_43:1743924-2865272 SUPER_33 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_27:4186600-4961599 RL_69 PLUS +? HAP1_SCAFFOLD_33:2947138-7285777 SUPER_33 PLUS +? HAP1_SCAFFOLD_48:463902-891196 SUPER_34 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_27:4961800-6692657 RL_69 MINUS -? HAP2_SCAFFOLD_31:113491-950375 RL_71 PLUS +? HAP1_SCAFFOLD_36:1-4518360 SUPER_34 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_31:1-113290 RL_71 MINUS +? HAP2_SCAFFOLD_32:3349211-4712026 SUPER_34 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_31:950576-1255819 RL_71 PLUS +? HAP2_SCAFFOLD_32:4712227-4820725 SUPER_34 PLUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_38:1209599-6096371 RL_71 PLUS -? HAP1_SCAFFOLD_48:463902-891196 RL_73 PLUS +? HAP2_SCAFFOLD_32:4820926-4963616 SUPER_34 PLUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_36:1-4518360 RL_73 PLUS +? HAP2_SCAFFOLD_32:4963817-5173517 SUPER_34 PLUS +? HAP1_SCAFFOLD_40:1-3594207 SUPER_35 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_32:3349211-4712026 RL_73 PLUS +? HAP1_SCAFFOLD_257:1-155167 SUPER_35 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_32:4712227-4820725 RL_73 PLUS +? HAP1_SCAFFOLD_452:1-93619 SUPER_35 MINUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_32:4820926-4963616 RL_73 PLUS +? HAP1_SCAFFOLD_58:1-576291 SUPER_35 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_32:4963817-5173517 RL_73 PLUS -? HAP1_SCAFFOLD_39:1-5759299 RL_75 PLUS -? HAP1_SCAFFOLD_40:1-3594207 RL_77 PLUS +? HAP1_SCAFFOLD_89:1-352771 SUPER_35 PLUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_257:1-155167 RL_77 PLUS +? HAP1_SCAFFOLD_169:1-211642 SUPER_35 PLUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_452:1-93619 RL_77 MINUS +? HAP1_SCAFFOLD_415:1-101441 SUPER_35 MINUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_58:1-576291 RL_77 PLUS +? HAP1_SCAFFOLD_40:3594408-5116557 SUPER_35 MINUS +? HAP1_SCAFFOLD_37:1-1386152 SUPER_36 PLUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_89:1-352771 RL_77 PLUS +? HAP1_SCAFFOLD_37:1386353-6178352 SUPER_36 PLUS +? HAP2_SCAFFOLD_31:113491-950375 SUPER_37 PLUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_169:1-211642 RL_77 PLUS +? HAP2_SCAFFOLD_31:1-113290 SUPER_37 MINUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_415:1-101441 RL_77 MINUS +? HAP2_SCAFFOLD_31:950576-1255819 SUPER_37 PLUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_40:3594408-5116557 RL_77 MINUS -? HAP2_SCAFFOLD_75:1-175271 W PLUS +? HAP1_SCAFFOLD_38:1209599-6096371 SUPER_37 PLUS +? HAP1_SCAFFOLD_39:1-5759299 SUPER_38 PLUS +? HAP2_SCAFFOLD_75:1-175271 SUPER_W PLUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_13:1-10773482 W PLUS +? HAP1_SCAFFOLD_13:1-10773482 SUPER_W PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_37:492238-4221727 W MINUS -? HAP1_SCAFFOLD_1:1-10770101 Z PLUS +? HAP2_SCAFFOLD_37:492238-4221727 SUPER_W MINUS +? HAP1_SCAFFOLD_1:1-10770101 SUPER_Z PLUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_1:10770302-15340751 Z PLUS +? HAP1_SCAFFOLD_1:10770302-15340751 SUPER_Z PLUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_1:15340952-18880918 Z PLUS +? HAP1_SCAFFOLD_1:15340952-18880918 SUPER_Z PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_37:1-33837 Z PLUS +? HAP2_SCAFFOLD_37:1-33837 SUPER_Z PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_37:34038-492037 Z PLUS +? HAP2_SCAFFOLD_37:34038-492037 SUPER_Z PLUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_1:18881119-21883956 Z PLUS +? HAP1_SCAFFOLD_1:18881119-21883956 SUPER_Z PLUS ? HAP1_SCAFFOLD_48:409325-463901 HAP1_SCAFFOLD_48 MINUS GAP TYPE-2 200 ? HAP1_SCAFFOLD_48:1-136441 HAP1_SCAFFOLD_48 PLUS diff --git a/tests/data/ilIthSala1_1/ilIthSala1_1-pretext-to-tpf.hap2.chromsomes.list.csv b/tests/data/ilIthSala1_1/ilIthSala1_1-pretext-to-tpf.hap2.chromsomes.list.csv new file mode 100644 index 0000000..045beb7 --- /dev/null +++ b/tests/data/ilIthSala1_1/ilIthSala1_1-pretext-to-tpf.hap2.chromsomes.list.csv @@ -0,0 +1,38 @@ +SUPER_1 +SUPER_2 +SUPER_3 +SUPER_4 +SUPER_5 +SUPER_6 +SUPER_7 +SUPER_8 +SUPER_9 +SUPER_10 +SUPER_11 +SUPER_12 +SUPER_13 +SUPER_14 +SUPER_15 +SUPER_16 +SUPER_17 +SUPER_18 +SUPER_19 +SUPER_20 +SUPER_21 +SUPER_22 +SUPER_23 +SUPER_24 +SUPER_25 +SUPER_26 +SUPER_27 +SUPER_28 +SUPER_29 +SUPER_30 +SUPER_31 +SUPER_32 +SUPER_33 +SUPER_34 +SUPER_35 +SUPER_36 +SUPER_37 +SUPER_38 diff --git a/tests/data/ilIthSala1_1/ilIthSala1_1-pretext-to-tpf_HAP2.tpf b/tests/data/ilIthSala1_1/ilIthSala1_1-pretext-to-tpf.hap2.tpf similarity index 85% rename from tests/data/ilIthSala1_1/ilIthSala1_1-pretext-to-tpf_HAP2.tpf rename to tests/data/ilIthSala1_1/ilIthSala1_1-pretext-to-tpf.hap2.tpf index 3501bdc..b2eec5e 100644 --- a/tests/data/ilIthSala1_1/ilIthSala1_1-pretext-to-tpf_HAP2.tpf +++ b/tests/data/ilIthSala1_1/ilIthSala1_1-pretext-to-tpf.hap2.tpf @@ -1,381 +1,381 @@ -? HAP2_SCAFFOLD_133:1-85228 RL_4 PLUS +? HAP1_SCAFFOLD_31:1-5280287 SUPER_1 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_1:10307431-12620842 RL_4 PLUS +? HAP2_SCAFFOLD_24:1-2061645 SUPER_1 MINUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_2:3110868-3220020 RL_4 PLUS +? HAP2_SCAFFOLD_44:1-2822575 SUPER_1 MINUS +? HAP2_SCAFFOLD_4:2883194-3278179 SUPER_2 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_1:12620843-12991430 RL_4 PLUS +? HAP2_SCAFFOLD_4:3278380-3654003 SUPER_2 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_1:3981907-10307230 RL_4 MINUS +? HAP2_SCAFFOLD_4:3654204-3700081 SUPER_2 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_1:1-3981706 RL_4 MINUS -? HAP2_SCAFFOLD_10:2556892-4566891 RL_6 PLUS +? HAP2_SCAFFOLD_4:3700282-6570079 SUPER_2 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_10:4567092-5852888 RL_6 PLUS +? HAP2_SCAFFOLD_4:6570280-7485273 SUPER_2 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_10:5853089-7574756 RL_6 PLUS +? HAP1_SCAFFOLD_19:5135558-6016270 SUPER_2 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_76:1-174910 RL_6 PLUS +? HAP2_SCAFFOLD_4:7485474-10514391 SUPER_2 MINUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_10:7574957-9164383 RL_6 PLUS +? HAP2_SCAFFOLD_51:1-646590 SUPER_2 MINUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_10:9164584-9801037 RL_6 PLUS +? HAP2_SCAFFOLD_4:1-2346384 SUPER_2 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_49:1-1029911 RL_6 MINUS +? HAP2_SCAFFOLD_4:2346585-2545579 SUPER_2 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_54:1-631727 RL_6 MINUS +? HAP2_SCAFFOLD_4:2545780-2882993 SUPER_2 PLUS +? HAP2_SCAFFOLD_133:1-85228 SUPER_3 PLUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_52:1-684000 RL_6 PLUS +? HAP2_SCAFFOLD_1:10307431-12620842 SUPER_3 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_10:1-852864 RL_6 PLUS +? HAP1_SCAFFOLD_2:3110868-3220020 SUPER_3 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_10:853065-2188655 RL_6 PLUS +? HAP2_SCAFFOLD_1:12620843-12991430 SUPER_3 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_10:2188856-2556691 RL_6 PLUS -? HAP2_SCAFFOLD_5:7936707-11032015 RL_8 MINUS +? HAP2_SCAFFOLD_1:3981907-10307230 SUPER_3 MINUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_5:6256003-7936506 RL_8 MINUS +? HAP2_SCAFFOLD_1:1-3981706 SUPER_3 MINUS +? HAP2_SCAFFOLD_10:2556892-4566891 SUPER_4 PLUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_4:5716901-11324647 RL_8 PLUS +? HAP2_SCAFFOLD_10:4567092-5852888 SUPER_4 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_5:1-1394010 RL_8 MINUS -? HAP2_SCAFFOLD_2:9010536-12580006 RL_10 PLUS +? HAP2_SCAFFOLD_10:5853089-7574756 SUPER_4 PLUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_5:3245824-5757832 RL_10 PLUS +? HAP2_SCAFFOLD_76:1-174910 SUPER_4 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_2:1-6614808 RL_10 MINUS -? HAP2_SCAFFOLD_3:1-749206 RL_12 PLUS +? HAP2_SCAFFOLD_10:7574957-9164383 SUPER_4 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_3:749407-808012 RL_12 PLUS +? HAP2_SCAFFOLD_10:9164584-9801037 SUPER_4 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_3:808213-1012022 RL_12 PLUS +? HAP2_SCAFFOLD_49:1-1029911 SUPER_4 MINUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_8:1158583-4693588 RL_12 PLUS +? HAP2_SCAFFOLD_54:1-631727 SUPER_4 MINUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_3:3995406-5873644 RL_12 PLUS +? HAP1_SCAFFOLD_52:1-684000 SUPER_4 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_3:5873845-12357806 RL_12 PLUS -? HAP2_SCAFFOLD_14:1-204514 RL_14 PLUS +? HAP2_SCAFFOLD_10:1-852864 SUPER_4 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_14:204715-3047362 RL_14 PLUS +? HAP2_SCAFFOLD_10:853065-2188655 SUPER_4 PLUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_6:3397395-8113000 RL_14 PLUS +? HAP2_SCAFFOLD_10:2188856-2556691 SUPER_4 PLUS +? HAP2_SCAFFOLD_2:9010536-12580006 SUPER_5 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_14:6867984-9006974 RL_14 PLUS -? HAP2_SCAFFOLD_12:6070389-9275957 RL_16 MINUS +? HAP1_SCAFFOLD_5:3245824-5757832 SUPER_5 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_12:4247985-6070188 RL_16 MINUS +? HAP2_SCAFFOLD_2:1-6614808 SUPER_5 MINUS +? HAP2_SCAFFOLD_35:1-3190653 SUPER_6 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_12:3281880-4247784 RL_16 MINUS +? HAP2_SCAFFOLD_35:3190854-4619674 SUPER_6 PLUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_7:7535744-11734208 RL_16 PLUS -? HAP2_SCAFFOLD_4:2883194-3278179 RL_18 PLUS +? HAP1_SCAFFOLD_10:5899052-6247260 SUPER_6 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_4:3278380-3654003 RL_18 PLUS +? HAP1_SCAFFOLD_10:6247461-9761274 SUPER_6 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_4:3654204-3700081 RL_18 PLUS +? HAP1_SCAFFOLD_10:9761475-11457375 SUPER_6 PLUS +? HAP2_SCAFFOLD_5:7936707-11032015 SUPER_7 MINUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_4:3700282-6570079 RL_18 PLUS +? HAP2_SCAFFOLD_5:6256003-7936506 SUPER_7 MINUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_4:6570280-7485273 RL_18 PLUS +? HAP1_SCAFFOLD_4:5716901-11324647 SUPER_7 PLUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_19:5135558-6016270 RL_18 PLUS +? HAP2_SCAFFOLD_5:1-1394010 SUPER_7 MINUS +? HAP2_SCAFFOLD_46:1-487386 SUPER_8 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_4:7485474-10514391 RL_18 MINUS +? HAP2_SCAFFOLD_46:487587-534977 SUPER_8 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_51:1-646590 RL_18 MINUS +? HAP2_SCAFFOLD_46:535178-2098177 SUPER_8 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_4:1-2346384 RL_18 PLUS +? HAP2_SCAFFOLD_39:1-3726805 SUPER_8 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_4:2346585-2545579 RL_18 PLUS +? HAP2_SCAFFOLD_62:1-282151 SUPER_8 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_4:2545780-2882993 RL_18 PLUS -? HAP2_SCAFFOLD_8:5635578-6519735 RL_20 MINUS +? HAP1_SCAFFOLD_59:150086-560463 SUPER_8 PLUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_9:4379774-5960241 RL_20 MINUS +? HAP1_SCAFFOLD_17:2710201-6330340 SUPER_8 MINUS +? HAP2_SCAFFOLD_8:5635578-6519735 SUPER_9 MINUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_8:1411363-4045825 RL_20 MINUS +? HAP1_SCAFFOLD_9:4379774-5960241 SUPER_9 MINUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_8:1-1411162 RL_20 MINUS +? HAP2_SCAFFOLD_8:1411363-4045825 SUPER_9 MINUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_8:6519936-7296979 RL_20 PLUS +? HAP2_SCAFFOLD_8:1-1411162 SUPER_9 MINUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_8:7297180-9360591 RL_20 PLUS +? HAP2_SCAFFOLD_8:6519936-7296979 SUPER_9 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_8:9360792-9383673 RL_20 PLUS +? HAP2_SCAFFOLD_8:7297180-9360591 SUPER_9 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_8:9383874-9669825 RL_20 PLUS +? HAP2_SCAFFOLD_8:9360792-9383673 SUPER_9 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_8:9670026-9897024 RL_20 PLUS -? HAP2_SCAFFOLD_35:1-3190653 RL_22 PLUS +? HAP2_SCAFFOLD_8:9383874-9669825 SUPER_9 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_35:3190854-4619674 RL_22 PLUS +? HAP2_SCAFFOLD_8:9670026-9897024 SUPER_9 PLUS +? HAP2_SCAFFOLD_6:1-4499799 SUPER_10 PLUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_10:5899052-6247260 RL_22 PLUS +? HAP2_SCAFFOLD_6:4500000-6965402 SUPER_10 PLUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_10:6247461-9761274 RL_22 PLUS +? HAP2_SCAFFOLD_6:6965603-10442365 SUPER_10 PLUS +? HAP2_SCAFFOLD_7:1-1041863 SUPER_11 PLUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_10:9761475-11457375 RL_22 PLUS -? HAP2_SCAFFOLD_6:1-4499799 RL_24 PLUS +? HAP2_SCAFFOLD_7:1042064-7674136 SUPER_11 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_6:4500000-6965402 RL_24 PLUS +? HAP2_SCAFFOLD_7:7674337-8706055 SUPER_11 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_6:6965603-10442365 RL_24 PLUS -? HAP2_SCAFFOLD_7:1-1041863 RL_26 PLUS +? HAP2_SCAFFOLD_7:8706256-10311773 SUPER_11 PLUS +? HAP2_SCAFFOLD_3:1-749206 SUPER_12 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_7:1042064-7674136 RL_26 PLUS +? HAP2_SCAFFOLD_3:749407-808012 SUPER_12 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_7:7674337-8706055 RL_26 PLUS +? HAP2_SCAFFOLD_3:808213-1012022 SUPER_12 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_7:8706256-10311773 RL_26 PLUS -? HAP2_SCAFFOLD_9:1-2560465 RL_28 PLUS +? HAP1_SCAFFOLD_8:1158583-4693588 SUPER_12 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_9:2560666-3663329 RL_28 PLUS +? HAP2_SCAFFOLD_3:3995406-5873644 SUPER_12 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_9:7037811-9838087 RL_28 MINUS +? HAP2_SCAFFOLD_3:5873845-12357806 SUPER_12 PLUS +? HAP2_SCAFFOLD_14:1-204514 SUPER_13 PLUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_14:4434201-7940897 RL_28 MINUS -? HAP2_SCAFFOLD_13:1-3105587 RL_30 PLUS +? HAP2_SCAFFOLD_14:204715-3047362 SUPER_13 PLUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_15:3301886-5508190 RL_30 PLUS +? HAP1_SCAFFOLD_6:3397395-8113000 SUPER_13 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_71:1-186908 RL_30 PLUS +? HAP2_SCAFFOLD_14:6867984-9006974 SUPER_13 PLUS +? HAP2_SCAFFOLD_12:6070389-9275957 SUPER_14 MINUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_13:4878933-8309013 RL_30 PLUS +? HAP2_SCAFFOLD_12:4247985-6070188 SUPER_14 MINUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_13:8309214-9213689 RL_30 PLUS -? HAP2_SCAFFOLD_18:1-631136 RL_32 PLUS +? HAP2_SCAFFOLD_12:3281880-4247784 SUPER_14 MINUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_18:631337-2213872 RL_32 PLUS +? HAP1_SCAFFOLD_7:7535744-11734208 SUPER_14 PLUS +? HAP2_SCAFFOLD_28:1-4015972 SUPER_15 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_52:1-641500 RL_32 MINUS +? HAP2_SCAFFOLD_28:4016173-5252912 SUPER_15 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_70:1-197286 RL_32 PLUS +? HAP2_SCAFFOLD_28:5253113-6616371 SUPER_15 PLUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_16:3046849-7345592 RL_32 PLUS +? HAP1_SCAFFOLD_42:1-3428000 SUPER_15 MINUS +? HAP2_SCAFFOLD_9:1-2560465 SUPER_16 PLUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_16:7345793-7731330 RL_32 PLUS +? HAP2_SCAFFOLD_9:2560666-3663329 SUPER_16 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_18:6966990-7090388 RL_32 PLUS +? HAP2_SCAFFOLD_9:7037811-9838087 SUPER_16 MINUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_18:7090589-8260419 RL_32 PLUS +? HAP1_SCAFFOLD_14:4434201-7940897 SUPER_16 MINUS +? HAP2_SCAFFOLD_13:1-3105587 SUPER_17 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_18:8260620-8361622 RL_32 PLUS +? HAP1_SCAFFOLD_15:3301886-5508190 SUPER_17 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_18:8361823-8385815 RL_32 PLUS +? HAP2_SCAFFOLD_71:1-186908 SUPER_17 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_18:8531267-8586728 RL_32 MINUS +? HAP2_SCAFFOLD_13:4878933-8309013 SUPER_17 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_18:8441418-8531066 RL_32 MINUS +? HAP2_SCAFFOLD_13:8309214-9213689 SUPER_17 PLUS +? HAP2_SCAFFOLD_18:1-631136 SUPER_18 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_18:8386016-8441217 RL_32 MINUS -? HAP2_SCAFFOLD_46:1-487386 RL_34 PLUS +? HAP2_SCAFFOLD_18:631337-2213872 SUPER_18 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_46:487587-534977 RL_34 PLUS +? HAP2_SCAFFOLD_52:1-641500 SUPER_18 MINUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_46:535178-2098177 RL_34 PLUS +? HAP2_SCAFFOLD_70:1-197286 SUPER_18 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_39:1-3726805 RL_34 PLUS +? HAP1_SCAFFOLD_16:3046849-7345592 SUPER_18 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_62:1-282151 RL_34 PLUS +? HAP1_SCAFFOLD_16:7345793-7731330 SUPER_18 PLUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_59:150086-560463 RL_34 PLUS +? HAP2_SCAFFOLD_18:6966990-7090388 SUPER_18 PLUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_17:2710201-6330340 RL_34 MINUS -? HAP2_SCAFFOLD_22:7145587-7866902 RL_36 MINUS +? HAP2_SCAFFOLD_18:7090589-8260419 SUPER_18 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_22:4059464-7145386 RL_36 MINUS +? HAP2_SCAFFOLD_18:8260620-8361622 SUPER_18 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_22:1-109153 RL_36 PLUS +? HAP2_SCAFFOLD_18:8361823-8385815 SUPER_18 PLUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_18:5089270-6563925 RL_36 PLUS +? HAP2_SCAFFOLD_18:8531267-8586728 SUPER_18 MINUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_22:1527875-2482189 RL_36 PLUS +? HAP2_SCAFFOLD_18:8441418-8531066 SUPER_18 MINUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_18:7231402-9087006 RL_36 PLUS -? HAP2_SCAFFOLD_17:1-142733 RL_38 PLUS +? HAP2_SCAFFOLD_18:8386016-8441217 SUPER_18 MINUS +? HAP2_SCAFFOLD_19:1-3838429 SUPER_19 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_17:142934-3379399 RL_38 PLUS +? HAP2_SCAFFOLD_19:3838630-4984371 SUPER_19 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_17:4847329-8719201 RL_38 MINUS +? HAP1_SCAFFOLD_24:5902434-6031780 SUPER_19 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_17:3444504-4847128 RL_38 MINUS -? HAP1_SCAFFOLD_21:1-368709 RL_40 PLUS +? HAP2_SCAFFOLD_19:7601514-7993373 SUPER_19 MINUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_21:368910-1787384 RL_40 PLUS +? HAP2_SCAFFOLD_19:5138743-7601313 SUPER_19 MINUS +? HAP2_SCAFFOLD_22:7145587-7866902 SUPER_20 MINUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_11:3345849-7654060 RL_40 MINUS +? HAP2_SCAFFOLD_22:4059464-7145386 SUPER_20 MINUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_11:2578309-3345648 RL_40 MINUS +? HAP2_SCAFFOLD_22:1-109153 SUPER_20 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_11:1886416-2578108 RL_40 MINUS +? HAP1_SCAFFOLD_18:5089270-6563925 SUPER_20 PLUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_21:7354199-9357017 RL_40 PLUS -? HAP2_SCAFFOLD_16:5278321-8903320 RL_42 PLUS +? HAP2_SCAFFOLD_22:1527875-2482189 SUPER_20 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_16:247009-5278120 RL_42 MINUS +? HAP1_SCAFFOLD_18:7231402-9087006 SUPER_20 PLUS +? HAP2_SCAFFOLD_23:423183-2071341 SUPER_21 MINUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_16:209321-246808 RL_42 MINUS +? HAP1_SCAFFOLD_23:1-518477 SUPER_21 MINUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_16:170802-209120 RL_42 MINUS +? HAP2_SCAFFOLD_23:2071542-4695257 SUPER_21 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_16:128969-170601 RL_42 MINUS +? HAP2_SCAFFOLD_61:1-296645 SUPER_21 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_16:1-128768 RL_42 MINUS -? HAP2_SCAFFOLD_23:423183-2071341 RL_44 MINUS +? HAP2_SCAFFOLD_56:1-503589 SUPER_21 PLUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_23:1-518477 RL_44 MINUS +? HAP2_SCAFFOLD_60:1-300576 SUPER_21 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_23:2071542-4695257 RL_44 PLUS +? HAP2_SCAFFOLD_23:4695458-4790879 SUPER_21 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_61:1-296645 RL_44 PLUS +? HAP2_SCAFFOLD_23:4791080-6793238 SUPER_21 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_56:1-503589 RL_44 PLUS +? HAP2_SCAFFOLD_23:6793439-7430343 SUPER_21 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_60:1-300576 RL_44 PLUS +? HAP1_SCAFFOLD_23:5348509-5785121 SUPER_21 MINUS +? HAP2_SCAFFOLD_16:5278321-8903320 SUPER_22 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_23:4695458-4790879 RL_44 PLUS +? HAP2_SCAFFOLD_16:247009-5278120 SUPER_22 MINUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_23:4791080-6793238 RL_44 PLUS +? HAP2_SCAFFOLD_16:209321-246808 SUPER_22 MINUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_23:6793439-7430343 RL_44 PLUS +? HAP2_SCAFFOLD_16:170802-209120 SUPER_22 MINUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_23:5348509-5785121 RL_44 MINUS -? HAP2_SCAFFOLD_19:1-3838429 RL_46 PLUS +? HAP2_SCAFFOLD_16:128969-170601 SUPER_22 MINUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_19:3838630-4984371 RL_46 PLUS +? HAP2_SCAFFOLD_16:1-128768 SUPER_22 MINUS +? HAP2_SCAFFOLD_17:1-142733 SUPER_23 PLUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_24:5902434-6031780 RL_46 PLUS +? HAP2_SCAFFOLD_17:142934-3379399 SUPER_23 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_19:7601514-7993373 RL_46 MINUS +? HAP2_SCAFFOLD_17:4847329-8719201 SUPER_23 MINUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_19:5138743-7601313 RL_46 MINUS -? HAP2_SCAFFOLD_20:1-4858042 RL_48 PLUS +? HAP2_SCAFFOLD_17:3444504-4847128 SUPER_23 MINUS +? HAP1_SCAFFOLD_21:1-368709 SUPER_24 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_20:4858243-8354552 RL_48 PLUS -? HAP2_SCAFFOLD_15:7474012-8295645 RL_50 PLUS +? HAP1_SCAFFOLD_21:368910-1787384 SUPER_24 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_15:6199106-7473811 RL_50 MINUS +? HAP2_SCAFFOLD_11:3345849-7654060 SUPER_24 MINUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_15:3489888-6198905 RL_50 MINUS +? HAP2_SCAFFOLD_11:2578309-3345648 SUPER_24 MINUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_15:1-3489687 RL_50 MINUS -? HAP2_SCAFFOLD_21:5571833-8296162 RL_52 MINUS +? HAP2_SCAFFOLD_11:1886416-2578108 SUPER_24 MINUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_21:5513287-5571632 RL_52 MINUS +? HAP1_SCAFFOLD_21:7354199-9357017 SUPER_24 PLUS +? HAP2_SCAFFOLD_20:1-4858042 SUPER_25 PLUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_26:3233665-3482153 RL_52 PLUS +? HAP2_SCAFFOLD_20:4858243-8354552 SUPER_25 PLUS +? HAP2_SCAFFOLD_45:1553712-2688743 SUPER_26 MINUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_21:2909077-5247368 RL_52 MINUS +? HAP2_SCAFFOLD_45:1-1553511 SUPER_26 MINUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_26:5822127-8847554 RL_52 PLUS -? HAP2_SCAFFOLD_41:1-86584 RL_54 PLUS +? HAP1_SCAFFOLD_28:1-3560270 SUPER_26 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_41:86785-3510707 RL_54 PLUS +? HAP2_SCAFFOLD_47:1-1606000 SUPER_26 PLUS +? HAP2_SCAFFOLD_26:2064328-6746038 SUPER_27 MINUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_27:8445732-8775055 RL_54 PLUS +? HAP2_SCAFFOLD_26:1950116-2064127 SUPER_27 MINUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_50:1-650000 RL_54 PLUS +? HAP2_SCAFFOLD_26:1-1949915 SUPER_27 MINUS +? HAP2_SCAFFOLD_21:5571833-8296162 SUPER_28 MINUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_38:1-4174185 RL_54 PLUS -? HAP2_SCAFFOLD_45:1553712-2688743 RL_56 MINUS +? HAP2_SCAFFOLD_21:5513287-5571632 SUPER_28 MINUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_45:1-1553511 RL_56 MINUS +? HAP1_SCAFFOLD_26:3233665-3482153 SUPER_28 PLUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_28:1-3560270 RL_56 PLUS +? HAP2_SCAFFOLD_21:2909077-5247368 SUPER_28 MINUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_47:1-1606000 RL_56 PLUS -? HAP2_SCAFFOLD_26:2064328-6746038 RL_58 MINUS +? HAP1_SCAFFOLD_26:5822127-8847554 SUPER_28 PLUS +? HAP2_SCAFFOLD_41:1-86584 SUPER_29 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_26:1950116-2064127 RL_58 MINUS +? HAP2_SCAFFOLD_41:86785-3510707 SUPER_29 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_26:1-1949915 RL_58 MINUS -? HAP2_SCAFFOLD_25:2526388-6902387 RL_60 MINUS +? HAP1_SCAFFOLD_27:8445732-8775055 SUPER_29 PLUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_128:1-263985 RL_60 MINUS +? HAP2_SCAFFOLD_50:1-650000 SUPER_29 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_25:326659-2526187 RL_60 MINUS +? HAP2_SCAFFOLD_38:1-4174185 SUPER_29 PLUS +? HAP2_SCAFFOLD_15:7474012-8295645 SUPER_30 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_25:1-326458 RL_60 MINUS -? HAP1_SCAFFOLD_31:1-5280287 RL_62 PLUS +? HAP2_SCAFFOLD_15:6199106-7473811 SUPER_30 MINUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_24:1-2061645 RL_62 MINUS +? HAP2_SCAFFOLD_15:3489888-6198905 SUPER_30 MINUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_44:1-2822575 RL_62 MINUS -? HAP2_SCAFFOLD_28:1-4015972 RL_64 PLUS +? HAP2_SCAFFOLD_15:1-3489687 SUPER_30 MINUS +? HAP2_SCAFFOLD_25:2526388-6902387 SUPER_31 MINUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_28:4016173-5252912 RL_64 PLUS +? HAP1_SCAFFOLD_128:1-263985 SUPER_31 MINUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_28:5253113-6616371 RL_64 PLUS +? HAP2_SCAFFOLD_25:326659-2526187 SUPER_31 MINUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_42:1-3428000 RL_64 MINUS -? HAP2_SCAFFOLD_34:3986289-5065535 RL_66 MINUS +? HAP2_SCAFFOLD_25:1-326458 SUPER_31 MINUS +? HAP1_SCAFFOLD_49:1-765000 SUPER_32 MINUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_34:1937674-3986088 RL_66 MINUS +? HAP2_SCAFFOLD_27:1-825719 SUPER_32 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_34:1820467-1937473 RL_66 MINUS +? HAP2_SCAFFOLD_27:825920-2573895 SUPER_32 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_34:1545836-1820266 RL_66 MINUS +? HAP2_SCAFFOLD_27:2574096-3855403 SUPER_32 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_34:1-1545635 RL_66 MINUS -? HAP2_SCAFFOLD_43:1-1743723 RL_68 PLUS +? HAP1_SCAFFOLD_35:4338841-5389440 SUPER_32 PLUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_33:1798778-2947137 RL_68 PLUS +? HAP1_SCAFFOLD_35:5389441-6914017 SUPER_32 PLUS +? HAP2_SCAFFOLD_43:1-1743723 SUPER_33 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_43:2865273-2923368 RL_68 PLUS +? HAP1_SCAFFOLD_33:1798778-2947137 SUPER_33 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_36:1-4608886 RL_68 PLUS -? HAP1_SCAFFOLD_49:1-765000 RL_70 MINUS +? HAP2_SCAFFOLD_43:2865273-2923368 SUPER_33 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_27:1-825719 RL_70 PLUS +? HAP2_SCAFFOLD_36:1-4608886 SUPER_33 PLUS +? HAP1_SCAFFOLD_45:1-1482000 SUPER_34 MINUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_27:825920-2573895 RL_70 PLUS +? HAP2_SCAFFOLD_32:1-2068272 SUPER_34 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_27:2574096-3855403 RL_70 PLUS +? HAP2_SCAFFOLD_32:2068473-2341340 SUPER_34 PLUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_35:4338841-5389440 RL_70 PLUS +? HAP2_SCAFFOLD_32:2341541-3349010 SUPER_34 PLUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_35:5389441-6914017 RL_70 PLUS -? HAP1_SCAFFOLD_38:1-896369 RL_72 PLUS +? HAP1_SCAFFOLD_36:4518561-6441740 SUPER_34 PLUS +? HAP2_SCAFFOLD_33:1640143-5146142 SUPER_35 MINUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_38:896570-1209398 RL_72 PLUS +? HAP2_SCAFFOLD_59:1-333807 SUPER_35 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_31:1256020-5025193 RL_72 PLUS +? HAP2_SCAFFOLD_170:1-73377 SUPER_35 MINUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_31:5025394-5656043 RL_72 PLUS +? HAP2_SCAFFOLD_123:1-91384 SUPER_35 PLUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_48:136442-409324 RL_72 MINUS -? HAP1_SCAFFOLD_45:1-1482000 RL_74 MINUS +? HAP2_SCAFFOLD_130:1-86703 SUPER_35 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_32:1-2068272 RL_74 PLUS +? HAP2_SCAFFOLD_57:1-375033 SUPER_35 MINUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_32:2068473-2341340 RL_74 PLUS +? HAP2_SCAFFOLD_33:1-1075191 SUPER_35 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_32:2341541-3349010 RL_74 PLUS +? HAP2_SCAFFOLD_33:1075392-1639942 SUPER_35 PLUS +? HAP2_SCAFFOLD_34:3986289-5065535 SUPER_36 MINUS GAP TYPE-2 200 -? HAP1_SCAFFOLD_36:4518561-6441740 RL_74 PLUS -? HAP2_SCAFFOLD_30:1149147-5781102 RL_76 MINUS +? HAP2_SCAFFOLD_34:1937674-3986088 SUPER_36 MINUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_30:1117745-1148946 RL_76 MINUS +? HAP2_SCAFFOLD_34:1820467-1937473 SUPER_36 MINUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_30:228417-1117544 RL_76 MINUS +? HAP2_SCAFFOLD_34:1545836-1820266 SUPER_36 MINUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_30:1-228216 RL_76 MINUS -? HAP2_SCAFFOLD_33:1640143-5146142 RL_78 MINUS +? HAP2_SCAFFOLD_34:1-1545635 SUPER_36 MINUS +? HAP1_SCAFFOLD_38:1-896369 SUPER_37 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_59:1-333807 RL_78 PLUS +? HAP1_SCAFFOLD_38:896570-1209398 SUPER_37 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_170:1-73377 RL_78 MINUS +? HAP2_SCAFFOLD_31:1256020-5025193 SUPER_37 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_123:1-91384 RL_78 PLUS +? HAP2_SCAFFOLD_31:5025394-5656043 SUPER_37 PLUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_130:1-86703 RL_78 PLUS +? HAP1_SCAFFOLD_48:136442-409324 SUPER_37 MINUS +? HAP2_SCAFFOLD_30:1149147-5781102 SUPER_38 MINUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_57:1-375033 RL_78 MINUS +? HAP2_SCAFFOLD_30:1117745-1148946 SUPER_38 MINUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_33:1-1075191 RL_78 PLUS +? HAP2_SCAFFOLD_30:228417-1117544 SUPER_38 MINUS GAP TYPE-2 200 -? HAP2_SCAFFOLD_33:1075392-1639942 RL_78 PLUS +? HAP2_SCAFFOLD_30:1-228216 SUPER_38 MINUS ? HAP2_SCAFFOLD_55:1-543105 HAP2_SCAFFOLD_55 PLUS ? HAP2_SCAFFOLD_58:1-348226 HAP2_SCAFFOLD_58 PLUS ? HAP2_SCAFFOLD_63:1-245045 HAP2_SCAFFOLD_63 PLUS diff --git a/tests/data/ilIthSala1_1/ilIthSala1_1-pretext-to-tpf_Haplotigs.tpf b/tests/data/ilIthSala1_1/ilIthSala1_1-pretext-to-tpf.haplotigs.tpf similarity index 100% rename from tests/data/ilIthSala1_1/ilIthSala1_1-pretext-to-tpf_Haplotigs.tpf rename to tests/data/ilIthSala1_1/ilIthSala1_1-pretext-to-tpf.haplotigs.tpf diff --git a/tests/data/ilIthSala1_1/ilIthSala1_1-pretext-to-tpf.log b/tests/data/ilIthSala1_1/ilIthSala1_1-pretext-to-tpf.log index fcc9024..fcef080 100644 --- a/tests/data/ilIthSala1_1/ilIthSala1_1-pretext-to-tpf.log +++ b/tests/data/ilIthSala1_1/ilIthSala1_1-pretext-to-tpf.log @@ -183,18 +183,18 @@ cut into: 309,695 HAP1_SCAFFOLD_40:5116558-5426252(+) Cut Haplotig -ilIthSala1_1-pretext-to-tpf_HAP1 +ilIthSala1_1-pretext-to-tpf.hap1 504,003,295 bp sequence (minus gaps) Autosomes: n = 38 - 14,311,964 RL_61 + 14,311,964 SUPER_1 ... ... - 5,759,299 RL_75 + 5,759,299 SUPER_38 374,425,016 bp total Named: n = 2 - 14,678,243 W - 22,375,193 Z + 14,678,243 SUPER_W + 22,375,193 SUPER_Z 37,053,436 bp total Unplaced: n = 791 @@ -203,13 +203,13 @@ ilIthSala1_1-pretext-to-tpf_HAP1 16,408 HAP1_SCAFFOLD_864 92,524,843 bp total -ilIthSala1_1-pretext-to-tpf_HAP2 +ilIthSala1_1-pretext-to-tpf.hap2 389,828,879 bp sequence (minus gaps) Autosomes: n = 38 - 13,185,411 RL_4 + 13,185,411 SUPER_3 ... ... - 5,064,735 RL_66 + 5,064,735 SUPER_36 347,504,210 bp total Unplaced: n = 1041 @@ -218,7 +218,7 @@ ilIthSala1_1-pretext-to-tpf_HAP2 5,267 HAP2_SCAFFOLD_1115 42,324,669 bp total -ilIthSala1_1-pretext-to-tpf_Haplotigs +ilIthSala1_1-pretext-to-tpf.haplotigs 309,695 bp sequence (minus gaps) n = 1 309,695 H_1 diff --git a/tests/data/iyExeIsch1/chrs.csv b/tests/data/iyExeIsch1/chrs.csv deleted file mode 100644 index a00cac0..0000000 --- a/tests/data/iyExeIsch1/chrs.csv +++ /dev/null @@ -1,12 +0,0 @@ -RL_1 -RL_2 -RL_3 -RL_4 -RL_5 -RL_6 -RL_7 -RL_8 -RL_9 -RL_10 -RL_11 -RL_12 diff --git a/tests/data/iyExeIsch1/iyExeIsch1-pretext-to-tpf.chr_report.csv b/tests/data/iyExeIsch1/iyExeIsch1-pretext-to-tpf.chr_report.csv new file mode 100644 index 0000000..4804f7e --- /dev/null +++ b/tests/data/iyExeIsch1/iyExeIsch1-pretext-to-tpf.chr_report.csv @@ -0,0 +1,13 @@ +assembly,seq_name,chr_name,localised,pretext_scaffold,length,length_minus_gaps +Primary,SUPER_1,1,true,Scaffold_1,30499120,30489920 +Primary,SUPER_2,2,true,Scaffold_4,28797786,28789386 +Primary,SUPER_3,3,true,Scaffold_2,28349879,28343679 +Primary,SUPER_4,4,true,Scaffold_3,27475874,27467074 +Primary,SUPER_5,5,true,Scaffold_8,26801871,26793271 +Primary,SUPER_6,6,true,Scaffold_5,23927040,23921040 +Primary,SUPER_7,7,true,Scaffold_7,22620837,22613237 +Primary,SUPER_8,8,true,Scaffold_6,20365201,20359401 +Primary,SUPER_9,9,true,Scaffold_9,18953628,18945228 +Primary,SUPER_10,10,true,Scaffold_11,18205039,18197439 +Primary,SUPER_11,11,true,Scaffold_12,17743748,17738148 +Primary,SUPER_12,12,true,Scaffold_10,16895040,16885640 diff --git a/tests/data/iyExeIsch1/iyExeIsch1-pretext-to-tpf.chromsomes.list.csv b/tests/data/iyExeIsch1/iyExeIsch1-pretext-to-tpf.chromsomes.list.csv new file mode 100644 index 0000000..e8450ab --- /dev/null +++ b/tests/data/iyExeIsch1/iyExeIsch1-pretext-to-tpf.chromsomes.list.csv @@ -0,0 +1,12 @@ +SUPER_1 +SUPER_2 +SUPER_3 +SUPER_4 +SUPER_5 +SUPER_6 +SUPER_7 +SUPER_8 +SUPER_9 +SUPER_10 +SUPER_11 +SUPER_12 diff --git a/tests/data/iyExeIsch1/iyExeIsch1-pretext-to-tpf.log b/tests/data/iyExeIsch1/iyExeIsch1-pretext-to-tpf.log index 6bb34c0..bf6969b 100644 --- a/tests/data/iyExeIsch1/iyExeIsch1-pretext-to-tpf.log +++ b/tests/data/iyExeIsch1/iyExeIsch1-pretext-to-tpf.log @@ -5,9 +5,9 @@ iyExeIsch1-pretext-to-tpf 283,906,128 bp sequence (minus gaps) Autosomes: n = 12 - 30,489,920 RL_1 + 30,489,920 SUPER_1 ... ... - 16,885,640 RL_10 + 16,885,640 SUPER_12 280,543,463 bp total Unplaced: n = 72 diff --git a/tests/data/iyExeIsch1/iyExeIsch1-pretext-to-tpf.tpf b/tests/data/iyExeIsch1/iyExeIsch1-pretext-to-tpf.tpf index 924bf92..d43e48e 100644 --- a/tests/data/iyExeIsch1/iyExeIsch1-pretext-to-tpf.tpf +++ b/tests/data/iyExeIsch1/iyExeIsch1-pretext-to-tpf.tpf @@ -1,931 +1,931 @@ -? scaffold_1:1-93024 RL_1 PLUS +? scaffold_1:1-93024 SUPER_1 PLUS GAP TYPE-2 200 -? scaffold_1:93225-232397 RL_1 PLUS +? scaffold_1:93225-232397 SUPER_1 PLUS GAP TYPE-2 200 -? scaffold_1:232598-261916 RL_1 PLUS +? scaffold_1:232598-261916 SUPER_1 PLUS GAP TYPE-2 200 -? scaffold_1:262117-906261 RL_1 PLUS +? scaffold_1:262117-906261 SUPER_1 PLUS GAP TYPE-2 200 -? scaffold_1:906462-1271115 RL_1 PLUS +? scaffold_1:906462-1271115 SUPER_1 PLUS GAP TYPE-2 200 -? scaffold_1:1271316-1363225 RL_1 PLUS +? scaffold_1:1271316-1363225 SUPER_1 PLUS GAP TYPE-2 200 -? scaffold_1:1363426-1927683 RL_1 PLUS +? scaffold_1:1363426-1927683 SUPER_1 PLUS GAP TYPE-2 200 -? scaffold_1:1927884-2719721 RL_1 PLUS +? scaffold_1:1927884-2719721 SUPER_1 PLUS GAP TYPE-2 200 -? scaffold_1:2719922-2974982 RL_1 PLUS +? scaffold_1:2719922-2974982 SUPER_1 PLUS GAP TYPE-2 200 -? scaffold_1:2975183-3501446 RL_1 PLUS +? scaffold_1:2975183-3501446 SUPER_1 PLUS GAP TYPE-2 200 -? scaffold_1:3501647-4582331 RL_1 PLUS +? scaffold_1:3501647-4582331 SUPER_1 PLUS GAP TYPE-2 200 -? scaffold_1:4582532-5130405 RL_1 PLUS +? scaffold_1:4582532-5130405 SUPER_1 PLUS GAP TYPE-2 200 -? scaffold_1:5130606-6223194 RL_1 PLUS +? scaffold_1:5130606-6223194 SUPER_1 PLUS GAP TYPE-2 200 -? scaffold_1:6223395-6416192 RL_1 PLUS +? scaffold_1:6223395-6416192 SUPER_1 PLUS GAP TYPE-2 200 -? scaffold_1:6416393-8134802 RL_1 PLUS +? scaffold_1:6416393-8134802 SUPER_1 PLUS GAP TYPE-2 200 -? scaffold_1:8135003-9835736 RL_1 PLUS +? scaffold_1:8135003-9835736 SUPER_1 PLUS GAP TYPE-2 200 -? scaffold_1:9835937-9869803 RL_1 PLUS +? scaffold_1:9835937-9869803 SUPER_1 PLUS GAP TYPE-2 200 -? scaffold_1:9870004-10131519 RL_1 PLUS +? scaffold_1:9870004-10131519 SUPER_1 PLUS GAP TYPE-2 200 -? scaffold_1:10131720-12025791 RL_1 PLUS +? scaffold_1:10131720-12025791 SUPER_1 PLUS GAP TYPE-2 200 -? scaffold_1:12025992-12486983 RL_1 PLUS +? scaffold_1:12025992-12486983 SUPER_1 PLUS GAP TYPE-2 200 -? scaffold_1:12487184-12673844 RL_1 PLUS +? scaffold_1:12487184-12673844 SUPER_1 PLUS GAP TYPE-2 200 -? scaffold_1:12674045-13499440 RL_1 PLUS +? scaffold_1:12674045-13499440 SUPER_1 PLUS GAP TYPE-2 200 -? scaffold_1:13499641-13520954 RL_1 PLUS +? scaffold_1:13499641-13520954 SUPER_1 PLUS GAP TYPE-2 200 -? scaffold_1:13521155-13868824 RL_1 PLUS +? scaffold_1:13521155-13868824 SUPER_1 PLUS GAP TYPE-2 200 -? scaffold_1:13869025-17020173 RL_1 PLUS +? scaffold_1:13869025-17020173 SUPER_1 PLUS GAP TYPE-2 200 -? scaffold_1:17020374-17082847 RL_1 PLUS +? scaffold_1:17020374-17082847 SUPER_1 PLUS GAP TYPE-2 200 -? scaffold_1:17083048-18696484 RL_1 PLUS +? scaffold_1:17083048-18696484 SUPER_1 PLUS GAP TYPE-2 200 -? scaffold_1:18696685-20498736 RL_1 PLUS +? scaffold_1:18696685-20498736 SUPER_1 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scaffold_37:1-151468 scaffold_37 PLUS diff --git a/tests/data/ngHelPoly1_1/chrs.csv b/tests/data/ngHelPoly1_1/chrs.csv deleted file mode 100644 index 6679872..0000000 --- a/tests/data/ngHelPoly1_1/chrs.csv +++ /dev/null @@ -1,6 +0,0 @@ -RL_1,RL_1_unloc_1,RL_1_unloc_2,RL_1_unloc_3,RL_1_unloc_4,RL_1_unloc_5,RL_1_unloc_6,RL_1_unloc_7,RL_1_unloc_8,RL_1_unloc_9,RL_1_unloc_10,RL_1_unloc_11,RL_1_unloc_12,RL_1_unloc_13 -RL_2,RL_2_unloc_1,RL_2_unloc_2,RL_2_unloc_3,RL_2_unloc_4,RL_2_unloc_5,RL_2_unloc_6,RL_2_unloc_7,RL_2_unloc_8,RL_2_unloc_9,RL_2_unloc_10,RL_2_unloc_11,RL_2_unloc_12 -RL_3,RL_3_unloc_1,RL_3_unloc_2,RL_3_unloc_3,RL_3_unloc_4,RL_3_unloc_5,RL_3_unloc_6,RL_3_unloc_7,RL_3_unloc_8,RL_3_unloc_9,RL_3_unloc_10 -RL_4,RL_4_unloc_1,RL_4_unloc_2,RL_4_unloc_3,RL_4_unloc_4,RL_4_unloc_5,RL_4_unloc_6,RL_4_unloc_7 -RL_5,RL_5_unloc_1,RL_5_unloc_2,RL_5_unloc_3,RL_5_unloc_4,RL_5_unloc_5,RL_5_unloc_6,RL_5_unloc_7,RL_5_unloc_8,RL_5_unloc_9,RL_5_unloc_10,RL_5_unloc_11 -X,X_unloc_1,X_unloc_2,X_unloc_3,X_unloc_4,X_unloc_5,X_unloc_6,X_unloc_7,X_unloc_8,X_unloc_9 diff --git a/tests/data/ngHelPoly1_1/ngHelPoly1_1-pretext-to-tpf.chr_report.csv b/tests/data/ngHelPoly1_1/ngHelPoly1_1-pretext-to-tpf.chr_report.csv new file mode 100644 index 0000000..b5d6688 --- /dev/null +++ b/tests/data/ngHelPoly1_1/ngHelPoly1_1-pretext-to-tpf.chr_report.csv @@ -0,0 +1,69 @@ +assembly,seq_name,chr_name,localised,pretext_scaffold,length,length_minus_gaps +Primary,SUPER_1,1,true,Scaffold_2,111496743,111372143 +Primary,SUPER_1_unloc_1,1,false,Scaffold_2,186682,186682 +Primary,SUPER_1_unloc_2,1,false,Scaffold_2,138556,138556 +Primary,SUPER_1_unloc_3,1,false,Scaffold_2,133463,133463 +Primary,SUPER_1_unloc_4,1,false,Scaffold_2,127299,127299 +Primary,SUPER_1_unloc_5,1,false,Scaffold_2,87811,87811 +Primary,SUPER_1_unloc_6,1,false,Scaffold_2,74661,74661 +Primary,SUPER_1_unloc_7,1,false,Scaffold_2,63850,63850 +Primary,SUPER_1_unloc_8,1,false,Scaffold_2,45706,45706 +Primary,SUPER_1_unloc_9,1,false,Scaffold_2,39000,39000 +Primary,SUPER_1_unloc_10,1,false,Scaffold_2,32831,32831 +Primary,SUPER_1_unloc_11,1,false,Scaffold_2,30467,30467 +Primary,SUPER_1_unloc_12,1,false,Scaffold_2,22500,22500 +Primary,SUPER_2,2,true,Scaffold_1,111625236,111505401 +Primary,SUPER_2_unloc_1,2,false,Scaffold_1,106894,106894 +Primary,SUPER_2_unloc_2,2,false,Scaffold_1,91000,91000 +Primary,SUPER_2_unloc_3,2,false,Scaffold_1,73122,73122 +Primary,SUPER_2_unloc_4,2,false,Scaffold_1,51495,51295 +Primary,SUPER_2_unloc_5,2,false,Scaffold_1,35664,35664 +Primary,SUPER_2_unloc_6,2,false,Scaffold_1,34759,34759 +Primary,SUPER_2_unloc_7,2,false,Scaffold_1,31639,31639 +Primary,SUPER_2_unloc_8,2,false,Scaffold_1,31016,31016 +Primary,SUPER_2_unloc_9,2,false,Scaffold_1,30954,30954 +Primary,SUPER_2_unloc_10,2,false,Scaffold_1,27908,27908 +Primary,SUPER_2_unloc_11,2,false,Scaffold_1,27272,27272 +Primary,SUPER_2_unloc_12,2,false,Scaffold_1,25315,25315 +Primary,SUPER_2_unloc_13,2,false,Scaffold_1,22766,22766 +Primary,SUPER_3,3,true,Scaffold_3,107430149,107316549 +Primary,SUPER_3_unloc_1,3,false,Scaffold_3,102685,102485 +Primary,SUPER_3_unloc_2,3,false,Scaffold_3,53857,53657 +Primary,SUPER_3_unloc_3,3,false,Scaffold_3,52676,52676 +Primary,SUPER_3_unloc_4,3,false,Scaffold_3,48934,48934 +Primary,SUPER_3_unloc_5,3,false,Scaffold_3,35218,35218 +Primary,SUPER_3_unloc_6,3,false,Scaffold_3,32382,32382 +Primary,SUPER_3_unloc_7,3,false,Scaffold_3,32002,32002 +Primary,SUPER_3_unloc_8,3,false,Scaffold_3,30128,30128 +Primary,SUPER_3_unloc_9,3,false,Scaffold_3,28287,28287 +Primary,SUPER_3_unloc_10,3,false,Scaffold_3,23842,23842 +Primary,SUPER_4,4,true,Scaffold_4,103419295,103319364 +Primary,SUPER_4_unloc_1,4,false,Scaffold_4,122658,122458 +Primary,SUPER_4_unloc_2,4,false,Scaffold_4,50865,50665 +Primary,SUPER_4_unloc_3,4,false,Scaffold_4,49378,49178 +Primary,SUPER_4_unloc_4,4,false,Scaffold_4,37442,37442 +Primary,SUPER_4_unloc_5,4,false,Scaffold_4,28543,28543 +Primary,SUPER_4_unloc_6,4,false,Scaffold_4,27941,27941 +Primary,SUPER_4_unloc_7,4,false,Scaffold_4,22178,22178 +Primary,SUPER_5,5,true,Scaffold_5,100359869,100249469 +Primary,SUPER_5_unloc_1,5,false,Scaffold_5,115661,115461 +Primary,SUPER_5_unloc_2,5,false,Scaffold_5,94924,94724 +Primary,SUPER_5_unloc_3,5,false,Scaffold_5,92437,92437 +Primary,SUPER_5_unloc_4,5,false,Scaffold_5,62538,62538 +Primary,SUPER_5_unloc_5,5,false,Scaffold_5,44445,44245 +Primary,SUPER_5_unloc_6,5,false,Scaffold_5,39728,39728 +Primary,SUPER_5_unloc_7,5,false,Scaffold_5,38131,38131 +Primary,SUPER_5_unloc_8,5,false,Scaffold_5,33495,33495 +Primary,SUPER_5_unloc_9,5,false,Scaffold_5,28719,28719 +Primary,SUPER_5_unloc_10,5,false,Scaffold_5,27650,27650 +Primary,SUPER_5_unloc_11,5,false,Scaffold_5,24129,24129 +Primary,SUPER_X,X,true,Scaffold_6,97362115,97240715 +Primary,SUPER_X_unloc_1,X,false,Scaffold_6,570302,570302 +Primary,SUPER_X_unloc_2,X,false,Scaffold_6,86197,86197 +Primary,SUPER_X_unloc_3,X,false,Scaffold_6,86044,85844 +Primary,SUPER_X_unloc_4,X,false,Scaffold_6,36000,36000 +Primary,SUPER_X_unloc_5,X,false,Scaffold_6,35747,35747 +Primary,SUPER_X_unloc_6,X,false,Scaffold_6,32953,32953 +Primary,SUPER_X_unloc_7,X,false,Scaffold_6,31915,31915 +Primary,SUPER_X_unloc_8,X,false,Scaffold_6,25768,25768 +Primary,SUPER_X_unloc_9,X,false,Scaffold_6,23993,23993 diff --git a/tests/data/ngHelPoly1_1/ngHelPoly1_1-pretext-to-tpf.chromsomes.list.csv b/tests/data/ngHelPoly1_1/ngHelPoly1_1-pretext-to-tpf.chromsomes.list.csv new file mode 100644 index 0000000..ada1d0d --- /dev/null +++ b/tests/data/ngHelPoly1_1/ngHelPoly1_1-pretext-to-tpf.chromsomes.list.csv @@ -0,0 +1,6 @@ +SUPER_1,SUPER_1_unloc_1,SUPER_1_unloc_2,SUPER_1_unloc_3,SUPER_1_unloc_4,SUPER_1_unloc_5,SUPER_1_unloc_6,SUPER_1_unloc_7,SUPER_1_unloc_8,SUPER_1_unloc_9,SUPER_1_unloc_10,SUPER_1_unloc_11,SUPER_1_unloc_12 +SUPER_2,SUPER_2_unloc_1,SUPER_2_unloc_2,SUPER_2_unloc_3,SUPER_2_unloc_4,SUPER_2_unloc_5,SUPER_2_unloc_6,SUPER_2_unloc_7,SUPER_2_unloc_8,SUPER_2_unloc_9,SUPER_2_unloc_10,SUPER_2_unloc_11,SUPER_2_unloc_12,SUPER_2_unloc_13 +SUPER_3,SUPER_3_unloc_1,SUPER_3_unloc_2,SUPER_3_unloc_3,SUPER_3_unloc_4,SUPER_3_unloc_5,SUPER_3_unloc_6,SUPER_3_unloc_7,SUPER_3_unloc_8,SUPER_3_unloc_9,SUPER_3_unloc_10 +SUPER_4,SUPER_4_unloc_1,SUPER_4_unloc_2,SUPER_4_unloc_3,SUPER_4_unloc_4,SUPER_4_unloc_5,SUPER_4_unloc_6,SUPER_4_unloc_7 +SUPER_5,SUPER_5_unloc_1,SUPER_5_unloc_2,SUPER_5_unloc_3,SUPER_5_unloc_4,SUPER_5_unloc_5,SUPER_5_unloc_6,SUPER_5_unloc_7,SUPER_5_unloc_8,SUPER_5_unloc_9,SUPER_5_unloc_10,SUPER_5_unloc_11 +SUPER_X,SUPER_X_unloc_1,SUPER_X_unloc_2,SUPER_X_unloc_3,SUPER_X_unloc_4,SUPER_X_unloc_5,SUPER_X_unloc_6,SUPER_X_unloc_7,SUPER_X_unloc_8,SUPER_X_unloc_9 diff --git a/tests/data/ngHelPoly1_1/ngHelPoly1_1-pretext-to-tpf_Haplotigs.tpf b/tests/data/ngHelPoly1_1/ngHelPoly1_1-pretext-to-tpf.haplotigs.tpf similarity index 100% rename from tests/data/ngHelPoly1_1/ngHelPoly1_1-pretext-to-tpf_Haplotigs.tpf rename to tests/data/ngHelPoly1_1/ngHelPoly1_1-pretext-to-tpf.haplotigs.tpf diff --git a/tests/data/ngHelPoly1_1/ngHelPoly1_1-pretext-to-tpf.log b/tests/data/ngHelPoly1_1/ngHelPoly1_1-pretext-to-tpf.log index 2107791..9a3afa6 100644 --- a/tests/data/ngHelPoly1_1/ngHelPoly1_1-pretext-to-tpf.log +++ b/tests/data/ngHelPoly1_1/ngHelPoly1_1-pretext-to-tpf.log @@ -59,13 +59,13 @@ ngHelPoly1_1-pretext-to-tpf 655,943,875 bp sequence (minus gaps) Autosomes: n = 5 - 112,354,969 RL_2 + 112,354,969 SUPER_1 ... ... - 100,850,726 RL_5 + 100,850,726 SUPER_5 536,714,629 bp total Named: n = 1 - 98,169,434 X + 98,169,434 SUPER_X Unplaced: n = 1208 190,492 scaffold_58 @@ -73,7 +73,7 @@ ngHelPoly1_1-pretext-to-tpf 1,000 scaffold_1564 21,059,812 bp total -ngHelPoly1_1-pretext-to-tpf_Haplotigs +ngHelPoly1_1-pretext-to-tpf.haplotigs 2,164,462 bp sequence (minus gaps) n = 24 263,000 H_1 diff --git a/tests/data/ngHelPoly1_1/ngHelPoly1_1-pretext-to-tpf.tpf b/tests/data/ngHelPoly1_1/ngHelPoly1_1-pretext-to-tpf.tpf index 64d5415..cc00e7e 100644 --- a/tests/data/ngHelPoly1_1/ngHelPoly1_1-pretext-to-tpf.tpf +++ b/tests/data/ngHelPoly1_1/ngHelPoly1_1-pretext-to-tpf.tpf @@ -1,6991 +1,6991 @@ -? scaffold_1:1-361914 RL_1 PLUS +? scaffold_2:1-219762 SUPER_1 PLUS GAP TYPE-2 200 -? scaffold_1:362115-469826 RL_1 PLUS +? scaffold_2:219963-327357 SUPER_1 PLUS GAP TYPE-2 200 -? scaffold_1:470027-538170 RL_1 PLUS +? scaffold_2:327558-369041 SUPER_1 PLUS GAP TYPE-2 200 -? scaffold_1:538371-1704927 RL_1 PLUS +? scaffold_2:369242-458324 SUPER_1 PLUS GAP TYPE-2 200 -? scaffold_133:1-84984 RL_1 PLUS +? scaffold_2:458525-509279 SUPER_1 PLUS GAP TYPE-2 200 -? scaffold_1:1705128-1962793 RL_1 PLUS +? scaffold_2:509480-618479 SUPER_1 PLUS GAP TYPE-2 200 -? scaffold_1:1962994-2067485 RL_1 PLUS +? scaffold_2:618680-656075 SUPER_1 PLUS GAP TYPE-2 200 -? scaffold_1:2067686-2171866 RL_1 PLUS +? 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scaffold_6:83485429-83700188 SUPER_X PLUS GAP TYPE-2 200 -? scaffold_6:83700389-83775558 X PLUS +? scaffold_6:83700389-83775558 SUPER_X PLUS GAP TYPE-2 200 -? scaffold_6:83775759-84033691 X PLUS +? scaffold_6:83775759-84033691 SUPER_X PLUS GAP TYPE-2 200 -? scaffold_6:84033892-84527743 X PLUS +? scaffold_6:84033892-84527743 SUPER_X PLUS GAP TYPE-2 200 -? scaffold_6:84527944-84612229 X PLUS +? scaffold_6:84527944-84612229 SUPER_X PLUS GAP TYPE-2 200 -? scaffold_6:84612430-84840822 X PLUS +? scaffold_6:84612430-84840822 SUPER_X PLUS GAP TYPE-2 200 -? scaffold_6:84841023-85108089 X PLUS +? scaffold_6:84841023-85108089 SUPER_X PLUS GAP TYPE-2 200 -? scaffold_6:85108290-85363596 X PLUS +? scaffold_6:85108290-85363596 SUPER_X PLUS GAP TYPE-2 200 -? scaffold_6:85363797-85642250 X PLUS +? scaffold_6:85363797-85642250 SUPER_X PLUS GAP TYPE-2 200 -? scaffold_250:1-43819 X PLUS -? scaffold_19:1-570302 X_unloc_1 PLUS -? scaffold_131:1-86197 X_unloc_2 PLUS -? scaffold_132:1-60900 X_unloc_3 PLUS +? scaffold_250:1-43819 SUPER_X PLUS +? scaffold_19:1-570302 SUPER_X_unloc_1 PLUS +? scaffold_131:1-86197 SUPER_X_unloc_2 PLUS +? scaffold_132:1-60900 SUPER_X_unloc_3 PLUS GAP TYPE-2 200 -? scaffold_132:61101-86044 X_unloc_3 PLUS -? scaffold_305:1-36000 X_unloc_4 PLUS -? scaffold_306:1-35747 X_unloc_5 MINUS -? scaffold_334:1-32953 X_unloc_6 PLUS -? scaffold_349:1-31915 X_unloc_7 PLUS -? scaffold_452:1-25768 X_unloc_8 PLUS -? scaffold_503:1-23993 X_unloc_9 PLUS +? scaffold_132:61101-86044 SUPER_X_unloc_3 PLUS +? scaffold_305:1-36000 SUPER_X_unloc_4 PLUS +? scaffold_306:1-35747 SUPER_X_unloc_5 MINUS +? scaffold_334:1-32953 SUPER_X_unloc_6 PLUS +? scaffold_349:1-31915 SUPER_X_unloc_7 PLUS +? scaffold_452:1-25768 SUPER_X_unloc_8 PLUS +? scaffold_503:1-23993 SUPER_X_unloc_9 PLUS ? scaffold_58:1-190492 scaffold_58 PLUS ? scaffold_84:1-128954 scaffold_84 PLUS ? scaffold_110:1-99521 scaffold_110 PLUS diff --git a/tests/data/nxCaeSini1_1/chrs.csv b/tests/data/nxCaeSini1_1/chrs.csv deleted file mode 100644 index f193e33..0000000 --- a/tests/data/nxCaeSini1_1/chrs.csv +++ /dev/null @@ -1,6 +0,0 @@ -RL_1 -RL_2,RL_2_unloc_1 -RL_3 -RL_4 -RL_5 -RL_6 diff --git a/tests/data/nxCaeSini1_1/nxCaeSini1_1-pretext-to-tpf.chr_report.csv b/tests/data/nxCaeSini1_1/nxCaeSini1_1-pretext-to-tpf.chr_report.csv new file mode 100644 index 0000000..e722a16 --- /dev/null +++ b/tests/data/nxCaeSini1_1/nxCaeSini1_1-pretext-to-tpf.chr_report.csv @@ -0,0 +1,8 @@ +assembly,seq_name,chr_name,localised,pretext_scaffold,length,length_minus_gaps +Primary,SUPER_1,1,true,Scaffold_1,34668837,34667637 +Primary,SUPER_2,2,true,Scaffold_2,28292709,28291083 +Primary,SUPER_2_unloc_1,2,false,Scaffold_2,193694,193694 +Primary,SUPER_3,3,true,Scaffold_3,27403670,27403070 +Primary,SUPER_4,4,true,Scaffold_4,22059136,22057736 +Primary,SUPER_5,5,true,Scaffold_5,20114748,20114148 +Primary,SUPER_6,6,true,Scaffold_6,19643377,19642777 diff --git a/tests/data/nxCaeSini1_1/nxCaeSini1_1-pretext-to-tpf.chromsomes.list.csv b/tests/data/nxCaeSini1_1/nxCaeSini1_1-pretext-to-tpf.chromsomes.list.csv new file mode 100644 index 0000000..918c89e --- /dev/null +++ b/tests/data/nxCaeSini1_1/nxCaeSini1_1-pretext-to-tpf.chromsomes.list.csv @@ -0,0 +1,6 @@ +SUPER_1 +SUPER_2,SUPER_2_unloc_1 +SUPER_3 +SUPER_4 +SUPER_5 +SUPER_6 diff --git a/tests/data/nxCaeSini1_1/nxCaeSini1_1-pretext-to-tpf_Haplotigs.tpf b/tests/data/nxCaeSini1_1/nxCaeSini1_1-pretext-to-tpf.haplotigs.tpf similarity index 100% rename from tests/data/nxCaeSini1_1/nxCaeSini1_1-pretext-to-tpf_Haplotigs.tpf rename to tests/data/nxCaeSini1_1/nxCaeSini1_1-pretext-to-tpf.haplotigs.tpf diff --git a/tests/data/nxCaeSini1_1/nxCaeSini1_1-pretext-to-tpf.log b/tests/data/nxCaeSini1_1/nxCaeSini1_1-pretext-to-tpf.log index 90545ec..1b16732 100644 --- a/tests/data/nxCaeSini1_1/nxCaeSini1_1-pretext-to-tpf.log +++ b/tests/data/nxCaeSini1_1/nxCaeSini1_1-pretext-to-tpf.log @@ -36,15 +36,15 @@ nxCaeSini1_1-pretext-to-tpf 152,385,837 bp sequence (minus gaps) Autosomes: n = 6 - 34,667,637 RL_1 + 34,667,637 SUPER_1 ... ... - 19,642,777 RL_6 + 19,642,777 SUPER_6 152,370,145 bp total Unplaced: n = 1 15,692 SCAFFOLD_15 -nxCaeSini1_1-pretext-to-tpf_Haplotigs +nxCaeSini1_1-pretext-to-tpf.haplotigs 54,697 bp sequence (minus gaps) n = 2 31,436 H_1 diff --git a/tests/data/nxCaeSini1_1/nxCaeSini1_1-pretext-to-tpf.tpf b/tests/data/nxCaeSini1_1/nxCaeSini1_1-pretext-to-tpf.tpf index f975574..26d8bd3 100644 --- a/tests/data/nxCaeSini1_1/nxCaeSini1_1-pretext-to-tpf.tpf +++ b/tests/data/nxCaeSini1_1/nxCaeSini1_1-pretext-to-tpf.tpf @@ -1,70 +1,70 @@ -? SCAFFOLD_1:1-15194280 RL_1 PLUS +? SCAFFOLD_1:1-15194280 SUPER_1 PLUS GAP TYPE-2 200 -? SCAFFOLD_1:15194481-22307237 RL_1 PLUS +? SCAFFOLD_1:15194481-22307237 SUPER_1 PLUS GAP TYPE-2 200 -? SCAFFOLD_1:22307438-22530762 RL_1 PLUS +? SCAFFOLD_1:22307438-22530762 SUPER_1 PLUS GAP TYPE-2 200 -? SCAFFOLD_1:22554024-25341640 RL_1 PLUS +? SCAFFOLD_1:22554024-25341640 SUPER_1 PLUS GAP TYPE-2 200 -? SCAFFOLD_1:25373277-27683976 RL_1 PLUS +? SCAFFOLD_1:25373277-27683976 SUPER_1 PLUS GAP TYPE-2 200 -? SCAFFOLD_1:27684177-33624271 RL_1 PLUS +? SCAFFOLD_1:27684177-33624271 SUPER_1 PLUS GAP TYPE-2 200 -? SCAFFOLD_7:1-1098863 RL_1 PLUS -? SCAFFOLD_2:1-3742205 RL_2 PLUS +? SCAFFOLD_7:1-1098863 SUPER_1 PLUS +? SCAFFOLD_2:1-3742205 SUPER_2 PLUS GAP TYPE-2 200 -? SCAFFOLD_2:3742406-4729991 RL_2 PLUS +? SCAFFOLD_2:3742406-4729991 SUPER_2 PLUS GAP TYPE-2 26 -? SCAFFOLD_2:4730018-5308486 RL_2 PLUS +? SCAFFOLD_2:4730018-5308486 SUPER_2 PLUS GAP TYPE-2 200 -? SCAFFOLD_2:5308687-5768768 RL_2 PLUS +? SCAFFOLD_2:5308687-5768768 SUPER_2 PLUS GAP TYPE-2 200 -? SCAFFOLD_2:10749502-13656628 RL_2 MINUS +? SCAFFOLD_2:10749502-13656628 SUPER_2 MINUS GAP TYPE-2 200 -? SCAFFOLD_2:5768769-10749301 RL_2 MINUS +? SCAFFOLD_2:5768769-10749301 SUPER_2 MINUS GAP TYPE-2 200 -? SCAFFOLD_2:13656629-19399672 RL_2 PLUS +? SCAFFOLD_2:13656629-19399672 SUPER_2 PLUS GAP TYPE-2 200 -? SCAFFOLD_2:19399873-27188695 RL_2 PLUS +? SCAFFOLD_2:19399873-27188695 SUPER_2 PLUS GAP TYPE-2 200 -? SCAFFOLD_11:1-81676 RL_2 PLUS +? SCAFFOLD_11:1-81676 SUPER_2 PLUS GAP TYPE-2 200 -? SCAFFOLD_2:27188896-28210433 RL_2 PLUS -? SCAFFOLD_8:1-193694 RL_2_unloc_1 PLUS -? SCAFFOLD_3:1-6221134 RL_3 PLUS +? SCAFFOLD_2:27188896-28210433 SUPER_2 PLUS +? SCAFFOLD_8:1-193694 SUPER_2_unloc_1 PLUS +? SCAFFOLD_3:1-6221134 SUPER_3 PLUS GAP TYPE-2 200 -? SCAFFOLD_3:6413103-18383159 RL_3 PLUS +? SCAFFOLD_3:6413103-18383159 SUPER_3 PLUS GAP TYPE-2 200 -? SCAFFOLD_3:18383360-27403470 RL_3 PLUS +? SCAFFOLD_3:18383360-27403470 SUPER_3 PLUS GAP TYPE-2 200 -? SCAFFOLD_3:6221335-6413102 RL_3 PLUS -? SCAFFOLD_10:1-92905 RL_4 MINUS +? SCAFFOLD_3:6221335-6413102 SUPER_3 PLUS +? SCAFFOLD_10:1-92905 SUPER_4 MINUS GAP TYPE-2 200 -? SCAFFOLD_4:1-4422562 RL_4 PLUS +? SCAFFOLD_4:1-4422562 SUPER_4 PLUS GAP TYPE-2 200 -? SCAFFOLD_4:4422763-11187190 RL_4 PLUS +? SCAFFOLD_4:4422763-11187190 SUPER_4 PLUS GAP TYPE-2 200 -? SCAFFOLD_4:11187391-17021166 RL_4 PLUS +? SCAFFOLD_4:11187391-17021166 SUPER_4 PLUS GAP TYPE-2 200 -? SCAFFOLD_4:17021367-18438881 RL_4 PLUS +? SCAFFOLD_4:17021367-18438881 SUPER_4 PLUS GAP TYPE-2 200 -? SCAFFOLD_4:18439082-21791878 RL_4 PLUS +? SCAFFOLD_4:18439082-21791878 SUPER_4 PLUS GAP TYPE-2 200 -? SCAFFOLD_14:1-26115 RL_4 PLUS +? SCAFFOLD_14:1-26115 SUPER_4 PLUS GAP TYPE-2 200 -? SCAFFOLD_9:1-147638 RL_4 PLUS -? SCAFFOLD_5:5243299-20070239 RL_5 MINUS +? SCAFFOLD_9:1-147638 SUPER_4 PLUS +? SCAFFOLD_5:5243299-20070239 SUPER_5 MINUS GAP TYPE-2 200 -? SCAFFOLD_5:1-5243098 RL_5 MINUS +? SCAFFOLD_5:1-5243098 SUPER_5 MINUS GAP TYPE-2 200 -? SCAFFOLD_12:1-32226 RL_5 PLUS +? SCAFFOLD_12:1-32226 SUPER_5 PLUS GAP TYPE-2 200 -? SCAFFOLD_16:1-11883 RL_5 PLUS -? SCAFFOLD_6:1-13471268 RL_6 PLUS +? SCAFFOLD_16:1-11883 SUPER_5 PLUS +? SCAFFOLD_6:1-13471268 SUPER_6 PLUS GAP TYPE-2 200 -? SCAFFOLD_6:13471469-14666665 RL_6 PLUS +? SCAFFOLD_6:13471469-14666665 SUPER_6 PLUS GAP TYPE-2 200 -? SCAFFOLD_6:14666866-19557021 RL_6 PLUS +? SCAFFOLD_6:14666866-19557021 SUPER_6 PLUS GAP TYPE-2 200 -? SCAFFOLD_6:19557222-19643377 RL_6 PLUS +? SCAFFOLD_6:19557222-19643377 SUPER_6 PLUS ? SCAFFOLD_15:1-15692 SCAFFOLD_15 PLUS diff --git a/tests/data/nxCaeSpej1/chrs.csv b/tests/data/nxCaeSpej1/chrs.csv deleted file mode 100644 index a6207da..0000000 --- a/tests/data/nxCaeSpej1/chrs.csv +++ /dev/null @@ -1,6 +0,0 @@ -I_II -II_I -III -IV -V -X diff --git a/tests/data/nxCaeSpej1/nxCaeSpej1-pretext-to-tpf.chr_report.csv b/tests/data/nxCaeSpej1/nxCaeSpej1-pretext-to-tpf.chr_report.csv new file mode 100644 index 0000000..a3f29ec --- /dev/null +++ b/tests/data/nxCaeSpej1/nxCaeSpej1-pretext-to-tpf.chr_report.csv @@ -0,0 +1,7 @@ +assembly,seq_name,chr_name,localised,pretext_scaffold,length,length_minus_gaps +Primary,SUPER_I_II,I_II,true,Scaffold_6,7368313,7367313 +Primary,SUPER_II_I,II_I,true,Scaffold_2,10008113,10007913 +Primary,SUPER_III,III,true,Scaffold_5,8501270,8500470 +Primary,SUPER_IV,IV,true,Scaffold_4,8761581,8760981 +Primary,SUPER_V,V,true,Scaffold_3,9627512,9627112 +Primary,SUPER_X,X,true,Scaffold_1,10893641,10893641 diff --git a/tests/data/nxCaeSpej1/nxCaeSpej1-pretext-to-tpf.chromsomes.list.csv b/tests/data/nxCaeSpej1/nxCaeSpej1-pretext-to-tpf.chromsomes.list.csv new file mode 100644 index 0000000..a62ee0e --- /dev/null +++ b/tests/data/nxCaeSpej1/nxCaeSpej1-pretext-to-tpf.chromsomes.list.csv @@ -0,0 +1,6 @@ +SUPER_I_II +SUPER_II_I +SUPER_III +SUPER_IV +SUPER_V +SUPER_X diff --git a/tests/data/nxCaeSpej1/nxCaeSpej1-pretext-to-tpf_Haplotigs.tpf b/tests/data/nxCaeSpej1/nxCaeSpej1-pretext-to-tpf.haplotigs.tpf similarity index 100% rename from tests/data/nxCaeSpej1/nxCaeSpej1-pretext-to-tpf_Haplotigs.tpf rename to tests/data/nxCaeSpej1/nxCaeSpej1-pretext-to-tpf.haplotigs.tpf diff --git a/tests/data/nxCaeSpej1/nxCaeSpej1-pretext-to-tpf.log b/tests/data/nxCaeSpej1/nxCaeSpej1-pretext-to-tpf.log index 58417d9..b2b7f5a 100644 --- a/tests/data/nxCaeSpej1/nxCaeSpej1-pretext-to-tpf.log +++ b/tests/data/nxCaeSpej1/nxCaeSpej1-pretext-to-tpf.log @@ -12,15 +12,15 @@ nxCaeSpej1-pretext-to-tpf 55,157,430 bp sequence (minus gaps) Named: n = 6 - 7,367,313 I_II - 10,007,913 II_I - 8,500,470 III - 8,760,981 IV - 9,627,112 V - 10,893,641 X + 7,367,313 SUPER_I_II + 10,007,913 SUPER_II_I + 8,500,470 SUPER_III + 8,760,981 SUPER_IV + 9,627,112 SUPER_V + 10,893,641 SUPER_X 55,157,430 bp total -nxCaeSpej1-pretext-to-tpf_Haplotigs +nxCaeSpej1-pretext-to-tpf.haplotigs 81,747 bp sequence (minus gaps) n = 4 31,487 H_1 diff --git a/tests/data/nxCaeSpej1/nxCaeSpej1-pretext-to-tpf.tpf b/tests/data/nxCaeSpej1/nxCaeSpej1-pretext-to-tpf.tpf index 5a68321..37008f0 100644 --- a/tests/data/nxCaeSpej1/nxCaeSpej1-pretext-to-tpf.tpf +++ b/tests/data/nxCaeSpej1/nxCaeSpej1-pretext-to-tpf.tpf @@ -1,36 +1,36 @@ -? SCAFFOLD_6:1-1386439 I_II PLUS +? SCAFFOLD_6:1-1386439 SUPER_I_II PLUS GAP TYPE-2 200 -? SCAFFOLD_6:1386640-1627205 I_II PLUS +? SCAFFOLD_6:1386640-1627205 SUPER_I_II PLUS GAP TYPE-2 200 -? SCAFFOLD_6:1627406-1717055 I_II PLUS +? SCAFFOLD_6:1627406-1717055 SUPER_I_II PLUS GAP TYPE-2 200 -? SCAFFOLD_6:1717256-6085064 I_II PLUS +? SCAFFOLD_6:1717256-6085064 SUPER_I_II PLUS GAP TYPE-2 200 -? SCAFFOLD_6:6085265-7297636 I_II PLUS +? SCAFFOLD_6:6085265-7297636 SUPER_I_II PLUS GAP TYPE-2 200 -? SCAFFOLD_7:1-70477 I_II MINUS -? SCAFFOLD_2:1-1901822 II_I PLUS +? SCAFFOLD_7:1-70477 SUPER_I_II MINUS +? SCAFFOLD_2:1-1901822 SUPER_II_I PLUS GAP TYPE-2 200 -? SCAFFOLD_2:1902023-10008113 II_I PLUS -? SCAFFOLD_5:1-1181218 III PLUS +? SCAFFOLD_2:1902023-10008113 SUPER_II_I PLUS +? SCAFFOLD_5:1-1181218 SUPER_III PLUS GAP TYPE-2 200 -? SCAFFOLD_5:1181419-1616919 III PLUS +? SCAFFOLD_5:1181419-1616919 SUPER_III PLUS GAP TYPE-2 200 -? SCAFFOLD_5:1617120-1888091 III PLUS +? SCAFFOLD_5:1617120-1888091 SUPER_III PLUS GAP TYPE-2 200 -? SCAFFOLD_5:1888292-2794432 III PLUS +? SCAFFOLD_5:1888292-2794432 SUPER_III PLUS GAP TYPE-2 200 -? SCAFFOLD_5:2794633-8501270 III PLUS -? SCAFFOLD_4:1-983863 IV PLUS +? SCAFFOLD_5:2794633-8501270 SUPER_III PLUS +? SCAFFOLD_4:1-983863 SUPER_IV PLUS GAP TYPE-2 200 -? SCAFFOLD_4:984064-7397053 IV PLUS +? SCAFFOLD_4:984064-7397053 SUPER_IV PLUS GAP TYPE-2 200 -? SCAFFOLD_4:7397254-7537345 IV PLUS +? SCAFFOLD_4:7397254-7537345 SUPER_IV PLUS GAP TYPE-2 200 -? SCAFFOLD_4:7537546-8761581 IV PLUS -? SCAFFOLD_3:1-2508188 V PLUS +? SCAFFOLD_4:7537546-8761581 SUPER_IV PLUS +? SCAFFOLD_3:1-2508188 SUPER_V PLUS GAP TYPE-2 200 -? SCAFFOLD_3:2508389-7110895 V PLUS +? SCAFFOLD_3:2508389-7110895 SUPER_V PLUS GAP TYPE-2 200 -? SCAFFOLD_3:7121011-9637427 V PLUS -? SCAFFOLD_1:1-10893641 X PLUS +? SCAFFOLD_3:7121011-9637427 SUPER_V PLUS +? SCAFFOLD_1:1-10893641 SUPER_X PLUS