Changed test files for updated output format

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

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

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