Skip to content

Commit

Permalink
adding files for v302 update
Browse files Browse the repository at this point in the history
  • Loading branch information
@NullModel
NullModel committed Jul 17, 2014
1 parent a9925c6 commit 36d6274
Show file tree
Hide file tree
Showing 13 changed files with 408 additions and 0 deletions.
5 changes: 5 additions & 0 deletions src/hg/mouseStuff/lavToPsl/tests/expected/newStyleLastz.bed
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,5 @@
##aligner=lastz.v1.03.46 M=50 T=2 O=400 E=30 Q=hg19.susScr3.chrM.Q.txt --output=hg19.susScr3.chrM.lav
##matrix=lastz.v1.03.46 16 79,-84,-55,-128,-84,100,-174,-55,-55,-174,100,-84,-128,-55,-84,79
##gapPenalties=lastz.v1.03.46 O=400 E=30
##blastzParms=O=400,E=30,K=3000,L=3000,M=50
hg19_chrM 575 16024 susScr3_chrM 496 + 575 16024 0 97 55,138,101,61,29,77,79,128,35,27,75,20,106,27,51,62,21,14,15,22,26,48,123,135,54,33,61,20,5,83,62,10,37,39,292,88,17,278,6,3,24,1065,123,31,35,26,15,30,953,18,15,34,21,20,68,9,71,86,36,17,1531,84,14,38,687,10,19,28,116,14,7,1513,402,13,37,836,14,1004,29,14,10,587,6,1178,245,8,264,77,692,18,427,17,31,13,16,36,15, 0,56,194,297,358,389,467,547,675,711,738,813,834,948,975,1027,1090,1113,1127,1142,1164,1190,1238,1361,1498,1554,1587,1649,1669,1675,1759,1821,1833,1871,1910,2202,2291,2308,2586,2596,2599,2623,3689,3812,3843,3878,3916,3931,3961,4914,4937,4953,4987,5009,5030,5098,5107,5178,5264,5301,5329,6860,6944,6959,6997,7689,7715,7735,7765,7884,7908,7915,9428,9830,9843,9880,10718,10732,11737,11766,11785,11795,12382,12391,13577,13822,13831,14095,14172,14864,14885,15313,15331,15362,15379,15397,15434,
5 changes: 5 additions & 0 deletions src/hg/mouseStuff/lavToPsl/tests/expected/newStyleLastz.psl
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,5 @@
##aligner=lastz.v1.03.46 M=50 T=2 O=400 E=30 Q=hg19.susScr3.chrM.Q.txt --output=hg19.susScr3.chrM.lav
##matrix=lastz.v1.03.46 16 79,-84,-55,-128,-84,100,-174,-55,-55,-174,100,-84,-128,-55,-84,79
##gapPenalties=lastz.v1.03.46 O=400 E=30
##blastzParms=O=400,E=30,K=3000,L=3000,M=50
11494 3816 0 0 49 131 47 139 + susScr3_chrM 16613 1172 16613 hg19_chrM 16571 575 16024 97 55,138,101,61,29,77,79,128,35,27,75,20,106,27,51,62,21,14,15,22,26,48,123,135,54,33,61,20,5,83,62,10,37,39,292,88,17,278,6,3,24,1065,123,31,35,26,15,30,953,18,15,34,21,20,68,9,71,86,36,17,1531,84,14,38,687,10,19,28,116,14,7,1513,402,13,37,836,14,1004,29,14,10,587,6,1178,245,8,264,77,692,18,427,17,31,13,16,36,15, 1172,1227,1367,1468,1530,1559,1636,1715,1847,1882,1910,1991,2011,2117,2153,2204,2266,2287,2302,2320,2344,2371,2421,2545,2680,2734,2768,2829,2851,2856,2939,3002,3012,3049,3089,3385,3473,3491,3770,3776,3785,3812,4877,5001,5033,5069,5095,5113,5152,6110,6128,6143,6178,6199,6219,6288,6298,6370,6457,6493,6510,8047,8135,8149,8188,8875,8885,8904,8932,9048,9062,9082,10596,10999,11013,11053,11889,11905,12909,12940,12954,12967,13557,13563,14741,14987,14995,15262,15341,16036,16054,16481,16498,16533,16546,16562,16598, 575,631,769,872,933,964,1042,1122,1250,1286,1313,1388,1409,1523,1550,1602,1665,1688,1702,1717,1739,1765,1813,1936,2073,2129,2162,2224,2244,2250,2334,2396,2408,2446,2485,2777,2866,2883,3161,3171,3174,3198,4264,4387,4418,4453,4491,4506,4536,5489,5512,5528,5562,5584,5605,5673,5682,5753,5839,5876,5904,7435,7519,7534,7572,8264,8290,8310,8340,8459,8483,8490,10003,10405,10418,10455,11293,11307,12312,12341,12360,12370,12957,12966,14152,14397,14406,14670,14747,15439,15460,15888,15906,15937,15954,15972,16009,
5 changes: 5 additions & 0 deletions src/hg/mouseStuff/lavToPsl/tests/expected/oldStyleBlastz.bed
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,5 @@
##aligner=blastz.v7 M=50 T=2 O=400 E=30 Q=hg19.susScr3.blastz.q
##matrix=blastz.v7 16 79,-84,-55,-128,-84,100,-174,-55,-55,-174,100,-84,-128,-55,-84,79
##gapPenalties=blastz.v7 O=400 E=30
##blastzParms=O=400,E=30,K=3000,L=3000,M=50
hg19_chrM 575 16022 susScr3_chrM 496 + 575 16022 0 97 55,138,101,61,29,77,79,128,35,27,75,20,106,27,51,62,21,14,15,22,26,48,123,135,54,33,61,20,5,83,62,10,37,39,292,88,17,278,6,3,24,1065,123,31,35,26,15,30,953,18,15,34,21,20,68,9,71,86,36,17,1531,84,14,38,687,10,19,28,116,14,7,1513,402,13,37,836,14,1004,29,14,10,587,6,1178,245,8,264,77,692,18,427,17,31,13,16,36,13, 0,56,194,297,358,389,467,547,675,711,738,813,834,948,975,1027,1090,1113,1127,1142,1164,1190,1238,1361,1498,1554,1587,1649,1669,1675,1759,1821,1833,1871,1910,2202,2291,2308,2586,2596,2599,2623,3689,3812,3843,3878,3916,3931,3961,4914,4937,4953,4987,5009,5030,5098,5107,5178,5264,5301,5329,6860,6944,6959,6997,7689,7715,7735,7765,7884,7908,7915,9428,9830,9843,9880,10718,10732,11737,11766,11785,11795,12382,12391,13577,13822,13831,14095,14172,14864,14885,15313,15331,15362,15379,15397,15434,
5 changes: 5 additions & 0 deletions src/hg/mouseStuff/lavToPsl/tests/expected/oldStyleBlastz.psl
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,5 @@
##aligner=blastz.v7 M=50 T=2 O=400 E=30 Q=hg19.susScr3.blastz.q
##matrix=blastz.v7 16 79,-84,-55,-128,-84,100,-174,-55,-55,-174,100,-84,-128,-55,-84,79
##gapPenalties=blastz.v7 O=400 E=30
##blastzParms=O=400,E=30,K=3000,L=3000,M=50
11492 3816 0 0 49 131 47 139 + susScr3_chrM 16613 1172 16611 hg19_chrM 16571 575 16022 97 55,138,101,61,29,77,79,128,35,27,75,20,106,27,51,62,21,14,15,22,26,48,123,135,54,33,61,20,5,83,62,10,37,39,292,88,17,278,6,3,24,1065,123,31,35,26,15,30,953,18,15,34,21,20,68,9,71,86,36,17,1531,84,14,38,687,10,19,28,116,14,7,1513,402,13,37,836,14,1004,29,14,10,587,6,1178,245,8,264,77,692,18,427,17,31,13,16,36,13, 1172,1227,1367,1468,1530,1559,1636,1715,1847,1882,1910,1991,2011,2117,2153,2204,2266,2287,2302,2320,2344,2371,2421,2545,2680,2734,2768,2829,2851,2856,2939,3002,3012,3049,3089,3385,3473,3491,3770,3776,3785,3812,4877,5001,5033,5069,5095,5113,5152,6110,6128,6143,6178,6199,6219,6288,6298,6370,6457,6493,6510,8047,8135,8149,8188,8875,8885,8904,8932,9048,9062,9082,10596,10999,11013,11053,11889,11905,12909,12940,12954,12967,13557,13563,14741,14987,14995,15262,15341,16036,16054,16481,16498,16533,16546,16562,16598, 575,631,769,872,933,964,1042,1122,1250,1286,1313,1388,1409,1523,1550,1602,1665,1688,1702,1717,1739,1765,1813,1936,2073,2129,2162,2224,2244,2250,2334,2396,2408,2446,2485,2777,2866,2883,3161,3171,3174,3198,4264,4387,4418,4453,4491,4506,4536,5489,5512,5528,5562,5584,5605,5673,5682,5753,5839,5876,5904,7435,7519,7534,7572,8264,8290,8310,8340,8459,8483,8490,10003,10405,10418,10455,11293,11307,12312,12341,12360,12370,12957,12966,14152,14397,14406,14670,14747,15439,15460,15888,15906,15937,15954,15972,16009,
Binary file added src/hg/mouseStuff/lavToPsl/tests/expected/redmine12502.bed.gz
View file
Binary file not shown.
Binary file added src/hg/mouseStuff/lavToPsl/tests/expected/redmine12502.psl.gz
View file
Binary file not shown.
Binary file added src/hg/mouseStuff/lavToPsl/tests/input/hg19.chrom.sizes.gz
View file
Binary file not shown.
Binary file added src/hg/mouseStuff/lavToPsl/tests/input/mm10.chrom.sizes.gz
View file
Binary file not shown.
128 changes: 128 additions & 0 deletions src/hg/mouseStuff/lavToPsl/tests/input/newStyleLastz.lav
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,128 @@
#:lav
d {
"lastz.v1.03.46 hg19.chrM.fa susScr3.chrM.fa M=50 T=2 O=400 E=30 Q=hg19.susScr3.chrM.Q.txt --output=hg19.susScr3.chrM.lav
A C G T
79 -84 -55 -128
-84 100 -174 -55
-55 -174 100 -84
-128 -55 -84 79
O = 400, E = 30, K = 3000, L = 3000, M = 50"
}
#:lav
s {
"hg19.chrM.fa" 1 16571 0 1
"susScr3.chrM.fa" 1 16613 0 1
}
h {
">hg19_chrM"
">susScr3_chrM"
}
a {
s 660086
b 576 1173
e 16024 16613
l 576 1173 630 1227 78
l 632 1228 769 1365 77
l 770 1368 870 1468 78
l 873 1469 933 1529 87
l 934 1531 962 1559 72
l 965 1560 1041 1636 71
l 1043 1637 1121 1715 87
l 1123 1716 1250 1843 85
l 1251 1848 1285 1882 97
l 1287 1883 1313 1909 59
l 1314 1911 1388 1985 81
l 1389 1992 1408 2011 80
l 1410 2012 1515 2117 79
l 1524 2118 1550 2144 63
l 1551 2154 1601 2204 84
l 1603 2205 1664 2266 65
l 1666 2267 1686 2287 71
l 1689 2288 1702 2301 57
l 1703 2303 1717 2317 67
l 1718 2321 1739 2342 64
l 1740 2345 1765 2370 85
l 1766 2372 1813 2419 83
l 1814 2422 1936 2544 73
l 1937 2546 2071 2680 83
l 2074 2681 2127 2734 74
l 2130 2735 2162 2767 76
l 2163 2769 2223 2829 85
l 2225 2830 2244 2849 75
l 2245 2852 2249 2856 100
l 2251 2857 2333 2939 71
l 2335 2940 2396 3001 61
l 2397 3003 2406 3012 70
l 2409 3013 2445 3049 76
l 2447 3050 2485 3088 92
l 2486 3090 2777 3381 85
l 2778 3386 2865 3473 63
l 2867 3474 2883 3490 71
l 2884 3492 3161 3769 89
l 3162 3771 3167 3776 83
l 3172 3777 3174 3779 67
l 3175 3786 3198 3809 75
l 3199 3813 4263 4877 75
l 4265 4878 4387 5000 85
l 4388 5002 4418 5032 84
l 4419 5034 4453 5068 100
l 4454 5070 4479 5095 96
l 4492 5096 4506 5110 80
l 4507 5114 4536 5143 47
l 4537 5153 5489 6105 69
l 5490 6111 5507 6128 56
l 5513 6129 5527 6143 93
l 5529 6144 5562 6177 91
l 5563 6179 5583 6199 67
l 5585 6200 5604 6219 75
l 5606 6220 5673 6287 79
l 5674 6289 5682 6297 78
l 5683 6299 5753 6369 93
l 5754 6371 5839 6456 88
l 5840 6458 5875 6493 92
l 5877 6494 5893 6510 100
l 5905 6511 7435 8041 79
l 7436 8048 7519 8131 74
l 7520 8136 7533 8149 93
l 7535 8150 7572 8187 84
l 7573 8189 8259 8875 71
l 8265 8876 8274 8885 60
l 8291 8886 8309 8904 58
l 8311 8905 8338 8932 86
l 8341 8933 8456 9048 65
l 8460 9049 8473 9062 57
l 8484 9063 8490 9069 100
l 8491 9083 10003 10595 75
l 10004 10597 10405 10998 69
l 10406 11000 10418 11012 77
l 10419 11014 10455 11050 92
l 10456 11054 11291 11889 72
l 11294 11890 11307 11903 57
l 11308 11906 12311 12909 75
l 12313 12910 12341 12938 97
l 12342 12941 12355 12954 64
l 12361 12955 12370 12964 80
l 12371 12968 12957 13554 71
l 12958 13558 12963 13563 67
l 12967 13564 14144 14741 72
l 14153 14742 14397 14986 62
l 14398 14988 14405 14995 75
l 14407 14996 14670 15259 72
l 14671 15263 14747 15339 86
l 14748 15342 15439 16033 76
l 15440 16037 15457 16054 61
l 15461 16055 15887 16481 74
l 15889 16482 15905 16498 76
l 15907 16499 15937 16529 74
l 15938 16534 15950 16546 69
l 15955 16547 15970 16562 63
l 15973 16563 16008 16598 89
l 16010 16599 16024 16613 80
}
x {
n 0
}
m {
n 0
}
#:eof
128 changes: 128 additions & 0 deletions src/hg/mouseStuff/lavToPsl/tests/input/oldStyleBlastz.lav
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,128 @@
#:lav
d {
"blastz.v7 hg19.chrM.fa susScr3.chrM.fa M=50 T=2 O=400 E=30 Q=hg19.susScr3.blastz.q
A C G T
79 -84 -55 -128
-84 100 -174 -55
-55 -174 100 -84
-128 -55 -84 79
O = 400, E = 30, K = 3000, L = 3000, M = 50"
}
#:lav
s {
"hg19.chrM.fa" 1 16571 0 1
"susScr3.chrM.fa" 1 16613 0 1
}
h {
">hg19_chrM"
">susScr3_chrM"
}
a {
s 659907
b 576 1173
e 16022 16611
l 576 1173 630 1227 78
l 632 1228 769 1365 77
l 770 1368 870 1468 78
l 873 1469 933 1529 87
l 934 1531 962 1559 72
l 965 1560 1041 1636 71
l 1043 1637 1121 1715 87
l 1123 1716 1250 1843 85
l 1251 1848 1285 1882 97
l 1287 1883 1313 1909 59
l 1314 1911 1388 1985 81
l 1389 1992 1408 2011 80
l 1410 2012 1515 2117 79
l 1524 2118 1550 2144 63
l 1551 2154 1601 2204 84
l 1603 2205 1664 2266 65
l 1666 2267 1686 2287 71
l 1689 2288 1702 2301 57
l 1703 2303 1717 2317 67
l 1718 2321 1739 2342 64
l 1740 2345 1765 2370 85
l 1766 2372 1813 2419 83
l 1814 2422 1936 2544 73
l 1937 2546 2071 2680 83
l 2074 2681 2127 2734 74
l 2130 2735 2162 2767 76
l 2163 2769 2223 2829 85
l 2225 2830 2244 2849 75
l 2245 2852 2249 2856 100
l 2251 2857 2333 2939 71
l 2335 2940 2396 3001 61
l 2397 3003 2406 3012 70
l 2409 3013 2445 3049 76
l 2447 3050 2485 3088 92
l 2486 3090 2777 3381 85
l 2778 3386 2865 3473 63
l 2867 3474 2883 3490 71
l 2884 3492 3161 3769 89
l 3162 3771 3167 3776 83
l 3172 3777 3174 3779 67
l 3175 3786 3198 3809 75
l 3199 3813 4263 4877 75
l 4265 4878 4387 5000 85
l 4388 5002 4418 5032 84
l 4419 5034 4453 5068 100
l 4454 5070 4479 5095 96
l 4492 5096 4506 5110 80
l 4507 5114 4536 5143 47
l 4537 5153 5489 6105 69
l 5490 6111 5507 6128 56
l 5513 6129 5527 6143 93
l 5529 6144 5562 6177 91
l 5563 6179 5583 6199 67
l 5585 6200 5604 6219 75
l 5606 6220 5673 6287 79
l 5674 6289 5682 6297 78
l 5683 6299 5753 6369 93
l 5754 6371 5839 6456 88
l 5840 6458 5875 6493 92
l 5877 6494 5893 6510 100
l 5905 6511 7435 8041 79
l 7436 8048 7519 8131 74
l 7520 8136 7533 8149 93
l 7535 8150 7572 8187 84
l 7573 8189 8259 8875 71
l 8265 8876 8274 8885 60
l 8291 8886 8309 8904 58
l 8311 8905 8338 8932 86
l 8341 8933 8456 9048 65
l 8460 9049 8473 9062 57
l 8484 9063 8490 9069 100
l 8491 9083 10003 10595 75
l 10004 10597 10405 10998 69
l 10406 11000 10418 11012 77
l 10419 11014 10455 11050 92
l 10456 11054 11291 11889 72
l 11294 11890 11307 11903 57
l 11308 11906 12311 12909 75
l 12313 12910 12341 12938 97
l 12342 12941 12355 12954 64
l 12361 12955 12370 12964 80
l 12371 12968 12957 13554 71
l 12958 13558 12963 13563 67
l 12967 13564 14144 14741 72
l 14153 14742 14397 14986 62
l 14398 14988 14405 14995 75
l 14407 14996 14670 15259 72
l 14671 15263 14747 15339 86
l 14748 15342 15439 16033 76
l 15440 16037 15457 16054 61
l 15461 16055 15887 16481 74
l 15889 16482 15905 16498 76
l 15907 16499 15937 16529 74
l 15938 16534 15950 16546 69
l 15955 16547 15970 16562 63
l 15973 16563 16008 16598 89
l 16010 16599 16022 16611 77
}
x {
n 0
}
m {
n 0
}
#:eof
Binary file added src/hg/mouseStuff/lavToPsl/tests/input/redmine12502.lav.gz
View file
Binary file not shown.
35 changes: 35 additions & 0 deletions src/hg/mouseStuff/lavToPsl/tests/input/trimEndsBug.lav
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,35 @@
#:lav
d {
normalize-lav 133851895 160039680
}
d {
"restore_rpts applied to:
lastz.v1.03.02 /dev/shm/blastz.KRxyCp/s1.strip.fa /dev/shm/blastz.KRxyCp/s2.strip.rev.fa B=0 H=2000
A C G T
91 -114 -31 -123
-114 100 -125 -31
-31 -125 100 -114
-123 -31 -114 91
O = 400, E = 30, K = 3000, L = 3000, M = 0"
}
#:lav
s {
"/scratch/data/hg19/nib/chr12.nib" 1 133851895
"/scratch/data/mm10/nib/chr3.nib-" 1 160039680
}
h {
">/scratch/data/hg19/nib/chr12.nib:120000001-133851895:___"
">/scratch/data/mm10/nib/chr3.nib:120000001-130000000:___ (reverse complement)"
}
a {
s 3892
b 132879984 37732617
e 132880140 37732773
l 132879984 37732617 132879983 37732616 0
l 132879984 37732631 132880085 37732732 68
l 132880100 37732733 132880140 37732773 63
}
m {
n 0
}
#:eof
Loading

0 comments on commit 36d6274

Please sign in to comment.