02336754147822f5aa61ba13277123b2cc629001 markd Thu May 20 08:38:55 2021 -0700 Moved pslMap, pslMapPostChain, pslRc, pslSwap to src/utils, as they do not have hg/lib dependencies. diff --git src/utils/pslMap/tests/input/kgMRna.psl src/utils/pslMap/tests/input/kgMRna.psl new file mode 100644 index 0000000..d7bd1f8 --- /dev/null +++ src/utils/pslMap/tests/input/kgMRna.psl @@ -0,0 +1,22 @@ +2251 4 0 0 1 1 2 7768 - AB000114 2263 7 2263 chr9 136372045 90517946 90527969 4 225,997,956,77, 0,226,1223,2179, 90517946,90518171,90520309,90527892, +2049 2 0 0 0 0 9 19870 + AB000115 2058 7 2058 chr1 246127941 78508741 78530662 10 108,60,427,49,196,153,172,101,175,610, 7,115,175,602,651,847,1000,1172,1273,1448, 78508741,78516183,78516244,78517228,78517997,78523614,78525309,78529298,78529712,78530052, +5153 12 0 0 2 12 19 171648 - AB000220 5177 0 5177 chr7 158545518 79983905 80160718 21 787,803,200,971,131,68,158,42,89,223,145,70,115,143,120,91,120,63,161,141,524, 0,787,1595,1802,2773,2904,2972,3130,3172,3261,3484,3629,3699,3814,3957,4077,4168,4288,4351,4512,4653, 79983905,79984693,79985496,79985703,79990264,79992635,79999697,80002982,80006521,80030672,80039458,80042123,80044031,80045472,80047005,80051977,80059665,80068791,80069951,80158045,80160194, +3346 1 0 0 0 0 9 377952 - 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AB001106 4131 0 4131 chr14 105311216 52931246 52945779 16 375,7,177,35,31,1780,29,189,1046,74,83,50,50,97,58,41, 0,376,384,562,598,630,2411,2441,2631,3677,3751,3834,3884,3934,4031,4090, 52931246,52931621,52931628,52931805,52931840,52931871,52933651,52933680,52933869,52936541,52937629,52938164,52938908,52940426,52945680,52945738, +3114 0 0 0 0 0 5 6114 - AB001466 3114 0 3114 chr14 105311216 21815742 21824970 6 1255,90,723,141,279,626, 0,1255,1345,2068,2209,2488, 21815742,21818212,21818653,21819477,21819891,21824344, +2694 2 0 0 0 0 12 39269 + AB001563 2696 0 2696 chr4 191731959 2687761 2729726 13 123,585,78,113,243,154,180,252,199,273,289,184,23, 0,123,708,786,899,1142,1296,1476,1728,1927,2200,2489,2673, 2687761,2687885,2691143,2692898,2693152,2696178,2696449,2705461,2722846,2724038,2726926,2728286,2729703, +2225 0 0 0 0 0 9 6789 - AB002110 2225 0 2225 chr17 81860266 57072255 57081269 10 229,418,97,102,118,135,124,87,759,156, 0,229,647,744,846,964,1099,1223,1310,2069, 57072255,57072741,57073252,57073543,57073734,57073965,57077076,57077693,57078218,57081113, +1500 0 0 0 0 0 9 60340 - AB002134 1500 0 1500 chr4 191731959 68691252 68753092 10 344,143,260,178,39,158,68,119,122,69, 0,344,487,747,925,964,1122,1190,1309,1431, 68691252,68694829,68696358,68702301,68704180,68707269,68711655,68723165,68728654,68753023, +535 2 0 1 2 2 3 2968 - AB002283 607 7 547 chr9 136372045 135114525 135118031 6 219,161,52,88,4,14, 60,279,440,492,581,586, 135114525,135115032,135115564,135117925,135118013,135118017, +1765 1 0 0 0 0 2 2203 + BC053876 2068 279 2045 chr1 246127941 202415929 202419898 3 516,76,1174, 279,795,871, 202415929,202417680,202418724, +191 0 0 0 0 0 1 557 + BC053876 2068 95 286 chr1 246127941 202417754 202418502 2 62,129, 95,157, 202417754,202418373, +104 0 0 0 0 0 0 0 + BC053876 2068 0 104 chr1 246127941 202418627 202418731 1 104, 0, 202418627,