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/pslSwap/tests/expected/withSeqTest.psl src/utils/pslSwap/tests/expected/withSeqTest.psl new file mode 100644 index 0000000..6505043 --- /dev/null +++ src/utils/pslSwap/tests/expected/withSeqTest.psl @@ -0,0 +1,2 @@ +1246 6 0 0 7 47617 1 1 - chr12 49533 2 48871 chr5 4235 2982 4235 8 522,117,144,141,59,66,83,120, 662,3246,4014,6211,8412,9998,11682,49411, 2982,3504,3621,3765,3906,3966,4032,4115, aaaaattaaaaaaactatatagctgtgttaatcaaagcgcttattttgtacaataataatgaccttgaatttcttaaaaaaaattacaataagctacaagtatcaaagaagcgaagttatctggagtagtctatataggagctctttggactttcttttattatgctaaaatagtggtgcttttaggatttacattattgtactctccaatacaaagtatggggcatgttaaagtatacagtacaccattttcatacatgtacaacattggtggatgaagaatgtctcttagcagtaatactggatgtagcctctggttttaccagctgcaaactctaggactattatataagtaaaaatctctcttgtgatactggaaagtgattagaatgtgcaaactgatatagtagctttcatccgcctcttaaagggtaccaccacaggaaagtccatttaagatgttggtaggtttaacaaagttggaatgctggcactgttgaattgggcaacagttcttcagac,ctggctcagagctacaatgcatttagtatattaaagcagctgacatgatgactttttgcgagccttcccaggcactggagtttttctgttaatttgccgcactaggtcataaaagat,ctcattaacatttatttttgattttgcagaagattctaagaatgcacagttgttccattgtcttgctagattttgaccttgttccttccctacaactctttcatcttccaagtcacacttattaccaacaagaatcattggaac,atcatcagtgtctttaactcgaagaatctgttctctcaggtcttgtaaatcgttaaatgtggactgtgctgtgatggaataaactaatgcaaatccttgtccatttttcatgtataaatccctcattgctgtaaattgctc,cgttcctgcagtatccaagatttcaagcatacactgttgtgcatctacttcaacttgct,tctataagaatcttctatcgtaggatcgtatttttctacaaaaattccttgaacaaattgtacagt,caaagcagactttccaacgcctcctgagccaagaacgactagcttatactcacgcatgatgcaagcttgtcaaaacctagtac,tctgcgaacctctcacgctgtcaccgggtccctgcagccagcgtcgccccgcgctccccccgggtcgctactctaggcgccacggcggtcctgccgctgccgcgccgctccggctggttt, aaaaattaaaaaaactatatagctgtgttaatcaaagcgcttattttgtacaataataatgaccttgaatttcttaaaaaaaattacaataagctacaagtatcaaagaagcgaagttatctggagtagtctatataggagctctttggactttcttttattatgctaaaatagtggtgcttttaggatttacattattgtactctccaatacaaagtatggggcatgttaaagtatacagtacaccattttcatacatgtacaacattggtggatgaagaatgtctcttagcagtaatactggatgtagcctctggttttaccagctgcatactctaggactattatataagtaaaaatctctcttgtgatactggaaagtgattagaatgtgcaaactgatatagtagctttcatccgcctcttaaagggtaccaccacaggaaagtccatttaagatgttggtaggtttaacaaagttggaatgctggcactgttgaattgggcaacagttcttcagac,ctggctcagagctacaatgcatttagtatattaaagcagctgacatgatgactttttgcgagccttcccaggcactggagtttttctgttaatttgccgcactaggtcataaaagat,ctcattaacatttatttttgattttgcagaagattctaagaatgcacagttgttccattgtcttgctagattttgaccttgttccttccctacaactctttcatcttccaagtcacacttattaccaacaagaatcattggaac,atcatcagtgtctttaactcgaagaatctgttctctcaggtcttgtaaatcgttaaatgtggactgtgctgtgatggaataaactaatgcaaacccttgtccatttttcatgtataaatccctcattgctgtaaattgctc,cgttcctgcagtatccaagatttcaagcatacactgttgtgcatctacttcaacttgct,tctataagaatcttctatcgtaggatcgtatttttctacaaaaattccttgaacaaattgtacagt,caaagcagactttccaacgcctcgtgagccaagaacgactagcttatactcacgcatgatgcaagcttgtcaaaacctagtac,tctgcgaacctctcacgctgtcaccgggtctctgcagccagcgtcgccccgtgctccccgcgggtcgctactctaggcgccacggcggtcctgccgctgccgcgccgctccggctggttt, +2676 7 0 0 4 20558 0 0 + chr6:26744497-26767742 23245 2 23243 /cluster/data/hg17/nib/chr9.nib:97039092-97041775 2683 0 2683 5 246,2185,70,89,93, 2,253,7368,22267,23150, 0,246,2431,2501,2590, ggttaccgtcctttcctttattggatttctgaattttttaaaaagtaaaagtaaagcaatcattaagtagttcagataaaagaaaagcatctttacctgagttacccatcaggtctactctgacccaccctagcttctcccagaacaagcttctgggtatctaaaaaactattttcatactgatttcatgtaaagtcctctctaccatatgagtcaactaactatgagaacagtcttctcatacat,atgtacatagattctcacccacaattaaatctctcactgcagaacaggttttttggggcctgataagacaggagcttctaccaaaggttttctcagactcaaggtaagtatgggttttttcacctatgtgagttccctgatgtaccacaagagttgatcattgacaagcactcttcattcagacacttgcagtctttcctcagattgggtttttttttttgggtgcaaacccaagtaaggctctccaacgaatgcttttgccatacttaagacaaatatacaatttttcaccagtatggcttctctgatgggtaagtcagagttttgttagaagcttttttcacacttgctggggcttctccccagggtgggttttctgaggtccaatgagatgttcatactgtctgcagcacaactgacactgaaggcatttaaaaagttgttctccggtgtgaattctcttacaacgagaagggctgagcattagtagaaagctctctcacactcagtgcatttctaaggtttcccacttgtatgaatcctcttgtgagtgatcaaatttgagctcagacggtaagttttcaaaacctctgggcatctgtagatttctcgttggagtgaggatgaagtgttctgttagggcagctctctgggcaaagaatttctcatatttccaattgcaggctctctggtccccactgaattctgagctctgagcaaagtctgagatttgtcctcatcttaatgagttctctgatacataaataatttttaatattggtattacagcttctcgcctggtcaagacatctgtgaggcttctgacgcatggggagggctaagctcaagacctttttcactcacattacagacaaacggtttttcaccaatgtgtactgtctgatgttgaagaagggctgaactctggtggaagcttttatcacatacagtgtatttatagtgtagctcctctgtttgagttctcattttctgttgggcaacaaagtccattcctaggaggaagccactctcacacgcagaccactgatgtggtttctcttccatgtgaattctctgatgtacaataagatctgagctacagttaaagcttttttcatattcaaggcatttaaaagtgtgagtgtgagttgcctggtgcctaattaggttggcactccgagtaaaacttctcatacattccaggcatttatacggcttctcacctgtgtggactctctggtgcacgataaggtctgatttctggccaaagcatttttcacaggcaccacacttatagggcttctccccagtatgaactcttttatgtacaatgaaggctgaacggtgtcggtaacttttctcacacttattacatttgtagggcctttccccagtgtgagttctctggtggctaataagatctgatttcccactaaaagctttttcacactcgagacacttaaatggtttctcacctgtgtgagttcttcgatgccttatgaggtttgtacttctactgaagcatttgtcacactcactacatagatatggtttctcgccagtatggcttcgctggtggacaagcagatcagaactctgaccaaaattcttgccacaaatgtcacatgtatagaattttttacctgcatgtgttctctgatgtcctgaaagcgctaagtgatgccaaaagctcttctcacatttgctacatttataaggtttctcgtaattgtggatcctctggtgtgaagtaagatctgagctttggacaaaggttttctcacacatatcacatttataaggtttctccccagtatgggttctctcacacataataagagctaagttttcacagaagttttgcttgcattcaaggcactggtatatatgaccatctatctgaataatctcatgcatatgaataaaaatctttttacccttccgagggcatacattatatattttccttttttgagttctctgattacatttctcttctgaagtgtacattttctatggctctctcctagggagttttccgctggtcttcttgacccatcgttgccctcacagtcattttcttgataagaacttggaagatacatctgtttcaggcctttcaatcatgagcctctacaagtttccagcatcatatatgttaattccttacttggtatttccaacc,ctagaatccagatggaagaaaacatacattcctgatcctgacaatttgacttctcaaagaagatagcatt,cgtaacaagaaagactcaagaccatcttccttttggtttcaaaaggtctctagttcagaactattcacaacactcaattcttgcctctc,cctggcagccgccggcgccgcccctaggcctggggacagcacttccggttactctccggacactcgaatctgggcttcctggcggccgcagac, ggttaccgtcctttcctttattggatttctgaattttttaaaaagtaaaagtaaagcaatcattaagtagttcagataaaagaaaagcatctttacctgagttacccatcaggtctactctgacccgccctagcttctcccagaacaagcttctgggtatctaaaaaactattttcatactgatttcatgtaaagtcctctctaccatatgagtcaactaactatgagaacagtcttctcatacat,atgtacatagattctcacccacaattaaatctctcactgcagaacaggttttttggggcctgataagacaggagcttctaccaaaggttttctcagactcaaggtaagtatgggttttttcacctatgtgagttccctgatgtaccacaagagttgatcattgacaagcactcttcattcagacacttgcagtctttcctcagattgggtttttttttttgggtgcaaacccaagtaaggctctccaatgaatgcttttgccatacgtaagacaaatatacaatttttcaccagtatggcttctctgatgggtaagtcagagttttgttagaagcttttttcacacttgctggggcttctccccagggtgggttttctgaggtccaatgagatgttcatactgtctgcagcacaactgacactgaaggcatttaaaaagttgttctccggtgtgaattctcttacaacgagaagggctgagcattagtagaaagctctctcacactcagtgcatttctaaggtttcccacttgtatgaatcctcttgtgagtgatcaaatttgagctcagacggtaagttttcaaaacctctgggcatctgtagatttctcgttggagtgaggatgaagtgttctgttagggcagctctctgggcaaagaatttctcatatttccaattgcaggctctctggtccccactgaattctgagctctgagcaaagtctgagatttgtcctcatcttaatgagttctctgatacataaataatttttaatattggtattacagcttctcgcctggtcaagacatctgtgaggcttctgacgcatggggagggctaagctcaagacctttttcactcacattacagacaaacggtttttcaccaatgcgtactgtctgatgttgaagaagggctgaactctggtggaagcttttatcacatacagtgtatttatagtgtagctcctctgtttgagttctcattttctgttgggcaacaaagtccattcctaggaggaagccactctcacacgcagaccactgatgtggtttctcttccatgtgaattctctgatgtacaataagatctgagctacagttaaagcttttttcatattcaaggcatttaaaagtgtgagtgtgagttgcctggtgcctaattaggttggcactccgagtaaaacttctcatacattccaggcatttatacggcttctcacctgtgtggactctctggtgcacgataaggtctgatttctggccaaagcatttttcacaggcaccacacttatagggcttctccccagtatgaactcttttatgtacaatgaaggctgaacggtgtcggtaacttttctcacacttattacatttgtagggcctttccccagtgtgagttctctggtggctaataagatctgatttcccactaaaagctttttcacactcgagacacttaaatggtttctcacctgtgtgagttcttcgatgccttatgaggtttgtacttctactgaagcatttgtcacactcactacatagatatggtttctcgccagtatggcttcgctggtggacaagcagatcagaactctgaccaaaattcttgccacaaatgtcacatgtatagaattttttacctgcatgtgttctctgatgtcctgaaagcactaagtgatgccaaaagctcttctcacatttgctacatttataaggtttctcgtaattgtggatcctctggtgtgaagtaagatctgagctttggacaaaggttttctcacacatatcacatttataaggtttctccccagtatgggttctctcacacataataagagctaagttttcacacaagttttgcttgcattcaaggcactggtatatatgaccatctatctgaataatctcatgcatatgaataaaaatctttttacccttccgagggcatacattatatattttccttttttgagttctctgattacatttctcttctgaagtgtacattttctatggctctctcctagggagttttccgctggtcttcttgacccatcgttgccctcacagtcattttcttgataagaacttggaagatacatctgtttcaggcctttcaatcatgagcctctacaagtttccagcatcatatatgttaattccttacttggtatttccaacc,ctagaatccagatggaagaaaacatacattcctgatcctgactatttgacttctcaaagaagatagcatt,cgtaacaagaaagactcaagaccatcttccttttggtttcaaaaggtctctagttcagaactattcacaacactcaattcttgcctctc,cctggcagccgccggcgccgcccctaggcctggggacagcacttccggttactctccggacactcgaatctgggcttcctggcggccgcagac,