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/withSeqNoRcTest.psl src/utils/pslSwap/tests/expected/withSeqNoRcTest.psl new file mode 100644 index 0000000..da5d60f --- /dev/null +++ src/utils/pslSwap/tests/expected/withSeqNoRcTest.psl @@ -0,0 +1,2 @@ +1246 6 0 0 7 47617 1 1 +- chr12 49533 2 48871 chr5 4235 2982 4235 8 120,83,66,59,141,144,117,522, 2,37768,39469,41062,43181,45375,46170,48349, 0,120,203,270,329,470,614,731, aaaccagccggagcggcgcggcagcggcaggaccgccgtggcgcctagagtagcgacccggggggagcgcggggcgacgctggctgcagggacccggtgacagcgtgagaggttcgcaga,gtactaggttttgacaagcttgcatcatgcgtgagtataagctagtcgttcttggctcaggaggcgttggaaagtctgctttg,actgtacaatttgttcaaggaatttttgtagaaaaatacgatcctacgatagaagattcttataga,agcaagttgaagtagatgcacaacagtgtatgcttgaaatcttggatactgcaggaacg,gagcaatttacagcaatgagggatttatacatgaaaaatggacaaggatttgcattagtttattccatcacagcacagtccacatttaacgatttacaagacctgagagaacagattcttcgagttaaagacactgatgat,gttccaatgattcttgttggtaataagtgtgacttggaagatgaaagagttgtagggaaggaacaaggtcaaaatctagcaagacaatggaacaactgtgcattcttagaatcttctgcaaaatcaaaaataaatgttaatgag,atcttttatgacctagtgcggcaaattaacagaaaaactccagtgcctgggaaggctcgcaaaaagtcatcatgtcagctgctttaatatactaaatgcattgtagctctgagccag,gtctgaagaactgttgcccaattcaacagtgccagcattccaactttgttaaacctaccaacatcttaaatggactttcctgtggtggtaccctttaagaggcggatgaaagctactatatcagtttgcacattctaatcactttccagtatcacaagagagatttttacttatataatagtcctagagtttgcagctggtaaaaccagaggctacatccagtattactgctaagagacattcttcatccaccaatgttgtacatgtatgaaaatggtgtactgtatactttaacatgccccatactttgtattggagagtacaataatgtaaatcctaaaagcaccactattttagcataataaaagaaagtccaaagagctcctatatagactactccagataacttcgcttctttgatacttgtagcttattgtaattttttttaagaaattcaaggtcattattattgtacaaaataagcgctttgattaacacagctatatagtttttttaattttt, aaaccagccggagcggcgcggcagcggcaggaccgccgtggcgcctagagtagcgacccgcggggagcacggggcgacgctggctgcagagacccggtgacagcgtgagaggttcgcaga,gtactaggttttgacaagcttgcatcatgcgtgagtataagctagtcgttcttggctcacgaggcgttggaaagtctgctttg,actgtacaatttgttcaaggaatttttgtagaaaaatacgatcctacgatagaagattcttataga,agcaagttgaagtagatgcacaacagtgtatgcttgaaatcttggatactgcaggaacg,gagcaatttacagcaatgagggatttatacatgaaaaatggacaagggtttgcattagtttattccatcacagcacagtccacatttaacgatttacaagacctgagagaacagattcttcgagttaaagacactgatgat,gttccaatgattcttgttggtaataagtgtgacttggaagatgaaagagttgtagggaaggaacaaggtcaaaatctagcaagacaatggaacaactgtgcattcttagaatcttctgcaaaatcaaaaataaatgttaatgag,atcttttatgacctagtgcggcaaattaacagaaaaactccagtgcctgggaaggctcgcaaaaagtcatcatgtcagctgctttaatatactaaatgcattgtagctctgagccag,gtctgaagaactgttgcccaattcaacagtgccagcattccaactttgttaaacctaccaacatcttaaatggactttcctgtggtggtaccctttaagaggcggatgaaagctactatatcagtttgcacattctaatcactttccagtatcacaagagagatttttacttatataatagtcctagagtatgcagctggtaaaaccagaggctacatccagtattactgctaagagacattcttcatccaccaatgttgtacatgtatgaaaatggtgtactgtatactttaacatgccccatactttgtattggagagtacaataatgtaaatcctaaaagcaccactattttagcataataaaagaaagtccaaagagctcctatatagactactccagataacttcgcttctttgatacttgtagcttattgtaattttttttaagaaattcaaggtcattattattgtacaaaataagcgctttgattaacacagctatatagtttttttaattttt, +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,