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,