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/hg/pslSwap/tests/input/withSeq.psl src/hg/pslSwap/tests/input/withSeq.psl
deleted file mode 100644
index 8831969..0000000
--- src/hg/pslSwap/tests/input/withSeq.psl
+++ /dev/null
@@ -1,2 +0,0 @@
-1246	6	0	0	1	1	7	47617	-	chr5	4235	2982	4235	chr12	49533	2	48871	8	120,83,66,59,141,144,117,522,	0,120,203,270,329,470,614,731,	2,37768,39469,41062,43181,45375,46170,48349,	aaaccagccggagcggcgcggcagcggcaggaccgccgtggcgcctagagtagcgacccgcggggagcacggggcgacgctggctgcagagacccggtgacagcgtgagaggttcgcaga,gtactaggttttgacaagcttgcatcatgcgtgagtataagctagtcgttcttggctcacgaggcgttggaaagtctgctttg,actgtacaatttgttcaaggaatttttgtagaaaaatacgatcctacgatagaagattcttataga,agcaagttgaagtagatgcacaacagtgtatgcttgaaatcttggatactgcaggaacg,gagcaatttacagcaatgagggatttatacatgaaaaatggacaagggtttgcattagtttattccatcacagcacagtccacatttaacgatttacaagacctgagagaacagattcttcgagttaaagacactgatgat,gttccaatgattcttgttggtaataagtgtgacttggaagatgaaagagttgtagggaaggaacaaggtcaaaatctagcaagacaatggaacaactgtgcattcttagaatcttctgcaaaatcaaaaataaatgttaatgag,atcttttatgacctagtgcggcaaattaacagaaaaactccagtgcctgggaaggctcgcaaaaagtcatcatgtcagctgctttaatatactaaatgcattgtagctctgagccag,gtctgaagaactgttgcccaattcaacagtgccagcattccaactttgttaaacctaccaacatcttaaatggactttcctgtggtggtaccctttaagaggcggatgaaagctactatatcagtttgcacattctaatcactttccagtatcacaagagagatttttacttatataatagtcctagagtatgcagctggtaaaaccagaggctacatccagtattactgctaagagacattcttcatccaccaatgttgtacatgtatgaaaatggtgtactgtatactttaacatgccccatactttgtattggagagtacaataatgtaaatcctaaaagcaccactattttagcataataaaagaaagtccaaagagctcctatatagactactccagataacttcgcttctttgatacttgtagcttattgtaattttttttaagaaattcaaggtcattattattgtacaaaataagcgctttgattaacacagctatatagtttttttaattttt,	aaaccagccggagcggcgcggcagcggcaggaccgccgtggcgcctagagtagcgacccggggggagcgcggggcgacgctggctgcagggacccggtgacagcgtgagaggttcgcaga,gtactaggttttgacaagcttgcatcatgcgtgagtataagctagtcgttcttggctcaggaggcgttggaaagtctgctttg,actgtacaatttgttcaaggaatttttgtagaaaaatacgatcctacgatagaagattcttataga,agcaagttgaagtagatgcacaacagtgtatgcttgaaatcttggatactgcaggaacg,gagcaatttacagcaatgagggatttatacatgaaaaatggacaaggatttgcattagtttattccatcacagcacagtccacatttaacgatttacaagacctgagagaacagattcttcgagttaaagacactgatgat,gttccaatgattcttgttggtaataagtgtgacttggaagatgaaagagttgtagggaaggaacaaggtcaaaatctagcaagacaatggaacaactgtgcattcttagaatcttctgcaaaatcaaaaataaatgttaatgag,atcttttatgacctagtgcggcaaattaacagaaaaactccagtgcctgggaaggctcgcaaaaagtcatcatgtcagctgctttaatatactaaatgcattgtagctctgagccag,gtctgaagaactgttgcccaattcaacagtgccagcattccaactttgttaaacctaccaacatcttaaatggactttcctgtggtggtaccctttaagaggcggatgaaagctactatatcagtttgcacattctaatcactttccagtatcacaagagagatttttacttatataatagtcctagagtttgcagctggtaaaaccagaggctacatccagtattactgctaagagacattcttcatccaccaatgttgtacatgtatgaaaatggtgtactgtatactttaacatgccccatactttgtattggagagtacaataatgtaaatcctaaaagcaccactattttagcataataaaagaaagtccaaagagctcctatatagactactccagataacttcgcttctttgatacttgtagcttattgtaattttttttaagaaattcaaggtcattattattgtacaaaataagcgctttgattaacacagctatatagtttttttaattttt,
-2676	7	0	0	0	0	4	20558	+	/cluster/data/hg17/nib/chr9.nib:97039092-97041775	2683	0	2683	chr6:26744497-26767742	23245	2	23243	5	246,2185,70,89,93,	0,246,2431,2501,2590,	2,253,7368,22267,23150,	ggttaccgtcctttcctttattggatttctgaattttttaaaaagtaaaagtaaagcaatcattaagtagttcagataaaagaaaagcatctttacctgagttacccatcaggtctactctgacccgccctagcttctcccagaacaagcttctgggtatctaaaaaactattttcatactgatttcatgtaaagtcctctctaccatatgagtcaactaactatgagaacagtcttctcatacat,atgtacatagattctcacccacaattaaatctctcactgcagaacaggttttttggggcctgataagacaggagcttctaccaaaggttttctcagactcaaggtaagtatgggttttttcacctatgtgagttccctgatgtaccacaagagttgatcattgacaagcactcttcattcagacacttgcagtctttcctcagattgggtttttttttttgggtgcaaacccaagtaaggctctccaatgaatgcttttgccatacgtaagacaaatatacaatttttcaccagtatggcttctctgatgggtaagtcagagttttgttagaagcttttttcacacttgctggggcttctccccagggtgggttttctgaggtccaatgagatgttcatactgtctgcagcacaactgacactgaaggcatttaaaaagttgttctccggtgtgaattctcttacaacgagaagggctgagcattagtagaaagctctctcacactcagtgcatttctaaggtttcccacttgtatgaatcctcttgtgagtgatcaaatttgagctcagacggtaagttttcaaaacctctgggcatctgtagatttctcgttggagtgaggatgaagtgttctgttagggcagctctctgggcaaagaatttctcatatttccaattgcaggctctctggtccccactgaattctgagctctgagcaaagtctgagatttgtcctcatcttaatgagttctctgatacataaataatttttaatattggtattacagcttctcgcctggtcaagacatctgtgaggcttctgacgcatggggagggctaagctcaagacctttttcactcacattacagacaaacggtttttcaccaatgcgtactgtctgatgttgaagaagggctgaactctggtggaagcttttatcacatacagtgtatttatagtgtagctcctctgtttgagttctcattttctgttgggcaacaaagtccattcctaggaggaagccactctcacacgcagaccactgatgtggtttctcttccatgtgaattctctgatgtacaataagatctgagctacagttaaagcttttttcatattcaaggcatttaaaagtgtgagtgtgagttgcctggtgcctaattaggttggcactccgagtaaaacttctcatacattccaggcatttatacggcttctcacctgtgtggactctctggtgcacgataaggtctgatttctggccaaagcatttttcacaggcaccacacttatagggcttctccccagtatgaactcttttatgtacaatgaaggctgaacggtgtcggtaacttttctcacacttattacatttgtagggcctttccccagtgtgagttctctggtggctaataagatctgatttcccactaaaagctttttcacactcgagacacttaaatggtttctcacctgtgtgagttcttcgatgccttatgaggtttgtacttctactgaagcatttgtcacactcactacatagatatggtttctcgccagtatggcttcgctggtggacaagcagatcagaactctgaccaaaattcttgccacaaatgtcacatgtatagaattttttacctgcatgtgttctctgatgtcctgaaagcactaagtgatgccaaaagctcttctcacatttgctacatttataaggtttctcgtaattgtggatcctctggtgtgaagtaagatctgagctttggacaaaggttttctcacacatatcacatttataaggtttctccccagtatgggttctctcacacataataagagctaagttttcacacaagttttgcttgcattcaaggcactggtatatatgaccatctatctgaataatctcatgcatatgaataaaaatctttttacccttccgagggcatacattatatattttccttttttgagttctctgattacatttctcttctgaagtgtacattttctatggctctctcctagggagttttccgctggtcttcttgacccatcgttgccctcacagtcattttcttgataagaacttggaagatacatctgtttcaggcctttcaatcatgagcctctacaagtttccagcatcatatatgttaattccttacttggtatttccaacc,ctagaatccagatggaagaaaacatacattcctgatcctgactatttgacttctcaaagaagatagcatt,cgtaacaagaaagactcaagaccatcttccttttggtttcaaaaggtctctagttcagaactattcacaacactcaattcttgcctctc,cctggcagccgccggcgccgcccctaggcctggggacagcacttccggttactctccggacactcgaatctgggcttcctggcggccgcagac,	ggttaccgtcctttcctttattggatttctgaattttttaaaaagtaaaagtaaagcaatcattaagtagttcagataaaagaaaagcatctttacctgagttacccatcaggtctactctgacccaccctagcttctcccagaacaagcttctgggtatctaaaaaactattttcatactgatttcatgtaaagtcctctctaccatatgagtcaactaactatgagaacagtcttctcatacat,atgtacatagattctcacccacaattaaatctctcactgcagaacaggttttttggggcctgataagacaggagcttctaccaaaggttttctcagactcaaggtaagtatgggttttttcacctatgtgagttccctgatgtaccacaagagttgatcattgacaagcactcttcattcagacacttgcagtctttcctcagattgggtttttttttttgggtgcaaacccaagtaaggctctccaacgaatgcttttgccatacttaagacaaatatacaatttttcaccagtatggcttctctgatgggtaagtcagagttttgttagaagcttttttcacacttgctggggcttctccccagggtgggttttctgaggtccaatgagatgttcatactgtctgcagcacaactgacactgaaggcatttaaaaagttgttctccggtgtgaattctcttacaacgagaagggctgagcattagtagaaagctctctcacactcagtgcatttctaaggtttcccacttgtatgaatcctcttgtgagtgatcaaatttgagctcagacggtaagttttcaaaacctctgggcatctgtagatttctcgttggagtgaggatgaagtgttctgttagggcagctctctgggcaaagaatttctcatatttccaattgcaggctctctggtccccactgaattctgagctctgagcaaagtctgagatttgtcctcatcttaatgagttctctgatacataaataatttttaatattggtattacagcttctcgcctggtcaagacatctgtgaggcttctgacgcatggggagggctaagctcaagacctttttcactcacattacagacaaacggtttttcaccaatgtgtactgtctgatgttgaagaagggctgaactctggtggaagcttttatcacatacagtgtatttatagtgtagctcctctgtttgagttctcattttctgttgggcaacaaagtccattcctaggaggaagccactctcacacgcagaccactgatgtggtttctcttccatgtgaattctctgatgtacaataagatctgagctacagttaaagcttttttcatattcaaggcatttaaaagtgtgagtgtgagttgcctggtgcctaattaggttggcactccgagtaaaacttctcatacattccaggcatttatacggcttctcacctgtgtggactctctggtgcacgataaggtctgatttctggccaaagcatttttcacaggcaccacacttatagggcttctccccagtatgaactcttttatgtacaatgaaggctgaacggtgtcggtaacttttctcacacttattacatttgtagggcctttccccagtgtgagttctctggtggctaataagatctgatttcccactaaaagctttttcacactcgagacacttaaatggtttctcacctgtgtgagttcttcgatgccttatgaggtttgtacttctactgaagcatttgtcacactcactacatagatatggtttctcgccagtatggcttcgctggtggacaagcagatcagaactctgaccaaaattcttgccacaaatgtcacatgtatagaattttttacctgcatgtgttctctgatgtcctgaaagcgctaagtgatgccaaaagctcttctcacatttgctacatttataaggtttctcgtaattgtggatcctctggtgtgaagtaagatctgagctttggacaaaggttttctcacacatatcacatttataaggtttctccccagtatgggttctctcacacataataagagctaagttttcacagaagttttgcttgcattcaaggcactggtatatatgaccatctatctgaataatctcatgcatatgaataaaaatctttttacccttccgagggcatacattatatattttccttttttgagttctctgattacatttctcttctgaagtgtacattttctatggctctctcctagggagttttccgctggtcttcttgacccatcgttgccctcacagtcattttcttgataagaacttggaagatacatctgtttcaggcctttcaatcatgagcctctacaagtttccagcatcatatatgttaattccttacttggtatttccaacc,ctagaatccagatggaagaaaacatacattcctgatcctgacaatttgacttctcaaagaagatagcatt,cgtaacaagaaagactcaagaccatcttccttttggtttcaaaaggtctctagttcagaactattcacaacactcaattcttgcctctc,cctggcagccgccggcgccgcccctaggcctggggacagcacttccggttactctccggacactcgaatctgggcttcctggcggccgcagac,