Commits for markd

v415_preview2 to v415_base (2021-05-17 to 2021-05-24) v415

90032ba9f879592a33cec272f160941f98b9b98d Wed May 19 04:20:59 2021 -0700

• remove dependency on stringify being compiled
  • src/hg/utils/pslMap/makefile - lines changed 1, context: html, text, full: html, text

02336754147822f5aa61ba13277123b2cc629001 Thu May 20 08:38:55 2021 -0700

• Moved pslMap, pslMapPostChain, pslRc, pslSwap to src/utils, as they do not have hg/lib dependencies.
  • src/hg/makefile - lines changed 2, context: html, text, full: html, text
  • src/hg/pslSwap/makefile - lines changed 6, context: html, text, full: html, text
  • src/hg/pslSwap/pslSwap.c - lines changed 57, context: html, text, full: html, text
  • src/hg/pslSwap/tests/.gitignore - lines changed 1, context: html, text, full: html, text
  • src/hg/pslSwap/tests/expected/mrnaNoRcTest.psl - lines changed 7, context: html, text, full: html, text
  • src/hg/pslSwap/tests/expected/mrnaTest.psl - lines changed 7, context: html, text, full: html, text
  • src/hg/pslSwap/tests/expected/transTest.psl - lines changed 12, context: html, text, full: html, text
  • src/hg/pslSwap/tests/expected/withSeqNoRcTest.psl - lines changed 2, context: html, text, full: html, text
  • src/hg/pslSwap/tests/expected/withSeqTest.psl - lines changed 2, context: html, text, full: html, text
  • src/hg/pslSwap/tests/input/mrna.psl - lines changed 7, context: html, text, full: html, text
  • src/hg/pslSwap/tests/input/trans.psl - lines changed 12, context: html, text, full: html, text
  • src/hg/pslSwap/tests/input/withSeq.psl - lines changed 2, context: html, text, full: html, text
  • src/hg/pslSwap/tests/makefile - lines changed 54, context: html, text, full: html, text
  • src/hg/utils/makefile - lines changed 3, context: html, text, full: html, text
  • src/hg/utils/pslMap/README - lines changed 64, context: html, text, full: html, text
  • src/hg/utils/pslMap/makefile - lines changed 14, context: html, text, full: html, text
  • src/hg/utils/pslMap/pslMap.c - lines changed 405, context: html, text, full: html, text
  • src/hg/utils/pslMap/tests/.gitignore - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/pslMap/tests/expected/gapBoth.psl - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/pslMap/tests/expected/kgProt.psl - lines changed 5, context: html, text, full: html, text
  • src/hg/utils/pslMap/tests/expected/mrnaMapOver.mapinfo - lines changed 3, context: html, text, full: html, text
  • src/hg/utils/pslMap/tests/expected/mrnaMapOver.psl - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/pslMap/tests/expected/mrnaMapOverChain.mapping.psl - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/pslMap/tests/expected/mrnaMapOverSwap.mapinfo - lines changed 3, context: html, text, full: html, text
  • src/hg/utils/pslMap/tests/expected/mrnaMapOverSwap.mapping.psl - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/pslMap/tests/expected/mrnaMrnaMap.psl - lines changed 7, context: html, text, full: html, text
  • src/hg/utils/pslMap/tests/expected/mrnaMrnaXMap.psl - lines changed 17, context: html, text, full: html, text
  • src/hg/utils/pslMap/tests/expected/negQChain.psl - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/pslMap/tests/expected/retroParent.mapinfo - lines changed 5, context: html, text, full: html, text
  • src/hg/utils/pslMap/tests/expected/retroParent.psl - lines changed 4, context: html, text, full: html, text
  • src/hg/utils/pslMap/tests/expected/testMapFileWithInQName.psl - lines changed 17, context: html, text, full: html, text
  • src/hg/utils/pslMap/tests/input/README - lines changed 35, context: html, text, full: html, text
  • src/hg/utils/pslMap/tests/input/gapBothMRna.psl - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/pslMap/tests/input/gapBothProtMRna.blast - lines changed 218, context: html, text, full: html, text
  • src/hg/utils/pslMap/tests/input/gencode.blocks.qName-psl - lines changed 17, context: html, text, full: html, text
  • src/hg/utils/pslMap/tests/input/gencode.src.psl - lines changed 5, context: html, text, full: html, text
  • src/hg/utils/pslMap/tests/input/kgMRna.psl - lines changed 22, context: html, text, full: html, text
  • src/hg/utils/pslMap/tests/input/kgProtMRna.blast - lines changed 2239, context: html, text, full: html, text
  • src/hg/utils/pslMap/tests/input/mm6ToHg17.chain - lines changed 237, context: html, text, full: html, text
  • src/hg/utils/pslMap/tests/input/mm6ToHg17.psl - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/pslMap/tests/input/mrnaRefSeq.psl - lines changed 7, context: html, text, full: html, text
  • src/hg/utils/pslMap/tests/input/mrnaRefSeqX.psl - lines changed 17, context: html, text, full: html, text
  • src/hg/utils/pslMap/tests/input/mrnaToMm6.psl - lines changed 2, context: html, text, full: html, text
  • src/hg/utils/pslMap/tests/input/negQ.chain - lines changed 632, context: html, text, full: html, text
  • src/hg/utils/pslMap/tests/input/negQ.refSeq.psl - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/pslMap/tests/input/parent.psl - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/pslMap/tests/input/refSeqGen.psl - lines changed 2, context: html, text, full: html, text
  • src/hg/utils/pslMap/tests/input/retro.psl - lines changed 4, context: html, text, full: html, text
  • src/hg/utils/pslMap/tests/makefile - lines changed 107, context: html, text, full: html, text
  • src/hg/utils/pslMap/usage.txt - lines changed 64, context: html, text, full: html, text
  • src/hg/utils/pslMapPostChain/makefile - lines changed 3, context: html, text, full: html, text
  • src/hg/utils/pslMapPostChain/pslMapPostChain.c - lines changed 323, context: html, text, full: html, text
  • src/hg/utils/pslMapPostChain/tests/expected/C57B6NJ-1504TransMapTest.psl - lines changed 21, context: html, text, full: html, text
  • src/hg/utils/pslMapPostChain/tests/input/C57B6NJ-1504.transMap-cases.psl - lines changed 51, context: html, text, full: html, text
  • src/hg/utils/pslMapPostChain/tests/makefile - lines changed 20, context: html, text, full: html, text
  • src/hg/utils/pslRc/makefile - lines changed 3, context: html, text, full: html, text
  • src/hg/utils/pslRc/pslRc.c - lines changed 55, context: html, text, full: html, text
  • src/hg/utils/pslRc/tests/expected/mrnaTest.psl - lines changed 7, context: html, text, full: html, text
  • src/hg/utils/pslRc/tests/expected/transTest.psl - lines changed 12, context: html, text, full: html, text
  • src/hg/utils/pslRc/tests/expected/withSeqTest.psl - lines changed 2, context: html, text, full: html, text
  • src/hg/utils/pslRc/tests/makefile - lines changed 36, context: html, text, full: html, text
  • src/userApps/fetchKentSource.sh - lines changed 1, context: html, text, full: html, text
  • src/utils/makefile - lines changed 4, context: html, text, full: html, text
  • src/utils/pslMap/README - lines changed 64, context: html, text, full: html, text
  • src/utils/pslMap/makefile - lines changed 14, context: html, text, full: html, text
  • src/utils/pslMap/pslMap.c - lines changed 405, context: html, text, full: html, text
  • src/utils/pslMap/tests/.gitignore - lines changed 1, context: html, text, full: html, text
  • src/utils/pslMap/tests/expected/gapBoth.psl - lines changed 1, context: html, text, full: html, text
  • src/utils/pslMap/tests/expected/kgProt.psl - lines changed 5, context: html, text, full: html, text
  • src/utils/pslMap/tests/expected/mrnaMapOver.mapinfo - lines changed 3, context: html, text, full: html, text
  • src/utils/pslMap/tests/expected/mrnaMapOver.psl - lines changed 1, context: html, text, full: html, text
  • src/utils/pslMap/tests/expected/mrnaMapOverChain.mapping.psl - lines changed 1, context: html, text, full: html, text
  • src/utils/pslMap/tests/expected/mrnaMapOverSwap.mapinfo - lines changed 3, context: html, text, full: html, text
  • src/utils/pslMap/tests/expected/mrnaMapOverSwap.mapping.psl - lines changed 1, context: html, text, full: html, text
  • src/utils/pslMap/tests/expected/mrnaMrnaMap.psl - lines changed 7, context: html, text, full: html, text
  • src/utils/pslMap/tests/expected/mrnaMrnaXMap.psl - lines changed 17, context: html, text, full: html, text
  • src/utils/pslMap/tests/expected/negQChain.psl - lines changed 1, context: html, text, full: html, text
  • src/utils/pslMap/tests/expected/retroParent.mapinfo - lines changed 5, context: html, text, full: html, text
  • src/utils/pslMap/tests/expected/retroParent.psl - lines changed 4, context: html, text, full: html, text
  • src/utils/pslMap/tests/expected/testMapFileWithInQName.psl - lines changed 17, context: html, text, full: html, text
  • src/utils/pslMap/tests/input/README - lines changed 35, context: html, text, full: html, text
  • src/utils/pslMap/tests/input/gapBothMRna.psl - lines changed 1, context: html, text, full: html, text
  • src/utils/pslMap/tests/input/gapBothProtMRna.blast - lines changed 218, context: html, text, full: html, text
  • src/utils/pslMap/tests/input/gencode.blocks.qName-psl - lines changed 17, context: html, text, full: html, text
  • src/utils/pslMap/tests/input/gencode.src.psl - lines changed 5, context: html, text, full: html, text
  • src/utils/pslMap/tests/input/kgMRna.psl - lines changed 22, context: html, text, full: html, text
  • src/utils/pslMap/tests/input/kgProtMRna.blast - lines changed 2239, context: html, text, full: html, text
  • src/utils/pslMap/tests/input/mm6ToHg17.chain - lines changed 237, context: html, text, full: html, text
  • src/utils/pslMap/tests/input/mm6ToHg17.psl - lines changed 1, context: html, text, full: html, text
  • src/utils/pslMap/tests/input/mrnaRefSeq.psl - lines changed 7, context: html, text, full: html, text
  • src/utils/pslMap/tests/input/mrnaRefSeqX.psl - lines changed 17, context: html, text, full: html, text
  • src/utils/pslMap/tests/input/mrnaToMm6.psl - lines changed 2, context: html, text, full: html, text
  • src/utils/pslMap/tests/input/negQ.chain - lines changed 632, context: html, text, full: html, text
  • src/utils/pslMap/tests/input/negQ.refSeq.psl - lines changed 1, context: html, text, full: html, text
  • src/utils/pslMap/tests/input/parent.psl - lines changed 1, context: html, text, full: html, text
  • src/utils/pslMap/tests/input/refSeqGen.psl - lines changed 2, context: html, text, full: html, text
  • src/utils/pslMap/tests/input/retro.psl - lines changed 4, context: html, text, full: html, text
  • src/utils/pslMap/tests/makefile - lines changed 107, context: html, text, full: html, text
  • src/utils/pslMap/usage.txt - lines changed 64, context: html, text, full: html, text
  • src/utils/pslMapPostChain/makefile - lines changed 3, context: html, text, full: html, text
  • src/utils/pslMapPostChain/pslMapPostChain.c - lines changed 323, context: html, text, full: html, text
  • src/utils/pslMapPostChain/tests/expected/C57B6NJ-1504TransMapTest.psl - lines changed 21, context: html, text, full: html, text
  • src/utils/pslMapPostChain/tests/input/C57B6NJ-1504.transMap-cases.psl - lines changed 51, context: html, text, full: html, text
  • src/utils/pslMapPostChain/tests/makefile - lines changed 20, context: html, text, full: html, text
  • src/utils/pslRc/makefile - lines changed 3, context: html, text, full: html, text
  • src/utils/pslRc/pslRc.c - lines changed 55, context: html, text, full: html, text
  • src/utils/pslRc/tests/expected/mrnaTest.psl - lines changed 7, context: html, text, full: html, text
  • src/utils/pslRc/tests/expected/transTest.psl - lines changed 12, context: html, text, full: html, text
  • src/utils/pslRc/tests/expected/withSeqTest.psl - lines changed 2, context: html, text, full: html, text
  • src/utils/pslRc/tests/makefile - lines changed 36, context: html, text, full: html, text
  • src/utils/pslSwap/makefile - lines changed 6, context: html, text, full: html, text
  • src/utils/pslSwap/pslSwap.c - lines changed 57, context: html, text, full: html, text
  • src/utils/pslSwap/tests/.gitignore - lines changed 1, context: html, text, full: html, text
  • src/utils/pslSwap/tests/expected/mrnaNoRcTest.psl - lines changed 7, context: html, text, full: html, text
  • src/utils/pslSwap/tests/expected/mrnaTest.psl - lines changed 7, context: html, text, full: html, text
  • src/utils/pslSwap/tests/expected/transTest.psl - lines changed 12, context: html, text, full: html, text
  • src/utils/pslSwap/tests/expected/withSeqNoRcTest.psl - lines changed 2, context: html, text, full: html, text
  • src/utils/pslSwap/tests/expected/withSeqTest.psl - lines changed 2, context: html, text, full: html, text
  • src/utils/pslSwap/tests/input/mrna.psl - lines changed 7, context: html, text, full: html, text
  • src/utils/pslSwap/tests/input/trans.psl - lines changed 12, context: html, text, full: html, text
  • src/utils/pslSwap/tests/input/withSeq.psl - lines changed 2, context: html, text, full: html, text
  • src/utils/pslSwap/tests/makefile - lines changed 54, context: html, text, full: html, text

be7a9450777b54bf7a4796f6cb4502b692d4aa86 Thu May 20 09:00:59 2021 -0700

• place were psl tests were executed was missed in the previous commit
  • src/hg/utils/makefile - lines changed 2, context: html, text, full: html, text