Commits for markd

v323_preview2 to v323_base (2015-09-28 to 2015-10-05) v323

• fixed broken test psl now caught by pslCheck
  
  • src/hg/pslCDnaFilter/tests/expected/ignoreIntronsTest/drop.psl - lines changed 1, context: html, text, full: html, text
  • src/hg/pslCDnaFilter/tests/expected/noIgnoreIntronsTest/keep.psl - lines changed 1, context: html, text, full: html, text
  • src/hg/pslCDnaFilter/tests/input/ignoreIntrons.psl - lines changed 1, context: html, text, full: html, text
• fixed various problems detected by making pslCheck more stringent
  
  • src/hg/utils/gff3ToPsl/tests/expected/grch38ToGrch37Test.psl - lines changed 18, context: html, text, full: html, text
  • src/hg/utils/gff3ToPsl/tests/expected/patch1test.psl - lines changed 264, context: html, text, full: html, text
  • src/hg/utils/pslMap/pslMap.c - lines changed 2, 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.mapping.psl - lines changed 1, 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/retro.psl - lines changed 4, context: html, text, full: html, text
  • src/inc/psl.h - lines changed 3, context: html, text, full: html, text
  • src/lib/psl.c - lines changed 35, context: html, text, full: html, text
• fixed memory leak that didn't matter
  
  • src/hg/utils/overlapSelect/chromAnnMap.c - lines changed 1, context: html, text, full: html, text
• GENCODE V23
  
  • src/hg/makeDb/doc/hg38/hg38.txt - lines changed 45, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/gencodeLoad.mk - lines changed 5, context: html, text, full: html, text
  • src/hg/makeDb/schema/all.joiner - lines changed 85, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/trackDb.wgEncode.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeSuper.html - lines changed 5, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV23.html - lines changed 333, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV23.ra - lines changed 272, context: html, text, full: html, text
• GENCODE VM7 import
  
  • src/hg/makeDb/doc/mm10.txt - lines changed 44, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/gencodeLoad.mk - lines changed 10, context: html, text, full: html, text
  • src/hg/makeDb/schema/all.joiner - lines changed 85, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm10/trackDb.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm10/wgEncodeGencodeSuper.html - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm10/wgEncodeGencodeVM7.html - lines changed 311, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm10/wgEncodeGencodeVM7.ra - lines changed 267, context: html, text, full: html, text
• updated mouse GENCODE to have same filters and highlighting as human
  
  • src/hg/makeDb/trackDb/mouse/mm10/wgEncodeGencodeVM7.ra - lines changed 10, context: html, text, full: html, text