Commits for markd

v318_base to v319_preview (2015-06-22 to 2015-06-29) v319

• add geneId to transmap gene table, with backwards compatibilty for current transmap tracks (RM 14574)
  
  • src/hg/hgc/transMapClick.c - lines changed 3, context: html, text, full: html, text
  • src/hg/inc/transMapGene.h - lines changed 10, context: html, text, full: html, text
  • src/hg/inc/transMapInfo.h - lines changed 2, context: html, text, full: html, text
  • src/hg/inc/transMapSrc.h - lines changed 2, context: html, text, full: html, text
  • src/hg/lib/transMapGene.as - lines changed 3, context: html, text, full: html, text
  • src/hg/lib/transMapGene.c - lines changed 27, context: html, text, full: html, text
  • src/hg/lib/transMapGene.sql - lines changed 5, context: html, text, full: html, text
  • src/hg/lib/transMapInfo.c - lines changed 3, context: html, text, full: html, text
  • src/hg/lib/transMapSrc.c - lines changed 4, context: html, text, full: html, text
• add option to gtfToGenePred to include gene and transcript version number that now part of their GTF files in the gene/transcripts ids (no redmine)
  
  • src/hg/inc/genePred.h - lines changed 3, context: html, text, full: html, text
  • src/hg/lib/genePred.c - lines changed 36, context: html, text, full: html, text
  • src/hg/utils/gtfToGenePred/gtfToGenePred.c - lines changed 32, context: html, text, full: html, text
  • src/hg/utils/gtfToGenePred/tests/expected/ensemblWithVersions.gp - lines changed 4, context: html, text, full: html, text
  • src/hg/utils/gtfToGenePred/tests/expected/ensemblWithVersions.info - lines changed 5, context: html, text, full: html, text
  • src/hg/utils/gtfToGenePred/tests/expected/ensemblWithVersionsGeneName2.gp - lines changed 4, context: html, text, full: html, text
  • src/hg/utils/gtfToGenePred/tests/expected/ensemblWithVersionsGeneName2.info - lines changed 5, context: html, text, full: html, text
  • src/hg/utils/gtfToGenePred/tests/input/ensemblSplicedStop.gp - lines changed 102, context: html, text, full: html, text
  • src/hg/utils/gtfToGenePred/tests/input/ensemblSplicedStop.gtf - lines changed 102, context: html, text, full: html, text
  • src/hg/utils/gtfToGenePred/tests/input/ensemblWithVersions.gtf - lines changed 38, context: html, text, full: html, text
  • src/hg/utils/gtfToGenePred/tests/makefile - lines changed 20, context: html, text, full: html, text
  • src/inc/gff.h - lines changed 3, context: html, text, full: html, text
  • src/lib/gff.c - lines changed 6, context: html, text, full: html, text
• fix click through on snake tracks to other genomes in mysql backed HAL browsers (no redmine)
  
  • src/hg/hgc/hgc.c - lines changed 13, context: html, text, full: html, text
• fixed buffer overflow in extreme test case (no readmind)
  
  • src/hg/lib/genePred.c - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/gtfToGenePred/gtfToGenePred.c - lines changed 1, context: html, text, full: html, text
• fixed skipping calculation of PSL match statistic in chainToPsl because of bogus code that was just hacked around instead of fixed. (no redmine)
  
  • src/hg/mouseStuff/chainToPsl/chainToPsl.c - lines changed 11, context: html, text, full: html, text
• fix pslStats computation of query coverage. It was not counting based aligned to Ns (no redmine)
  
  • src/hg/pslStats/pslStats.c - lines changed 1, context: html, text, full: html, text
  • src/hg/pslStats/tests/expected/cdna2cdnaAlignTest.stats - lines changed 1, context: html, text, full: html, text
  • src/hg/pslStats/tests/expected/cdna2cdnaQueryTest.stats - lines changed 1, context: html, text, full: html, text