File Changes for markd

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

• src/hg/hgc/hgc.c
  • lines changed 13, 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/transMapClick.c
  • lines changed 3, context: html, text, full: html, text
    add geneId to transmap gene table, with backwards compatibilty for current transmap tracks (RM 14574)
    
• src/hg/inc/genePred.h
  • lines changed 3, 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/transMapGene.h
  • lines changed 10, context: html, text, full: html, text
    add geneId to transmap gene table, with backwards compatibilty for current transmap tracks (RM 14574)
    
• src/hg/inc/transMapInfo.h
  • lines changed 2, context: html, text, full: html, text
    add geneId to transmap gene table, with backwards compatibilty for current transmap tracks (RM 14574)
    
• src/hg/inc/transMapSrc.h
  • lines changed 2, context: html, text, full: html, text
    add geneId to transmap gene table, with backwards compatibilty for current transmap tracks (RM 14574)
    
• src/hg/lib/genePred.c
  • lines changed 36, 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)
    
  • lines changed 1, context: html, text, full: html, text
    fixed buffer overflow in extreme test case (no readmind)
    
• src/hg/lib/transMapGene.as
  • lines changed 3, context: html, text, full: html, text
    add geneId to transmap gene table, with backwards compatibilty for current transmap tracks (RM 14574)
    
• src/hg/lib/transMapGene.c
  • lines changed 27, context: html, text, full: html, text
    add geneId to transmap gene table, with backwards compatibilty for current transmap tracks (RM 14574)
    
• src/hg/lib/transMapGene.sql
  • lines changed 5, context: html, text, full: html, text
    add geneId to transmap gene table, with backwards compatibilty for current transmap tracks (RM 14574)
    
• src/hg/lib/transMapInfo.c
  • lines changed 3, context: html, text, full: html, text
    add geneId to transmap gene table, with backwards compatibilty for current transmap tracks (RM 14574)
    
• src/hg/lib/transMapSrc.c
  • lines changed 4, context: html, text, full: html, text
    add geneId to transmap gene table, with backwards compatibilty for current transmap tracks (RM 14574)
    
• src/hg/mouseStuff/chainToPsl/chainToPsl.c
  • lines changed 11, 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/pslStats/pslStats.c
  • lines changed 1, 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/tests/expected/cdna2cdnaAlignTest.stats
  • lines changed 1, 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/tests/expected/cdna2cdnaQueryTest.stats
  • lines changed 1, context: html, text, full: html, text
    fix pslStats computation of query coverage. It was not counting based aligned to Ns (no redmine)
    
• src/hg/utils/gtfToGenePred/gtfToGenePred.c
  • lines changed 32, 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)
    
  • lines changed 1, context: html, text, full: html, text
    fixed buffer overflow in extreme test case (no readmind)
    
• src/hg/utils/gtfToGenePred/tests/expected/ensemblWithVersions.gp
  • 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/utils/gtfToGenePred/tests/expected/ensemblWithVersions.info
  • lines changed 5, 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/utils/gtfToGenePred/tests/expected/ensemblWithVersionsGeneName2.gp
  • 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/utils/gtfToGenePred/tests/expected/ensemblWithVersionsGeneName2.info
  • lines changed 5, 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/utils/gtfToGenePred/tests/input/ensemblSplicedStop.gp
  • lines changed 102, 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/utils/gtfToGenePred/tests/input/ensemblSplicedStop.gtf
  • lines changed 102, 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/utils/gtfToGenePred/tests/input/ensemblWithVersions.gtf
  • lines changed 38, 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/utils/gtfToGenePred/tests/makefile
  • lines changed 20, 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/inc/gff.h
  • lines changed 3, 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/lib/gff.c
  • lines changed 6, 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)