Commits for braney

v326_preview to v326_preview2 (2015-11-23 to 2015-11-30) v326

• tweak mm10 snp142 HTML files #15934
  
  • src/hg/makeDb/trackDb/mouse/snp142.html - lines changed 5, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/snp142.shared.html - lines changed 42, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/snp142Common.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/snp142Mult.html - lines changed 1, context: html, text, full: html, text
• remove mouseStuff/chainStats... program never useful (no redmine)
  
  • src/hg/mouseStuff/chainStats/chainStats.c - lines changed 215, context: html, text, full: html, text
  • src/hg/mouseStuff/chainStats/makefile - lines changed 3, context: html, text, full: html, text
• support htslib for sam/bam/cram/tabix support #14717
  
  • src/hg/encode3/encodeDataWarehouse/lib/edwLib.c - lines changed 8, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/utils/edwBamFilter/edwBamFilter.c - lines changed 12, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/utils/edwBamRemoveChrom/edwBamRemoveChrom.c - lines changed 12, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/utils/edwBamStats/edwBamStats.c - lines changed 28, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/utils/edwSamRepeatAnalysis/edwSamRepeatAnalysis.c - lines changed 8, context: html, text, full: html, text
  • src/hg/encode3/validateFiles/validateFiles.c - lines changed 17, context: html, text, full: html, text
  • src/hg/hgTables/bam.c - lines changed 10, context: html, text, full: html, text
  • src/hg/hgTracks/bamTrack.c - lines changed 12, context: html, text, full: html, text
  • src/hg/hgc/bamClick.c - lines changed 4, context: html, text, full: html, text
  • src/hg/inc/hgBam.h - lines changed 4, context: html, text, full: html, text
  • src/hg/lib/hgBam.c - lines changed 22, context: html, text, full: html, text
  • src/inc/bamFile.h - lines changed 22, context: html, text, full: html, text
  • src/inc/common.mk - lines changed 16, context: html, text, full: html, text
  • src/inc/linefile.h - lines changed 18, context: html, text, full: html, text
  • src/lib/bamFile.c - lines changed 58, context: html, text, full: html, text
  • src/lib/knetUdc.c - lines changed 9, context: html, text, full: html, text
  • src/lib/linefile.c - lines changed 50, context: html, text, full: html, text
• remove chainStats from makefile
  
  • src/hg/mouseStuff/makefile - lines changed 1, context: html, text, full: html, text
• pipelineTester needs INT_MAX from limits.h thqt is normally included by
  tabix.h
  
  • src/lib/tests/pipelineTester.c - lines changed 1, context: html, text, full: html, text