Commits for braney

v320_base to v321_preview (2015-08-03 to 2015-08-21) v321

• first cut at bigPsl support in the browser. #14241
  
  • src/hg/hgTrackUi/hgTrackUi.c - lines changed 2, context: html, text, full: html, text
  • src/hg/hgTracks/bigBedTrack.c - lines changed 8, context: html, text, full: html, text
  • src/hg/hgTracks/cds.c - lines changed 5, context: html, text, full: html, text
  • src/hg/hgTracks/hgTracks.c - lines changed 5, context: html, text, full: html, text
  • src/hg/hgTracks/hgTracks.h - lines changed 1, context: html, text, full: html, text
  • src/hg/hgTracks/simpleTracks.c - lines changed 9, context: html, text, full: html, text
  • src/hg/hgc/hgc.c - lines changed 46, context: html, text, full: html, text
  • src/hg/lib/bigPsl.as - lines changed 6, context: html, text, full: html, text
  • src/hg/lib/hui.c - lines changed 1, context: html, text, full: html, text
  • src/hg/lib/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/lib/trackDbCustom.c - lines changed 1, context: html, text, full: html, text
  • src/hg/lib/trackHub.c - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/tagTypes.tab - lines changed 35, context: html, text, full: html, text
  • src/hg/utils/pslToBigPsl/makefile - lines changed 4, context: html, text, full: html, text
  • src/hg/utils/pslToBigPsl/pslToBigPsl.c - lines changed 289, context: html, text, full: html, text
• left out bigPsl.c in my earlier bigPsl check in. #14241
  
  • src/hg/inc/bigPsl.h - lines changed 88, context: html, text, full: html, text
  • src/hg/lib/bigPsl.c - lines changed 336, context: html, text, full: html, text
• small bigPsl fix #14241
  
  • src/hg/hgc/hgc.c - lines changed 1, context: html, text, full: html, text
• increase a number that causes beds with more than 1024 blocks to not
  validate, even though they work fine after validation #14241
  
  • src/lib/basicBed.c - lines changed 1, context: html, text, full: html, text
• fix regex for hgsid to match current hgsid format (now
  number_alphanumber whereas it used to just be a number ) #15820
  
  • src/hg/js/ajax.js - lines changed 2, context: html, text, full: html, text
• do a better job of bigPsl support (query gaps) #14241
  
  • src/hg/hgTracks/bigBedTrack.c - lines changed 32, context: html, text, full: html, text
• a couple of test tracks using bigPsl #14241
  
  • src/hg/makeDb/trackDb/human/hg38/trackDb.ra - lines changed 37, context: html, text, full: html, text
• more polish for bigPsl support. hgc alignments work now #14241
  
  • src/hg/hgTracks/bigBedTrack.c - lines changed 2, context: html, text, full: html, text
  • src/hg/hgc/hgc.c - lines changed 75, context: html, text, full: html, text
  • src/hg/lib/bigPsl.c - lines changed 7, context: html, text, full: html, text
  • src/hg/utils/bigPslToPsl/bigPslToPsl.c - lines changed 61, context: html, text, full: html, text
  • src/hg/utils/bigPslToPsl/makefile - lines changed 3, context: html, text, full: html, text
  • src/hg/utils/pslToBigPsl/pslToBigPsl.c - lines changed 5, context: html, text, full: html, text
• some tweaks to introduce mafSnp mode to hg38 100way #14277
  
  • src/hg/hgTracks/mafTrack.c - lines changed 2, context: html, text, full: html, text
  • src/hg/hgTracks/mafTrack.h - lines changed 9, context: html, text, full: html, text
  • src/hg/hgTracks/wigMafTrack.c - lines changed 13, context: html, text, full: html, text