Commits for braney

v342_preview to v342_preview2 (2016-11-14 to 2016-11-28) v342

c4c419da6f898053370b2b8b31a165c7cda9b5a0 Mon Nov 14 12:58:24 2016 -0800

• score in chains is double, not unsigned
  • src/hg/lib/bigChain.as - lines changed 1, context: html, text, full: html, text

e585df1a1af3538bd2e41bb2fb3e2e1157ca9b16 Tue Nov 15 15:41:19 2016 -0800

• mention CRAM in section about BAM in trackDb doc
  • src/hg/htdocs/goldenPath/help/trackDb/trackDbDoc.html - lines changed 2, context: html, text, full: html, text
  • src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.v1.html - lines changed 2, context: html, text, full: html, text
  • src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml - lines changed 7, context: html, text, full: html, text

6fe08e419d9eaf9c40eac041dc9d8d2ba42f3061 Wed Nov 16 17:12:00 2016 -0800

• fix problem with snake track height when there's an error message or no items in track.
  • src/hg/hgTracks/snakeTrack.c - lines changed 2, context: html, text, full: html, text

dccdf29485000ddce07f65a431d52a51ffd158cf Wed Nov 16 18:41:22 2016 -0800

• add support for protein psls in bigPsl
  • src/hg/hgTracks/bigBedTrack.c - lines changed 15, context: html, text, full: html, text
  • src/hg/hgTracks/cds.c - lines changed 3, context: html, text, full: html, text
  • src/hg/hgc/hgc.c - lines changed 28, context: html, text, full: html, text
  • src/hg/inc/bigPsl.h - lines changed 6, context: html, text, full: html, text
  • src/hg/lib/bigPsl.as - lines changed 1, context: html, text, full: html, text
  • src/hg/lib/bigPsl.c - lines changed 20, context: html, text, full: html, text
  • src/hg/utils/pslToBigPsl/pslToBigPsl.c - lines changed 11, context: html, text, full: html, text
  • src/lib/psl.c - lines changed 2, context: html, text, full: html, text

2b3b809dcbcd3f3827965f1cae071c6e470db6fe Wed Nov 16 19:31:11 2016 -0800

• fix up bigPslToPsl to use the new API.
  • src/hg/utils/bigPslToPsl/bigPslToPsl.c - lines changed 2, context: html, text, full: html, text

a7455028205c94b674aa9d495558b1bac2845fdf Fri Nov 18 13:36:45 2016 -0800

• tagStorm file support for track hubs. NEEEDS DOC!!!
  • src/hg/cirm/cdw/cdwWebBrowse/cdwWebBrowse.c - lines changed 2, context: html, text, full: html, text
  • src/hg/lib/hui.c - lines changed 16, context: html, text, full: html, text
  • src/hg/lib/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/lib/tagRepo.c - lines changed 130, context: html, text, full: html, text
  • src/inc/tagStorm.h - lines changed 3, context: html, text, full: html, text
  • src/lib/tagStorm.c - lines changed 8, context: html, text, full: html, text

40fc79826f7de636f623e2c6dbe2c49e3d191e78 Fri Nov 18 16:10:12 2016 -0800

• oops, left this out
  • src/hg/inc/tagRepo.h - lines changed 10, context: html, text, full: html, text

3a5ceb6cf9b3a4869e57ab621d1143fbd0573a5a Wed Nov 23 17:01:52 2016 -0800

• implements blat results to custom track using bigPsl. Requires hg.conf variable useBlatBigPsl=on, otherwise old behavior exists
  • src/hg/hgBlat/hgBlat.c - lines changed 89, context: html, text, full: html, text
  • src/hg/hgc/hgc.c - lines changed 30, context: html, text, full: html, text
  • src/hg/lib/bigPsl.c - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/hgLoadBed/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/pslToBigPsl/makefile - lines changed 14, context: html, text, full: html, text
  • src/makefile - lines changed 1, context: html, text, full: html, text
  • src/utils/bedToBigBed/makefile - lines changed 14, context: html, text, full: html, text

464490ebad9e39144ad981f86d859219cc5c658d Thu Nov 24 06:57:31 2016 -0800

• add alpha,beta targets to pslToBigPsl and bedToBigBed makefiles
  • src/hg/utils/pslToBigPsl/makefile - lines changed 48, context: html, text, full: html, text
  • src/utils/bedToBigBed/makefile - lines changed 48, context: html, text, full: html, text