Commits for braney

v333_preview to v333_preview2 (2016-05-09 to 2016-05-16) v333

3afb1ad18d251832c36c02910ba194a3996ab47a Mon May 9 14:56:22 2016 -0700

• some changes to bigPsl format
  
  • src/hg/hgTracks/bigBedTrack.c - lines changed 1, context: html, text, full: html, text
  • src/hg/hgc/hgc.c - lines changed 2, context: html, text, full: html, text
  • src/hg/inc/bigPsl.h - lines changed 2, context: html, text, full: html, text
  • src/hg/lib/bigPsl.as - lines changed 2, context: html, text, full: html, text
  • src/hg/lib/bigPsl.c - lines changed 8, context: html, text, full: html, text
  • src/hg/utils/pslToBigPsl/pslToBigPsl.c - lines changed 124, context: html, text, full: html, text

05118fa9e5d2e7b81a874c983f1571ca7df9d346 Mon May 9 15:09:05 2016 -0700

• oops.. another bigPsl change
  
  • src/hg/utils/bigPslToPsl/bigPslToPsl.c - lines changed 1, context: html, text, full: html, text

b4310bdbb2d4a0b1979f4fb1c8fc45ed521426d3 Mon May 9 15:37:39 2016 -0700

• get genbank data from hgFixed
  
  • src/hg/utils/refSeqGet/refSeqGet.c - lines changed 1, context: html, text, full: html, text

3377b968b5f797ef07f454f5a5fb125668f6c2e4 Tue May 10 12:10:55 2016 -0700

• fix a problem that shows up if neither samtabix or htslib are installed
  
  • src/hg/lib/hgBam.c - lines changed 13, context: html, text, full: html, text

57275b00fff2a36640700b50ec2af37af42fca97 Tue May 10 15:10:21 2016 -0700

• changes to document new big* formats
  
  • src/hg/htdocs/FAQ/FAQformat.html - lines changed 126, context: html, text, full: html, text
  • src/hg/htdocs/goldenPath/help/bigPsl.html - lines changed 4, context: html, text, full: html, text
  • src/hg/htdocs/goldenPath/help/customTrackText.html - lines changed 3, context: html, text, full: html, text
  • src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html - lines changed 6, context: html, text, full: html, text
  • src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml - lines changed 3, context: html, text, full: html, text

f75c6a6591461c2d716288d0b278cadf938e6590 Tue May 10 18:48:27 2016 -0700

• more changes to doc new big* formats
  
  • src/hg/htdocs/FAQ/FAQformat.html - lines changed 3, context: html, text, full: html, text
  • src/hg/htdocs/goldenPath/help/bigChain.html - lines changed 3, context: html, text, full: html, text
  • src/hg/htdocs/goldenPath/help/bigMaf.html - lines changed 18, context: html, text, full: html, text
  • src/hg/htdocs/goldenPath/help/bigPsl.html - lines changed 11, context: html, text, full: html, text

52432fd218c9b33509078dd1514acd021d30439b Wed May 11 11:50:25 2016 -0700

• fix #17281 bug with stacked bars and only one dataset
  
  • src/hg/hgTracks/multiWig.c - lines changed 2, context: html, text, full: html, text

762c15a711cbc708476298a975dc324de82e992b Wed May 11 12:32:48 2016 -0700

• changed CRAM download pending message #14717
  
  • src/lib/bamFile.c - lines changed 1, context: html, text, full: html, text

72211d6e55ffad9e5f12048276243e79f33b71b1 Thu May 12 10:30:07 2016 -0700

• remove "canDoCoverage" hg.conf variable. Density graph is now always
  offered.
  
  • src/hg/inc/hui.h - lines changed 2, context: html, text, full: html, text
  • src/hg/lib/hui.c - lines changed 5, context: html, text, full: html, text

cc659a8d5b8669461e135d517eb59249de9dbbab Thu May 12 11:28:21 2016 -0700

• allow coverage wiggles for bigBeds
  
  • src/hg/lib/hui.c - lines changed 1, context: html, text, full: html, text

330109b998a61e1a9db6764b96f40dceb918ffc6 Thu May 12 16:08:34 2016 -0700

• a couple of changes in response to code review
  
  • src/hg/hgc/hgc.c - lines changed 5, context: html, text, full: html, text
  • src/hg/lib/customFactory.c - lines changed 1, context: html, text, full: html, text

237b5bec54fd46beff17c0271934593c15b3081b Thu May 12 17:16:42 2016 -0700

• back out hasty code change to allow density graphs on too many track
  types
  
  • src/hg/lib/hui.c - lines changed 1, context: html, text, full: html, text

fbcba9729a66e8b13f23ee55da62f6b716cea1d0 Fri May 13 11:52:29 2016 -0700

• Revert "remove "canDoCoverage" hg.conf variable. Density graph is now always"
  
  This reverts commit 72211d6e55ffad9e5f12048276243e79f33b71b1.
  
  • src/hg/inc/hui.h - lines changed 2, context: html, text, full: html, text
  • src/hg/lib/hui.c - lines changed 5, context: html, text, full: html, text

4e4629ec70e0b6635441790483d6d24bb30df91b Fri May 13 17:00:35 2016 -0700

• first cut at long range interaction track
  
  • src/hg/hgTracks/bedTrack.c - lines changed 14, context: html, text, full: html, text
  • src/hg/hgTracks/hgTracks.c - lines changed 7, context: html, text, full: html, text
  • src/hg/hgTracks/hgTracks.h - lines changed 3, context: html, text, full: html, text
  • src/hg/hgTracks/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/hgTracks/simpleTracks.c - lines changed 19, context: html, text, full: html, text
  • src/hg/lib/customFactory.c - lines changed 82, context: html, text, full: html, text
  • src/inc/bedTabix.h - lines changed 18, context: html, text, full: html, text
  • src/lib/bedTabix.c - lines changed 39, context: html, text, full: html, text
  • src/lib/makefile - lines changed 1, context: html, text, full: html, text

087cf4606b0df6c0c5b9db6df76ea8e15b1551c7 Fri May 13 17:22:30 2016 -0700

• oops... missed a file needed for bedTabix and longTabix
  
  • src/hg/hgTracks/connectTrack.c - lines changed 143, context: html, text, full: html, text

37f2949bd230359381df9070c80361bddc058fc3 Sat May 14 16:47:31 2016 -0700

• add some logic so genbank tables are retrieved from hgFixed in genbankDb
  is not in hg.conf and the table exists
  
  • src/hg/lib/genbank.c - lines changed 17, context: html, text, full: html, text