File Changes for braney

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

• src/hg/hgTracks/bedTrack.c
  • lines changed 14, 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/bigBedTrack.c
  • lines changed 1, context: html, text, full: html, text
    3afb1ad18d251832c36c02910ba194a3996ab47a Mon May 9 14:56:22 2016 -0700
    some changes to bigPsl format
    
• src/hg/hgTracks/connectTrack.c
  • lines changed 143, 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/hgTracks.c
  • lines changed 7, 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/hgTracks.h
  • lines changed 3, 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/makefile
  • lines changed 1, 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/multiWig.c
  • lines changed 2, 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/simpleTracks.c
  • lines changed 19, context: html, text, full: html, text
    4e4629ec70e0b6635441790483d6d24bb30df91b Fri May 13 17:00:35 2016 -0700
    first cut at long range interaction track
    
• src/hg/hgc/hgc.c
  • lines changed 2, context: html, text, full: html, text
    3afb1ad18d251832c36c02910ba194a3996ab47a Mon May 9 14:56:22 2016 -0700
    some changes to bigPsl format
    
  • lines changed 5, 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/htdocs/FAQ/FAQformat.html
  • lines changed 126, context: html, text, full: html, text
    57275b00fff2a36640700b50ec2af37af42fca97 Tue May 10 15:10:21 2016 -0700
    changes to document new big* formats
    
  • 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/goldenPath/help/bigChain.html
  • 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/goldenPath/help/bigMaf.html
  • lines changed 18, 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/goldenPath/help/bigPsl.html
  • lines changed 4, context: html, text, full: html, text
    57275b00fff2a36640700b50ec2af37af42fca97 Tue May 10 15:10:21 2016 -0700
    changes to document new big* formats
    
  • lines changed 11, 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/goldenPath/help/customTrackText.html
  • lines changed 3, context: html, text, full: html, text
    57275b00fff2a36640700b50ec2af37af42fca97 Tue May 10 15:10:21 2016 -0700
    changes to document new big* formats
    
• src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html
  • lines changed 6, context: html, text, full: html, text
    57275b00fff2a36640700b50ec2af37af42fca97 Tue May 10 15:10:21 2016 -0700
    changes to document new big* formats
    
• src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
  • lines changed 3, context: html, text, full: html, text
    57275b00fff2a36640700b50ec2af37af42fca97 Tue May 10 15:10:21 2016 -0700
    changes to document new big* formats
    
• src/hg/inc/bigPsl.h
  • lines changed 2, context: html, text, full: html, text
    3afb1ad18d251832c36c02910ba194a3996ab47a Mon May 9 14:56:22 2016 -0700
    some changes to bigPsl format
    
• src/hg/inc/hui.h
  • lines changed 2, 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.
    
  • lines changed 2, 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/lib/bigPsl.as
  • lines changed 2, context: html, text, full: html, text
    3afb1ad18d251832c36c02910ba194a3996ab47a Mon May 9 14:56:22 2016 -0700
    some changes to bigPsl format
    
• src/hg/lib/bigPsl.c
  • lines changed 8, context: html, text, full: html, text
    3afb1ad18d251832c36c02910ba194a3996ab47a Mon May 9 14:56:22 2016 -0700
    some changes to bigPsl format
    
• src/hg/lib/customFactory.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
    
  • lines changed 82, context: html, text, full: html, text
    4e4629ec70e0b6635441790483d6d24bb30df91b Fri May 13 17:00:35 2016 -0700
    first cut at long range interaction track
    
• src/hg/lib/genbank.c
  • lines changed 17, 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/hgBam.c
  • lines changed 13, 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/hui.c
  • lines changed 5, 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.
    
  • lines changed 1, context: html, text, full: html, text
    cc659a8d5b8669461e135d517eb59249de9dbbab Thu May 12 11:28:21 2016 -0700
    allow coverage wiggles for bigBeds
    
  • 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
    
  • lines changed 5, 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/utils/bigPslToPsl/bigPslToPsl.c
  • lines changed 1, context: html, text, full: html, text
    05118fa9e5d2e7b81a874c983f1571ca7df9d346 Mon May 9 15:09:05 2016 -0700
    oops.. another bigPsl change
    
• src/hg/utils/pslToBigPsl/pslToBigPsl.c
  • lines changed 124, context: html, text, full: html, text
    3afb1ad18d251832c36c02910ba194a3996ab47a Mon May 9 14:56:22 2016 -0700
    some changes to bigPsl format
    
• src/hg/utils/refSeqGet/refSeqGet.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/inc/bedTabix.h
  • lines changed 18, context: html, text, full: html, text
    4e4629ec70e0b6635441790483d6d24bb30df91b Fri May 13 17:00:35 2016 -0700
    first cut at long range interaction track
    
• src/lib/bamFile.c
  • lines changed 1, context: html, text, full: html, text
    762c15a711cbc708476298a975dc324de82e992b Wed May 11 12:32:48 2016 -0700
    changed CRAM download pending message #14717
    
• src/lib/bedTabix.c
  • lines changed 39, context: html, text, full: html, text
    4e4629ec70e0b6635441790483d6d24bb30df91b Fri May 13 17:00:35 2016 -0700
    first cut at long range interaction track
    
• src/lib/makefile
  • lines changed 1, context: html, text, full: html, text
    4e4629ec70e0b6635441790483d6d24bb30df91b Fri May 13 17:00:35 2016 -0700
    first cut at long range interaction track