All File Changes

v343_preview to v343_preview2 (2016-12-19 to 2017-01-03) v343

• LICENSE
  • lines changed 1, context: html, text, full: html, text
    6014a9a49ec62ba589d446570ebf9d894b62aa4c Mon Dec 19 14:53:58 2016 -0800
    fixed typo, refs #18559
• confs/hgwbeta.hg.conf
  • lines changed 1, context: html, text, full: html, text
    386ba1996399b07f8aee18ae07eb098f77a4092a Sun Dec 25 01:11:45 2016 -0800
    Installing updated hg.conf files from UCSC servers
• src/LICENSE
  • lines changed 1, context: html, text, full: html, text
    a01153325ae96ff8317ffc5b838b0c4d2d2d6812 Tue Jan 3 09:47:16 2017 -0800
    fixed typo, refs #18559
• src/hg/cirm/cdw/cdwMakeFileTags/cdwMakeFileTags.c
  • lines changed 190, context: html, text, full: html, text
    63a86151d3aeeedebf5b303118f526720e8d39f6 Mon Dec 19 22:15:39 2016 -0800
    Making cdwFileTags table use minimum sized database types.
  • lines changed 11, context: html, text, full: html, text
    86000a33c9b13f1382c1d8e02388a06d3b81451e Tue Dec 20 11:51:32 2016 -0800
    Adding sqlType to the -types output, and putting min before max.
• src/hg/cirm/cdw/cdwMakeValidFile/cdwMakeValidFile.c
  • lines changed 34, context: html, text, full: html, text
    17325ead43fb0dd51d1adf720f3c982a45e6dc5d Mon Dec 26 12:14:51 2016 -0800
    Checking chromosome sizes match declared assembly for bigBed and bigWig files.
  • lines changed 57, context: html, text, full: html, text
    cb58baca5f7b2918a9f335119f5d679ef09a92c5 Tue Dec 27 12:08:54 2016 -0800
    Checking chromosome/assembly agreement for bam files. Improving commenting and error message on similar check for bigWig/bigBed files.
• src/hg/cirm/cdw/cdwSummary/cdwSummary
  • lines changed 80, context: html, text, full: html, text
    4c1601a6b36300946259e6e90d417bb638aa77db Wed Dec 21 16:32:07 2016 -0800
    CIRM: adding a json export option to cdwSummary for a new js plotter
  • lines changed 15, context: html, text, full: html, text
    9b97fd666c3a49c36a4b54059e1a0b3c2ca46934 Fri Dec 23 14:32:08 2016 -0800
    CIRM: better handling of empty gene lists
• src/hg/cirm/cdw/cdwWebBrowse/cdwFlowCharts.c
  • lines changed 2, context: html, text, full: html, text
    d00fcf8e270eca6379c2d7f1ac40d4c100bd3a66 Mon Dec 19 10:25:53 2016 -0800
    Minor update to get the node linking feature where we want it, refs #17544
• src/hg/cirm/cdw/wrangle/kallistoToMatrix/kallistoToMatrix
  • lines changed 35, context: html, text, full: html, text
    56a11ad6564e8c3a4fef1e41f2d87dbc66dae7c6 Thu Dec 22 11:34:36 2016 -0800
    CIRM: Merging in Sol's changes to kallistoToMatrix
• src/hg/encode3/encodeDataWarehouse/utils/edwBamStats/edwBamStats.c
  • lines changed 1, context: html, text, full: html, text
    0e468e331193dda588bd7c2151997bbdbd4ef517 Tue Dec 27 12:07:28 2016 -0800
    Removing duplicate include file.
• src/hg/hgTables/joining.c
  • lines changed 22, context: html, text, full: html, text
    e47b56dbd11cb3936098df9694704fc8ea086a67 Wed Dec 21 15:11:55 2016 -0800
    hgTables was missing support for "comma" or "separator" field in non-primary field lines of all.joiner. refs #18586
  • lines changed 4, context: html, text, full: html, text
    799b4fefa8e3e5e1453ff8d79e7d1f23f3812546 Thu Dec 22 13:12:00 2016 -0800
    Piggyback on my last commit: get the real wordCount from chopString because the last separator might not have anything after it (null idWord -> SEGV). Trim spaces on the way into idHash as well as on the way out. refs #18586
• src/hg/hgVai/hgVai.c
  • lines changed 1, context: html, text, full: html, text
    07f19e67fafd6351ff6408c07c4e6b546f3cbb16 Mon Dec 19 11:03:05 2016 -0800
    Make hgVai's back-end default for include_intergenic the same as the UI default. refs #12216 note-23
• src/hg/htdocs/FAQ/FAQtracks.html
  • lines changed 12, context: html, text, full: html, text
    75376b4af0c0654f845369ee3ca3673ed8c5cf11 Wed Dec 21 13:23:06 2016 -0800
    Adding coord system blog to FAQ, refs #18527
• src/hg/htdocs/admin/maintenance.html
  • lines changed 68, context: html, text, full: html, text
    c7c72c8dabe4a0b0b6a6eb26bac1f9d876642d20 Wed Dec 21 14:52:31 2016 -0800
    Adding an under-maintenance page to put up in case of server problems, refs #9608
• src/hg/htdocs/goldenPath/help/bigMaf.html
  • lines changed 5, context: html, text, full: html, text
    f9967d6f83a3366bbd70007ca157d592aa5bb0c3 Tue Dec 20 13:58:56 2016 -0800
    fix up bigMaf documentation to use new mafToBigMaf utility
  • lines changed 6, context: html, text, full: html, text
    288c75cfcfc1f8d73bbb1ec41477695ed7f7ad6d Thu Dec 22 11:01:18 2016 -0800
    more tweaks to the bigMaf instructions
• src/hg/htdocs/goldenPath/help/customTrackText.html
  • lines changed 4, context: html, text, full: html, text
    9112d7880085b7950abba8e013b5f0cf0ffbd9ed Wed Dec 21 07:51:11 2016 -0800
    edited customtrackText.html per refs #18566
  • lines changed 6, context: html, text, full: html, text
    06b216d99af8a1c12e7f7152cd396b37183dbe7c Thu Dec 22 09:02:18 2016 -0800
    Small change in Custom Track User Guide about Gateway page refs #18580
• src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.v2.html
  • lines changed 4, context: html, text, full: html, text
    be27ca93c66e41f3b67887c3601d53bef22b3c54 Tue Jan 3 09:01:22 2017 -0800
    Promoting trackDb settings html priority colorByStrand autoScale from full to base given input from Ensembl
• src/hg/htdocs/goldenPath/help/wiggle.html
  • lines changed 11, context: html, text, full: html, text
    e734e57e3bb712d5edf742eec10843cdfa7b9d06 Wed Dec 21 11:51:53 2016 -0800
    Updating 1-start coordinate info for wiggle files, refs #17963
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 2, context: html, text, full: html, text
    06754b5a001e99e7921cb646300462559fda072e Mon Dec 19 14:43:29 2016 -0800
    Fixing GTEx url to point to hg38, no RM
• src/hg/js/cdwSummaryJs.js
  • lines changed 138, context: html, text, full: html, text
    aa3a3d7569db389a23850470026ace8ef7dda548 Tue Dec 27 10:34:35 2016 -0800
    Javascript for the cdwSummary pages, refs #16300
  • lines changed 8, context: html, text, full: html, text
    ed89083e1fd2d49f3fc7ef85c06c3077f8cefd5e Wed Dec 28 10:27:16 2016 -0800
    Passed jshint on cirm but failed on hgwdev, may need to update our jsHint code on the cirm machine. refs #16300
• src/hg/js/makefile
  • lines changed 2, context: html, text, full: html, text
    16943bb36521610c3600a4c1277d3fcadb77185b Tue Dec 27 10:35:36 2016 -0800
    Javascript for the cdwSummary pages adding to makefile, refs #16300
• src/hg/lib/hui.c
  • lines changed 2, context: html, text, full: html, text
    64b59a1531511c86e7fc369bc9f76ceaf14f8dd5 Fri Dec 23 14:03:07 2016 -0800
    fix a problem with hgc and tagStorm db's
• src/hg/lib/joiner.c
  • lines changed 28, context: html, text, full: html, text
    e25ec5b271d3ba3073de307e3d80bc2503ad7207 Thu Dec 22 11:49:14 2016 -0800
    tableExists was always opening a sql connection, but only rarely do we get a table with a sql wildcard that needs a sql query. So open a sql conn only when necessary -- speeds up all.joiner searches with many matches to tables in different databases like knownGene.
• src/hg/liftUp/liftUp.c
  • lines changed 13, context: html, text, full: html, text
    ef8001c7de45f170e6b17352f0e4ee89876edb83 Thu Dec 22 16:24:52 2016 -0800
    Adding bed3 option to liftUp, so that if the 6th field just happens coincidentally to be a -, it's not converted to a + by an overzealous reverse strand lift refs #18589
• src/hg/liftUp/test/expected/bed3Strand.bed
  • lines changed 2, context: html, text, full: html, text
    ef8001c7de45f170e6b17352f0e4ee89876edb83 Thu Dec 22 16:24:52 2016 -0800
    Adding bed3 option to liftUp, so that if the 6th field just happens coincidentally to be a -, it's not converted to a + by an overzealous reverse strand lift refs #18589
• src/hg/liftUp/test/input/contigRevStrand.lft
  • lines changed 1, context: html, text, full: html, text
    ef8001c7de45f170e6b17352f0e4ee89876edb83 Thu Dec 22 16:24:52 2016 -0800
    Adding bed3 option to liftUp, so that if the 6th field just happens coincidentally to be a -, it's not converted to a + by an overzealous reverse strand lift refs #18589
• src/hg/liftUp/test/makefile
  • lines changed 6, context: html, text, full: html, text
    ef8001c7de45f170e6b17352f0e4ee89876edb83 Thu Dec 22 16:24:52 2016 -0800
    Adding bed3 option to liftUp, so that if the 6th field just happens coincidentally to be a -, it's not converted to a + by an overzealous reverse strand lift refs #18589
• src/hg/makeDb/doc/mouseStrains/GCA_001624185.1_129S1_SvImJ_v1/GCA_001624185.1_129S1_SvImJ_v1.bigMaf.trackDb.txt
  • lines changed 9, context: html, text, full: html, text
    9b96e8d38040d3ace1786dac5c1a7456b88b50c2 Thu Dec 22 15:23:32 2016 -0800
    adding bigMaf.trackDb tracks refs #13553
• src/hg/makeDb/doc/mouseStrains/GCA_001624185.1_129S1_SvImJ_v1/GCA_001624185.1_129S1_SvImJ_v1.trackDb.txt
  • lines changed 2, context: html, text, full: html, text
    6d27c1a32d232379913cfd9ae1b72a93e2dbb40d Thu Dec 22 15:30:20 2016 -0800
    including the bigMaf.trackDb definitions refs #13553
• src/hg/makeDb/doc/mouseStrains/GCA_001624215.1_A_J_v1/GCA_001624215.1_A_J_v1.bigMaf.trackDb.txt
  • lines changed 9, context: html, text, full: html, text
    9b96e8d38040d3ace1786dac5c1a7456b88b50c2 Thu Dec 22 15:23:32 2016 -0800
    adding bigMaf.trackDb tracks refs #13553
• src/hg/makeDb/doc/mouseStrains/GCA_001624215.1_A_J_v1/GCA_001624215.1_A_J_v1.trackDb.txt
  • lines changed 2, context: html, text, full: html, text
    6d27c1a32d232379913cfd9ae1b72a93e2dbb40d Thu Dec 22 15:30:20 2016 -0800
    including the bigMaf.trackDb definitions refs #13553
• src/hg/makeDb/doc/mouseStrains/GCA_001624295.1_AKR_J_v1/GCA_001624295.1_AKR_J_v1.bigMaf.trackDb.txt
  • lines changed 9, context: html, text, full: html, text
    9b96e8d38040d3ace1786dac5c1a7456b88b50c2 Thu Dec 22 15:23:32 2016 -0800
    adding bigMaf.trackDb tracks refs #13553
• src/hg/makeDb/doc/mouseStrains/GCA_001624295.1_AKR_J_v1/GCA_001624295.1_AKR_J_v1.trackDb.txt
  • lines changed 2, context: html, text, full: html, text
    6d27c1a32d232379913cfd9ae1b72a93e2dbb40d Thu Dec 22 15:30:20 2016 -0800
    including the bigMaf.trackDb definitions refs #13553
• src/hg/makeDb/doc/mouseStrains/GCA_001624445.1_CAST_EiJ_v1/GCA_001624445.1_CAST_EiJ_v1.bigMaf.trackDb.txt
  • lines changed 9, context: html, text, full: html, text
    9b96e8d38040d3ace1786dac5c1a7456b88b50c2 Thu Dec 22 15:23:32 2016 -0800
    adding bigMaf.trackDb tracks refs #13553
• src/hg/makeDb/doc/mouseStrains/GCA_001624445.1_CAST_EiJ_v1/GCA_001624445.1_CAST_EiJ_v1.trackDb.txt
  • lines changed 2, context: html, text, full: html, text
    6d27c1a32d232379913cfd9ae1b72a93e2dbb40d Thu Dec 22 15:30:20 2016 -0800
    including the bigMaf.trackDb definitions refs #13553
• src/hg/makeDb/doc/mouseStrains/GCA_001624475.1_CBA_J_v1/GCA_001624475.1_CBA_J_v1.bigMaf.trackDb.txt
  • lines changed 9, context: html, text, full: html, text
    9b96e8d38040d3ace1786dac5c1a7456b88b50c2 Thu Dec 22 15:23:32 2016 -0800
    adding bigMaf.trackDb tracks refs #13553
• src/hg/makeDb/doc/mouseStrains/GCA_001624475.1_CBA_J_v1/GCA_001624475.1_CBA_J_v1.trackDb.txt
  • lines changed 2, context: html, text, full: html, text
    6d27c1a32d232379913cfd9ae1b72a93e2dbb40d Thu Dec 22 15:30:20 2016 -0800
    including the bigMaf.trackDb definitions refs #13553
• src/hg/makeDb/doc/mouseStrains/GCA_001624505.1_DBA_2J_v1/GCA_001624505.1_DBA_2J_v1.bigMaf.trackDb.txt
  • lines changed 9, context: html, text, full: html, text
    9b96e8d38040d3ace1786dac5c1a7456b88b50c2 Thu Dec 22 15:23:32 2016 -0800
    adding bigMaf.trackDb tracks refs #13553
• src/hg/makeDb/doc/mouseStrains/GCA_001624505.1_DBA_2J_v1/GCA_001624505.1_DBA_2J_v1.trackDb.txt
  • lines changed 2, context: html, text, full: html, text
    6d27c1a32d232379913cfd9ae1b72a93e2dbb40d Thu Dec 22 15:30:20 2016 -0800
    including the bigMaf.trackDb definitions refs #13553
• src/hg/makeDb/doc/mouseStrains/GCA_001624535.1_FVB_NJ_v1/GCA_001624535.1_FVB_NJ_v1.bigMaf.trackDb.txt
  • lines changed 9, context: html, text, full: html, text
    9b96e8d38040d3ace1786dac5c1a7456b88b50c2 Thu Dec 22 15:23:32 2016 -0800
    adding bigMaf.trackDb tracks refs #13553
• src/hg/makeDb/doc/mouseStrains/GCA_001624535.1_FVB_NJ_v1/GCA_001624535.1_FVB_NJ_v1.trackDb.txt
  • lines changed 2, context: html, text, full: html, text
    6d27c1a32d232379913cfd9ae1b72a93e2dbb40d Thu Dec 22 15:30:20 2016 -0800
    including the bigMaf.trackDb definitions refs #13553
• src/hg/makeDb/doc/mouseStrains/GCA_001624675.1_NOD_ShiLtJ_v1/GCA_001624675.1_NOD_ShiLtJ_v1.bigMaf.trackDb.txt
  • lines changed 9, context: html, text, full: html, text
    9b96e8d38040d3ace1786dac5c1a7456b88b50c2 Thu Dec 22 15:23:32 2016 -0800
    adding bigMaf.trackDb tracks refs #13553
• src/hg/makeDb/doc/mouseStrains/GCA_001624675.1_NOD_ShiLtJ_v1/GCA_001624675.1_NOD_ShiLtJ_v1.trackDb.txt
  • lines changed 2, context: html, text, full: html, text
    6d27c1a32d232379913cfd9ae1b72a93e2dbb40d Thu Dec 22 15:30:20 2016 -0800
    including the bigMaf.trackDb definitions refs #13553
• src/hg/makeDb/doc/mouseStrains/GCA_001624745.1_NZO_HlLtJ_v1/GCA_001624745.1_NZO_HlLtJ_v1.bigMaf.trackDb.txt
  • lines changed 9, context: html, text, full: html, text
    9b96e8d38040d3ace1786dac5c1a7456b88b50c2 Thu Dec 22 15:23:32 2016 -0800
    adding bigMaf.trackDb tracks refs #13553
• src/hg/makeDb/doc/mouseStrains/GCA_001624745.1_NZO_HlLtJ_v1/GCA_001624745.1_NZO_HlLtJ_v1.trackDb.txt
  • lines changed 2, context: html, text, full: html, text
    6d27c1a32d232379913cfd9ae1b72a93e2dbb40d Thu Dec 22 15:30:20 2016 -0800
    including the bigMaf.trackDb definitions refs #13553
• src/hg/makeDb/doc/mouseStrains/GCA_001624775.1_PWK_PhJ_v1/GCA_001624775.1_PWK_PhJ_v1.bigMaf.trackDb.txt
  • lines changed 9, context: html, text, full: html, text
    9b96e8d38040d3ace1786dac5c1a7456b88b50c2 Thu Dec 22 15:23:32 2016 -0800
    adding bigMaf.trackDb tracks refs #13553
• src/hg/makeDb/doc/mouseStrains/GCA_001624775.1_PWK_PhJ_v1/GCA_001624775.1_PWK_PhJ_v1.trackDb.txt
  • lines changed 2, context: html, text, full: html, text
    6d27c1a32d232379913cfd9ae1b72a93e2dbb40d Thu Dec 22 15:30:20 2016 -0800
    including the bigMaf.trackDb definitions refs #13553
• src/hg/makeDb/doc/mouseStrains/GCA_001624835.1_WSB_EiJ_v1/GCA_001624835.1_WSB_EiJ_v1.bigMaf.trackDb.txt
  • lines changed 9, context: html, text, full: html, text
    9b96e8d38040d3ace1786dac5c1a7456b88b50c2 Thu Dec 22 15:23:32 2016 -0800
    adding bigMaf.trackDb tracks refs #13553
• src/hg/makeDb/doc/mouseStrains/GCA_001624835.1_WSB_EiJ_v1/GCA_001624835.1_WSB_EiJ_v1.trackDb.txt
  • lines changed 2, context: html, text, full: html, text
    6d27c1a32d232379913cfd9ae1b72a93e2dbb40d Thu Dec 22 15:30:20 2016 -0800
    including the bigMaf.trackDb definitions refs #13553
• src/hg/makeDb/doc/mouseStrains/GCA_001624865.1_SPRET_EiJ_v1/GCA_001624865.1_SPRET_EiJ_v1.bigMaf.trackDb.txt
  • lines changed 9, context: html, text, full: html, text
    9b96e8d38040d3ace1786dac5c1a7456b88b50c2 Thu Dec 22 15:23:32 2016 -0800
    adding bigMaf.trackDb tracks refs #13553
• src/hg/makeDb/doc/mouseStrains/GCA_001624865.1_SPRET_EiJ_v1/GCA_001624865.1_SPRET_EiJ_v1.trackDb.txt
  • lines changed 2, context: html, text, full: html, text
    6d27c1a32d232379913cfd9ae1b72a93e2dbb40d Thu Dec 22 15:30:20 2016 -0800
    including the bigMaf.trackDb definitions refs #13553
• src/hg/makeDb/doc/mouseStrains/GCA_001632525.1_BALB_cJ_v1/GCA_001632525.1_BALB_cJ_v1.bigMaf.trackDb.txt
  • lines changed 9, context: html, text, full: html, text
    9b96e8d38040d3ace1786dac5c1a7456b88b50c2 Thu Dec 22 15:23:32 2016 -0800
    adding bigMaf.trackDb tracks refs #13553
• src/hg/makeDb/doc/mouseStrains/GCA_001632525.1_BALB_cJ_v1/GCA_001632525.1_BALB_cJ_v1.trackDb.txt
  • lines changed 2, context: html, text, full: html, text
    6d27c1a32d232379913cfd9ae1b72a93e2dbb40d Thu Dec 22 15:30:20 2016 -0800
    including the bigMaf.trackDb definitions refs #13553
• src/hg/makeDb/doc/mouseStrains/GCA_001632555.1_C57BL_6NJ_v1/GCA_001632555.1_C57BL_6NJ_v1.bigMaf.trackDb.txt
  • lines changed 9, context: html, text, full: html, text
    9b96e8d38040d3ace1786dac5c1a7456b88b50c2 Thu Dec 22 15:23:32 2016 -0800
    adding bigMaf.trackDb tracks refs #13553
• src/hg/makeDb/doc/mouseStrains/GCA_001632555.1_C57BL_6NJ_v1/GCA_001632555.1_C57BL_6NJ_v1.trackDb.txt
  • lines changed 2, context: html, text, full: html, text
    6d27c1a32d232379913cfd9ae1b72a93e2dbb40d Thu Dec 22 15:30:20 2016 -0800
    including the bigMaf.trackDb definitions refs #13553
• src/hg/makeDb/doc/mouseStrains/GCA_001632575.1_C3H_HeJ_v1/GCA_001632575.1_C3H_HeJ_v1.bigMaf.trackDb.txt
  • lines changed 9, context: html, text, full: html, text
    9b96e8d38040d3ace1786dac5c1a7456b88b50c2 Thu Dec 22 15:23:32 2016 -0800
    adding bigMaf.trackDb tracks refs #13553
• src/hg/makeDb/doc/mouseStrains/GCA_001632575.1_C3H_HeJ_v1/GCA_001632575.1_C3H_HeJ_v1.trackDb.txt
  • lines changed 2, context: html, text, full: html, text
    6d27c1a32d232379913cfd9ae1b72a93e2dbb40d Thu Dec 22 15:30:20 2016 -0800
    including the bigMaf.trackDb definitions refs #13553
• src/hg/makeDb/doc/mouseStrains/GCA_001632615.1_LP_J_v1/GCA_001632615.1_LP_J_v1.bigMaf.trackDb.txt
  • lines changed 9, context: html, text, full: html, text
    9b96e8d38040d3ace1786dac5c1a7456b88b50c2 Thu Dec 22 15:23:32 2016 -0800
    adding bigMaf.trackDb tracks refs #13553
• src/hg/makeDb/doc/mouseStrains/GCA_001632615.1_LP_J_v1/GCA_001632615.1_LP_J_v1.trackDb.txt
  • lines changed 2, context: html, text, full: html, text
    6d27c1a32d232379913cfd9ae1b72a93e2dbb40d Thu Dec 22 15:30:20 2016 -0800
    including the bigMaf.trackDb definitions refs #13553
• src/hg/makeDb/doc/mouseStrains/makefile
  • lines changed 2, context: html, text, full: html, text
    f65d252a9b81c35f152134d6200a3f111c83dccf Thu Dec 22 15:25:20 2016 -0800
    adding in the bigMaf.trackDb installs refs #13553
• src/hg/makeDb/doc/mouseStrains/mm10/mm10.bigMaf.trackDb.txt
  • lines changed 9, context: html, text, full: html, text
    9b96e8d38040d3ace1786dac5c1a7456b88b50c2 Thu Dec 22 15:23:32 2016 -0800
    adding bigMaf.trackDb tracks refs #13553
• src/hg/makeDb/doc/mouseStrains/mm10/mm10.trackDb.txt
  • lines changed 1, context: html, text, full: html, text
    6d27c1a32d232379913cfd9ae1b72a93e2dbb40d Thu Dec 22 15:30:20 2016 -0800
    including the bigMaf.trackDb definitions refs #13553
• src/hg/makeDb/doc/mouseStrains/rn6/rn6.bigMaf.trackDb.txt
  • lines changed 9, context: html, text, full: html, text
    9b96e8d38040d3ace1786dac5c1a7456b88b50c2 Thu Dec 22 15:23:32 2016 -0800
    adding bigMaf.trackDb tracks refs #13553
• src/hg/makeDb/doc/mouseStrains/rn6/rn6.trackDb.txt
  • lines changed 1, context: html, text, full: html, text
    6d27c1a32d232379913cfd9ae1b72a93e2dbb40d Thu Dec 22 15:30:20 2016 -0800
    including the bigMaf.trackDb definitions refs #13553
• src/hg/makeDb/schema/all.joiner
  • lines changed 2, context: html, text, full: html, text
    ad1cf0cc166a6d5b0a3e81a580e5144f37a4a016 Thu Dec 22 12:19:07 2016 -0800
    Move knownToRefSeq way up in the field list for knownGeneId -- when connecting knownGene to omimId tables, keggPathway was taking precedence but has low coverage of knownGene, so most results were missed. refs #18586
• src/hg/makeDb/trackDb/crispr.html
  • lines changed 2, context: html, text, full: html, text
    2070590ef7e8b7ecb3603fc93fdf1caf2f6c287b Thu Dec 15 14:13:17 2016 -0800
    cosmetics. crispr tracks: added a space btw elements in 200bp, italicized species name and changed spelling of grey to american version, gray
• src/hg/makeDb/trackDb/human/hg19/crispr.html
  • lines changed 2, context: html, text, full: html, text
    2070590ef7e8b7ecb3603fc93fdf1caf2f6c287b Thu Dec 15 14:13:17 2016 -0800
    cosmetics. crispr tracks: added a space btw elements in 200bp, italicized species name and changed spelling of grey to american version, gray
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSunyAlbanyTiling.html
  • lines changed 1, context: html, text, full: html, text
    885ff69b88b7ef3dd8f673e26bb8d6185b92d3b3 Wed Dec 21 16:00:18 2016 -0800
    Fixing bad url for hg19 wgEncodeSunyAlbanyTiling
  • lines changed 1, context: html, text, full: html, text
    d5d91c8eae971b41443da13eda10ad167bf6a217 Wed Dec 21 16:37:07 2016 -0800
    Fixing 2nd bad url wgEncodeSunyAlbanyTiling, refs #18587
• src/hg/makeDb/trackDb/human/hg38/crispr.html
  • lines changed 2, context: html, text, full: html, text
    2070590ef7e8b7ecb3603fc93fdf1caf2f6c287b Thu Dec 15 14:13:17 2016 -0800
    cosmetics. crispr tracks: added a space btw elements in 200bp, italicized species name and changed spelling of grey to american version, gray
• src/hg/makeDb/trackDb/human/hg38/hg38Patch9.html
  • lines changed 93, context: html, text, full: html, text
    645462b2959eda28a5c5c817849612e60089dc1b Wed Dec 21 14:00:05 2016 -0800
    added color key to track description page hg38Patch9.html per refs #18274
• src/hg/makeDb/trackDb/spAnnot.html
  • lines changed 4, context: html, text, full: html, text
    b92e607fec4a99cdc76cce9d8299f270a586f5e6 Tue Dec 20 07:01:58 2016 -0800
    changing uniprot annotations track doc after complaint from UniProt, no redmine
• src/hg/makeDb/trackDb/trackDb.ra
  • lines changed 0, context: html, text, full: html, text
    2070590ef7e8b7ecb3603fc93fdf1caf2f6c287b Thu Dec 15 14:13:17 2016 -0800
    cosmetics. crispr tracks: added a space btw elements in 200bp, italicized species name and changed spelling of grey to american version, gray
• src/hg/utils/bigMafToMaf/bigMafToMaf.c
  • lines changed 64, context: html, text, full: html, text
    90f26ce1f4bd4f69b53d11569d4c4efc0c3386b7 Tue Dec 20 12:41:19 2016 -0800
    make some utilities to turn mafs into bigMafs
  • lines changed 4, context: html, text, full: html, text
    8b5faf8487826c2d273b3f22b500a3ef0c94d8bf Tue Dec 20 13:39:36 2016 -0800
    a few more tweaks to get bigMafToMaf into the utils
• src/hg/utils/bigMafToMaf/makefile
  • lines changed 3, context: html, text, full: html, text
    90f26ce1f4bd4f69b53d11569d4c4efc0c3386b7 Tue Dec 20 12:41:19 2016 -0800
    make some utilities to turn mafs into bigMafs
• src/hg/utils/hubCheck/tests/makefile
  • lines changed 1, context: html, text, full: html, text
    c4085691bbf14edaf06118a0bdb6f1addda9f72a Tue Dec 20 13:40:18 2016 -0800
    keep the hubCheck test silent
• src/hg/utils/mafToBigMaf/mafToBigMaf.c
  • lines changed 82, context: html, text, full: html, text
    90f26ce1f4bd4f69b53d11569d4c4efc0c3386b7 Tue Dec 20 12:41:19 2016 -0800
    make some utilities to turn mafs into bigMafs
• src/hg/utils/mafToBigMaf/makefile
  • lines changed 3, context: html, text, full: html, text
    90f26ce1f4bd4f69b53d11569d4c4efc0c3386b7 Tue Dec 20 12:41:19 2016 -0800
    make some utilities to turn mafs into bigMafs
• src/hg/utils/mafToBigMaf/tests/input/chrom.sizes
  • lines changed 455, context: html, text, full: html, text
    90f26ce1f4bd4f69b53d11569d4c4efc0c3386b7 Tue Dec 20 12:41:19 2016 -0800
    make some utilities to turn mafs into bigMafs
• src/hg/utils/mafToBigMaf/tests/input/test1.maf
  • lines changed 2351, context: html, text, full: html, text
    90f26ce1f4bd4f69b53d11569d4c4efc0c3386b7 Tue Dec 20 12:41:19 2016 -0800
    make some utilities to turn mafs into bigMafs
• src/hg/utils/mafToBigMaf/tests/makefile
  • lines changed 23, context: html, text, full: html, text
    90f26ce1f4bd4f69b53d11569d4c4efc0c3386b7 Tue Dec 20 12:41:19 2016 -0800
    make some utilities to turn mafs into bigMafs
• src/hg/utils/makefile
  • lines changed 1, context: html, text, full: html, text
    90f26ce1f4bd4f69b53d11569d4c4efc0c3386b7 Tue Dec 20 12:41:19 2016 -0800
    make some utilities to turn mafs into bigMafs
  • lines changed 1, context: html, text, full: html, text
    8b5faf8487826c2d273b3f22b500a3ef0c94d8bf Tue Dec 20 13:39:36 2016 -0800
    a few more tweaks to get bigMafToMaf into the utils
• src/hg/utils/otto/clinvar/clinVarToBed
  • lines changed 1, context: html, text, full: html, text
    bfc69bf9af7bac40300e370781f201426ff0aa5d Thu Dec 22 11:45:56 2016 -0800
    Another change of the clinvar files require another change to the parser. No redmine.
• src/hg/utils/vai.pl
  • lines changed 22, context: html, text, full: html, text
    a7c9586b9cdeefd418f099915bf06c51981297f8 Tue Dec 20 11:53:25 2016 -0800
    Added command line options for filtering output by functional category. refs #12216 note-25
• src/inc/bamFile.h
  • lines changed 14, context: html, text, full: html, text
    29356d0b9520b11bb46d22f5c70b8b1a275b5116 Tue Dec 27 12:06:35 2016 -0800
    Removing bamChromInfo structure and the routines to free it. The routine that made it got deleted a while back for some reason, so I'm just tidying up.
• src/inc/maf.h
  • lines changed 3, context: html, text, full: html, text
    90f26ce1f4bd4f69b53d11569d4c4efc0c3386b7 Tue Dec 20 12:41:19 2016 -0800
    make some utilities to turn mafs into bigMafs
• src/lib/bamFile.c
  • lines changed 26, context: html, text, full: html, text
    29356d0b9520b11bb46d22f5c70b8b1a275b5116 Tue Dec 27 12:06:35 2016 -0800
    Removing bamChromInfo structure and the routines to free it. The routine that made it got deleted a while back for some reason, so I'm just tidying up.
• src/lib/maf.c
  • lines changed 17, context: html, text, full: html, text
    90f26ce1f4bd4f69b53d11569d4c4efc0c3386b7 Tue Dec 20 12:41:19 2016 -0800
    make some utilities to turn mafs into bigMafs
• src/product/installer/browserSetup.sh
  • lines changed 3, context: html, text, full: html, text
    8f0ef5ce242c9f91132c9453d192dc55ae5a2f4c Wed Dec 21 09:31:14 2016 -0800
    Updating browserSetup.sh to warn about .hg.conf file for using command line utils. Adding minimal hg.conf for users to copy, refs #14399
• src/product/minimal.hg.conf
  • lines changed 43, context: html, text, full: html, text
    8f0ef5ce242c9f91132c9453d192dc55ae5a2f4c Wed Dec 21 09:31:14 2016 -0800
    Updating browserSetup.sh to warn about .hg.conf file for using command line utils. Adding minimal hg.conf for users to copy, refs #14399
  • lines changed 2, context: html, text, full: html, text
    b81eb09770cbaa8190153d93edd5fb8ff77d18ec Wed Dec 21 10:09:43 2016 -0800
    Minor changes to minimal.hg.conf after feedback from Max.
• src/tagStorm/tagStormDeleteTags/tagStormDeleteTags.c
  • lines changed 1, context: html, text, full: html, text
    5333b9029b14fbbfa51362c5092de30b693ef7e3 Thu Dec 15 08:04:35 2016 -0800
    Minor improvement to usage message.
• src/tagStorm/tagStormQuery/tagStormQuery.c
  • lines changed 19, context: html, text, full: html, text
    8d9add6559b88bebf9ce119e14b970ab22a5df1e Tue Dec 20 15:11:21 2016 -0800
    Improving usage message.
• src/utils/qa/getPubHubContact.sh
  • lines changed 56, context: html, text, full: html, text
    51b0e05f3807e351efb2ff9a4870946175121722 Wed Dec 21 10:00:55 2016 -0800
    Adding usage message and ability to specify output directory per Jonathan's suggestion. Also setting qaConfig and other standard stuff at the top of the script. refs #18316
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    b46d0a109ce12a0d0e98567091bd02629a880caf Tue Jan 3 10:05:45 2017 -0800
    v343 preview2 refs #18555

• lines changed: 4275
• files changed: 103