All File Changes

v329_preview to v329_preview2 (2016-02-15 to 2016-02-22) v329

• src/browserbox/root/updateBrowser.sh
  • lines changed 14, context: html, text, full: html, text
    move logfile creation via tee a few lines down in gbib's
    updateBrowser.sh script. This is necessary because tee's exec will
    create a new subshell, which looks like an already running updateBrowser
    script and will trigger the main part to stop. refs #16838
    
• src/hg/cirm/cdw/wrangle/condenseMatrix/condenseMatrix
  • lines changed 4, context: html, text, full: html, text
    Adding in a different transcript to gene conversion, refs #16244
    
• src/hg/hgTracks/bigWarn.c
  • lines changed 15, context: html, text, full: html, text
    Fixes #16818. Gets better cross-all-windows error handling working for bigDataUrl/network tracks.
    
    Squashed commit of the following:
    
    commit cdf9db633c9018538aabf9c8346eabee63b5a3cf
    Author: Galt Barber <galt@soe.ucsc.edu>
    Date: Wed Feb 17 12:55:47 2016 -0800
    
    Fixed width in bigWarn.c and background in multiWig.c
    
    commit 3620dcd0912660fabbd993df4af119cc03676545
    Author: Galt Barber <galt@soe.ucsc.edu>
    Date: Tue Feb 16 11:53:32 2016 -0800
    
    Initial checking for multi-region all-windows warn. This is an attempt to handle timeout high-level errors better, when a track is taking too long to finish loading; and to handle the network errors across all of the windows together, i.e. using the entire screen width to display the errors, only diplaying the first error, and only drawing for the first window.
    
• src/hg/hgTracks/hgTracks.c
  • lines changed 2, context: html, text, full: html, text
    Fixes #16839. Assembly hubs not supported yet.
    
  • lines changed 42, context: html, text, full: html, text
    Fixes #16818. Gets better cross-all-windows error handling working for bigDataUrl/network tracks.
    
    Squashed commit of the following:
    
    commit cdf9db633c9018538aabf9c8346eabee63b5a3cf
    Author: Galt Barber <galt@soe.ucsc.edu>
    Date: Wed Feb 17 12:55:47 2016 -0800
    
    Fixed width in bigWarn.c and background in multiWig.c
    
    commit 3620dcd0912660fabbd993df4af119cc03676545
    Author: Galt Barber <galt@soe.ucsc.edu>
    Date: Tue Feb 16 11:53:32 2016 -0800
    
    Initial checking for multi-region all-windows warn. This is an attempt to handle timeout high-level errors better, when a track is taking too long to finish loading; and to handle the network errors across all of the windows together, i.e. using the entire screen width to display the errors, only diplaying the first error, and only drawing for the first window.
    
• src/hg/hgTracks/multiWig.c
  • lines changed 9, context: html, text, full: html, text
    Fixes #16818. Gets better cross-all-windows error handling working for bigDataUrl/network tracks.
    
    Squashed commit of the following:
    
    commit cdf9db633c9018538aabf9c8346eabee63b5a3cf
    Author: Galt Barber <galt@soe.ucsc.edu>
    Date: Wed Feb 17 12:55:47 2016 -0800
    
    Fixed width in bigWarn.c and background in multiWig.c
    
    commit 3620dcd0912660fabbd993df4af119cc03676545
    Author: Galt Barber <galt@soe.ucsc.edu>
    Date: Tue Feb 16 11:53:32 2016 -0800
    
    Initial checking for multi-region all-windows warn. This is an attempt to handle timeout high-level errors better, when a track is taking too long to finish loading; and to handle the network errors across all of the windows together, i.e. using the entire screen width to display the errors, only diplaying the first error, and only drawing for the first window.
    
• src/hg/hgTracks/simpleTracks.c
  • lines changed 15, context: html, text, full: html, text
    Filtering in OMIM tracks wasn't properly interacting with cart variables, refs #13349, #8377
    
• src/hg/hgc/hgc.c
  • lines changed 1, context: html, text, full: html, text
    Updating SNP links on OMIM tracks for hg19, hg38, refs #10501
    
  • lines changed 65, context: html, text, full: html, text
    fix up the links on the ncbiRefSeq hgc page
    
• src/hg/htdocs/FAQ/FAQformat.html
  • lines changed 3, context: html, text, full: html, text
    Minor fix FAQformat.html & credits.html via Code Review, refs #16826
    
• src/hg/htdocs/goldenPath/credits.html
  • lines changed 1, context: html, text, full: html, text
    Fixing link as per code review, refs #16827
    
  • lines changed 1, context: html, text, full: html, text
    Minor fix FAQformat.html & credits.html via Code Review, refs #16826
    
• src/hg/htdocs/indexNews.html
  • lines changed 1, context: html, text, full: html, text
    indexNews.html
    
• src/hg/js/d3.dendrograms.js
  • lines changed 257, context: html, text, full: html, text
    Added a bunch of cool test features. refs #16341
    
  • lines changed 264, context: html, text, full: html, text
    Adding some new features, making things pretty and some refactoring for speed, refs #16341
    
• src/hg/lib/hgFind.c
  • lines changed 176, context: html, text, full: html, text
    Simplified cytoBand search and loosened up termRegex to support horse.
    I removed some old functionality: the cytoBand search code used to cache
    the entire table, but it is never repetitively searched -- the code is
    invoked only for a user's search term. Also, keywords like "cen" and
    "qter" were supported but have been excluded by search regexes for years
    and noone has missed them. Now, use a regex to help parse the search
    term into chrom and band name, and look for an exact match in cytoBand.
    
• src/hg/liftOver/liftOver.c
  • lines changed 2, context: html, text, full: html, text
    Allow suppressing status messages from liftOver (with verbosity=0), but leave current behavior as default
    
• src/hg/makeDb/doc/hg38/hg38.txt
  • lines changed 19, context: html, text, full: html, text
    Added entry for GWIPS-viz Riboseq track; refs #16765
    
• src/hg/makeDb/trackDb/affyAllExonProbes.html
  • lines changed 1, context: html, text, full: html, text
    Fixing bad url for 7 assemblies, no refs
    
• src/hg/makeDb/trackDb/chicken/galGal2/rnaGene.html
  • lines changed 1, context: html, text, full: html, text
    Fixing bad url for 7 assemblies, no refs
    
• src/hg/makeDb/trackDb/drosophila/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    useless setting in ancient refGene override refs #13673
    
• src/hg/makeDb/trackDb/human/affyHuEx1.html
  • lines changed 1, context: html, text, full: html, text
    Fixing bad url for 7 assemblies, no refs
    
• src/hg/makeDb/trackDb/human/hg38/gwipsvizRiboseq.html
  • lines changed 98, context: html, text, full: html, text
    Made description page changes as specified by Audrey Michel; refs #16765
    
• src/hg/makeDb/trackDb/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    add CDS table reference to ncbiRefSeqPsl
    
  • lines changed 1, context: html, text, full: html, text
    Simplified cytoBand search and loosened up termRegex to support horse.
    I removed some old functionality: the cytoBand search code used to cache
    the entire table, but it is never repetitively searched -- the code is
    invoked only for a user's search term. Also, keywords like "cen" and
    "qter" were supported but have been excluded by search regexes for years
    and noone has missed them. Now, use a regex to help parse the search
    term into chrom and band name, and look for an exact match in cytoBand.
    
• src/hg/pslSomeRecords/pslSomeRecords.c
  • lines changed 5, context: html, text, full: html, text
    add "-not" option to pslSomeRecords
    
• src/hg/utils/automation/accRsu.pl
  • lines changed 48, context: html, text, full: html, text
    getting closer to final version refs #13673
    
• src/hg/utils/automation/doNcbiRefSeq.pl
  • lines changed 120, context: html, text, full: html, text
    cleaning up and trying on mm10 refs #13673
    
  • lines changed 53, context: html, text, full: html, text
    getting closer to final version refs #13673
    
• src/hg/utils/automation/gff3ToRefLink.pl
  • lines changed 173, context: html, text, full: html, text
    getting closer to final version refs #13673
    
• src/hg/utils/automation/ucscToINSDC.sh
  • lines changed 3, context: html, text, full: html, text
    fixup to work correctly for rheMac8 refs #16744
    
• src/hg/utils/gff3ToPsl/gff3ToPsl.c
  • lines changed 2, context: html, text, full: html, text
    fix gff3ToPsl to get the strands right
    
• src/hg/utils/gff3ToPsl/tests/expected/grch38ToGrch37Test.psl
  • lines changed 3, context: html, text, full: html, text
    fix gff3ToPsl to get the strands right
    
• src/hg/utils/gff3ToPsl/tests/expected/patch1test.psl
  • lines changed 62, context: html, text, full: html, text
    fix gff3ToPsl to get the strands right
    
• src/hg/utils/otto/omim/buildOmimTracks.csh
  • lines changed 143, context: html, text, full: html, text
    Updates for the OMIM pipeline, refs #8377, #14465, #16796
    
• src/hg/utils/otto/omim/buildOmimTracks.sh
  • lines changed 119, context: html, text, full: html, text
    Updates for the OMIM pipeline, refs #8377, #14465, #16796
    
• src/hg/utils/otto/omim/checkOmim.sh
  • lines changed 4, context: html, text, full: html, text
    Updates for the OMIM pipeline, refs #8377, #14465, #16796
    
• src/hg/utils/otto/omim/doOmimLocation/doOmimLocation.c
  • lines changed 9, context: html, text, full: html, text
    Updates for the OMIM pipeline, refs #8377, #14465, #16796
    
• src/hg/utils/otto/omim/makefile
  • lines changed 1, context: html, text, full: html, text
    Updates for the OMIM pipeline, refs #8377, #14465, #16796
    
• src/hg/utils/otto/omim/omimWrapper.sh
  • lines changed 2, context: html, text, full: html, text
    Updates for the OMIM pipeline, refs #8377, #14465, #16796
    
  • lines changed 2, context: html, text, full: html, text
    Quick fix - restoring the previous mail recipients
    
• src/lib/psl.c
  • lines changed 2, context: html, text, full: html, text
    fix gff3ToPsl to get the strands right
    
• src/utils/qa/updateTimesDb.csh
  • lines changed 106, context: html, text, full: html, text
    Replacing updateTimesDb.csh with a new script, updateTimesDb.sh. New script is written in bash. New script has the same functionality as the old one, but features an improved and more compact output format. refs #16553
    
• src/utils/qa/updateTimesDb.sh
  • lines changed 151, context: html, text, full: html, text
    Replacing updateTimesDb.csh with a new script, updateTimesDb.sh. New script is written in bash. New script has the same functionality as the old one, but features an improved and more compact output format. refs #16553
    
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    v329 preview2 refs #16821
    

• lines changed: 2006
• files changed: 45