All File Changes

v313_preview to v313_preview2 (2015-02-23 to 2015-03-02) v313

• src/hg/cirm/cdw/cdwMakeEnrichments/cdwMakeEnrichments.c
  • lines changed 3, context: html, text, full: html, text
    Doing enrichments on VCF files.
    
• src/hg/cirm/cdw/cdwMakeTrackViz/cdwMakeTrackViz.c
  • lines changed 6, context: html, text, full: html, text
    Doing a better job of prepping vcf files
    
  • lines changed 8, context: html, text, full: html, text
    Adding viz for narrowPeak and broadPeak files.
    
• src/hg/cirm/cdw/cdwMakeValidFile/cdwMakeValidFile.c
  • lines changed 43, context: html, text, full: html, text
    Improving handling of VCF files, delegating most of work to cdwVcfStats. Adding -redo command line option.
    
• src/hg/cirm/cdw/cdwQuery/cdwQuery.c
  • lines changed 6, context: html, text, full: html, text
    Renaming -format option to -out option to be more consistent with other utilities.
    
• src/hg/cirm/cdw/cdwReallyRemoveFiles/cdwReallyRemoveFiles.c
  • lines changed 4, context: html, text, full: html, text
    Adding cdwVcfFile and cdwTrackViz to list of tables things get ripped out of.
    
• src/hg/cirm/cdw/cdwSubmit/cdwSubmit.c
  • lines changed 4, context: html, text, full: html, text
    Ifdefing out some currently unused code.
    
• src/hg/cirm/cdw/cdwWebBrowse/cdwNavBar.html
  • lines changed 1, context: html, text, full: html, text
    Making time out same as genome browser's menu time out.
    
• src/hg/cirm/cdw/cdwWebBrowse/cdwWebBrowse.c
  • lines changed 15, context: html, text, full: html, text
    Expanding size fields can take in browse tracks table. Bumping version.
    
  • lines changed 4, context: html, text, full: html, text
    Changing to case-ignoring sort since that's the usual in a database and we're mixing database and local order.
    
  • lines changed 225, context: html, text, full: html, text
    Refactoring. Moving functions to library modules. Breaking up some larger functions.
    
  • lines changed 69, context: html, text, full: html, text
    More large function break-apart.
    
  • lines changed 28, context: html, text, full: html, text
    MOstly commenting and renaming.
    
  • lines changed 20, context: html, text, full: html, text
    Harmonized order of parameters to two show tables routines and bumped version number.
    
  • lines changed 343, context: html, text, full: html, text
    Adding a ton of useful web table handling stuff from cdwWebBrowse.c to hg/lib/tablesTables.c and it's header.
    
  • lines changed 9, context: html, text, full: html, text
    Added a little more explanitory text. Added enriched_in column.
    
  • lines changed 180, context: html, text, full: html, text
    Adding context parameter to wraps. Minor polish here and there.
    
• src/hg/cirm/cdw/inc/cdw.h
  • lines changed 90, context: html, text, full: html, text
    Adding cdwVcfFile table.
    
• src/hg/cirm/cdw/inc/cdwLib.h
  • lines changed 8, context: html, text, full: html, text
    Integrating VCF file statistics into system.
    
• src/hg/cirm/cdw/inc/cdwVcfFileFromRa.h
  • lines changed 18, context: html, text, full: html, text
    Adding cdwVcfFileFromRa auto-generated parser to help process output of cdwVcfStats.
    
• src/hg/cirm/cdw/lib/cdw.as
  • lines changed 30, context: html, text, full: html, text
    Adding cdwVcfFile table.
    
• src/hg/cirm/cdw/lib/cdw.c
  • lines changed 258, context: html, text, full: html, text
    Adding cdwVcfFile table.
    
• src/hg/cirm/cdw/lib/cdw.sql
  • lines changed 32, context: html, text, full: html, text
    Adding cdwVcfFile table.
    
• src/hg/cirm/cdw/lib/cdwLib.c
  • lines changed 51, context: html, text, full: html, text
    Integrating VCF file statistics into system.
    
• src/hg/cirm/cdw/lib/cdwValid.c
  • lines changed 1, context: html, text, full: html, text
    Allowing chrom fields in metadata.
    
• src/hg/cirm/cdw/lib/cdwVcfFileFromRa.c
  • lines changed 261, context: html, text, full: html, text
    Adding cdwVcfFileFromRa auto-generated parser to help process output of cdwVcfStats.
    
• src/hg/cirm/cdw/lib/makefile
  • lines changed 1, context: html, text, full: html, text
    Adding cdwVcfFileFromRa auto-generated parser to help process output of cdwVcfStats.
    
• src/hg/cirm/cdw/utils/cdwVcfStats/cdwVcfStats.c
  • lines changed 245, context: html, text, full: html, text
    Utility to gather stats on vcf files seems to work.
    
  • lines changed 6, context: html, text, full: html, text
    Rmoving snpPassCount
    
  • lines changed 27, context: html, text, full: html, text
    Removing stray '=' in ra output. Counting depth for record rather than genotype.
    
• src/hg/cirm/cdw/utils/cdwVcfStats/makefile
  • lines changed 4, context: html, text, full: html, text
    Utility to gather stats on vcf files seems to work.
    
• src/hg/cirm/cdw/wrangle/cdwWrangleIsaacInput/cdwWrangleIsaacInput.c
  • lines changed 93, context: html, text, full: html, text
    Wrangle tool to help create inputs.txt for baldwin lab submission.
    
• src/hg/cirm/cdw/wrangle/cdwWrangleIsaacInput/makefile
  • lines changed 4, context: html, text, full: html, text
    Wrangle tool to help create inputs.txt for baldwin lab submission.
    
• src/hg/htdocs/goldenPath/help/hubQuickStartAssembly.html
  • lines changed 4, context: html, text, full: html, text
    Adding note in blat assembly hub page about -mask gfServer effect lower-case seq. MLQ refs #14867
    
• src/hg/htdocs/goldenPath/help/twoBit.html
  • lines changed 5, context: html, text, full: html, text
    Adding note in twoBit.html about lower-case sequence refs #14867
    
• src/hg/htdocs/goldenPath/pubs.html
  • lines changed 26, context: html, text, full: html, text
    Added 2 pubs that Kate co-authored, updated PMID for existing pubs entry.
    
• src/hg/htdocs/indexNews.html
  • lines changed 1, context: html, text, full: html, text
    Fixing typo per code review. refs #14890
    
• src/hg/inc/grp.h
  • lines changed 3, context: html, text, full: html, text
    fix duplicated lines in group menu bug #14878
    
• src/hg/inc/jksql.h
  • lines changed 9, context: html, text, full: html, text
    Added functions to get all fields associated with a sqlResult as a slName list or as an array of char *'s.
    
• src/hg/inc/tablesTables.h
  • lines changed 12, context: html, text, full: html, text
    A new module for tables on the web mostly.
    
  • lines changed 37, context: html, text, full: html, text
    Adding a ton of useful web table handling stuff from cdwWebBrowse.c to hg/lib/tablesTables.c and it's header.
    
  • lines changed 10, context: html, text, full: html, text
    Adding context parameter to wraps. Minor polish here and there.
    
• src/hg/lib/cartTrackDb.c
  • lines changed 5, context: html, text, full: html, text
    fix duplicated lines in group menu bug #14878
    
• src/hg/lib/grp.c
  • lines changed 12, context: html, text, full: html, text
    fix duplicated lines in group menu bug #14878
    
• src/hg/lib/jksql.c
  • lines changed 26, context: html, text, full: html, text
    Added functions to get all fields associated with a sqlResult as a slName list or as an array of char *'s.
    
• src/hg/lib/makefile
  • lines changed 1, context: html, text, full: html, text
    Adding new tablesTables module.
    
• src/hg/lib/tablesTables.c
  • lines changed 27, context: html, text, full: html, text
    A new module for tables on the web mostly.
    
  • lines changed 338, context: html, text, full: html, text
    Adding a ton of useful web table handling stuff from cdwWebBrowse.c to hg/lib/tablesTables.c and it's header.
    
  • lines changed 12, context: html, text, full: html, text
    Adding context parameter to wraps. Minor polish here and there.
    
• src/hg/makeDb/doc/tarSyr2/initialBuild.txt
  • lines changed 28, context: html, text, full: html, text
    add search rule for gold table refs #14410
    
• src/hg/makeDb/doc/tarSyr2/lastzRuns.txt
  • lines changed 23, context: html, text, full: html, text
    rerun rhiRox1 with correct sequence refs #14560
    
• src/hg/makeDb/doc/tarSyr2/multiz17way.txt
  • lines changed 244, context: html, text, full: html, text
    done with the rework of this with the correct rhiRox1 sequence refs #14410
    
• src/hg/makeDb/trackDb/baboon/papAnu2/trackDb.chainNet.ra
  • lines changed 24, context: html, text, full: html, text
    adding overrides for chain nets on species to 17-way tarSyr2 refs #14410
    
• src/hg/makeDb/trackDb/baboon/papAnu2/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    adding overrides for chain nets on species to 17-way tarSyr2 refs #14410
    
• src/hg/makeDb/trackDb/bushbaby/otoGar3/trackDb.chainNet.ra
  • lines changed 25, context: html, text, full: html, text
    adding overrides for chain nets on species to 17-way tarSyr2 refs #14410
    
• src/hg/makeDb/trackDb/bushbaby/otoGar3/trackDb.ra
  • lines changed 5, context: html, text, full: html, text
    adding overrides for chain nets on species to 17-way tarSyr2 refs #14410
    
• src/hg/makeDb/trackDb/chimp/panTro4/trackDb.chainNet.ra
  • lines changed 55, context: html, text, full: html, text
    adding overrides for chain nets on species to 17-way tarSyr2 refs #14410
    
• src/hg/makeDb/trackDb/chimp/panTro4/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    adding overrides for chain nets on species to 17-way tarSyr2 refs #14410
    
• src/hg/makeDb/trackDb/drosophila/dm6/refGene.html
  • lines changed 74, context: html, text, full: html, text
    all of the RefSeq genes for dm6 were contributed to GenBank by FlyBase. They asked for credit
    
• src/hg/makeDb/trackDb/drosophila/dm6/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    all of the RefSeq genes for dm6 were contributed to GenBank by FlyBase. They asked for credit
    
• src/hg/makeDb/trackDb/ebola/trackDb.ncbiGene.ra
  • lines changed 2, context: html, text, full: html, text
    adding overrides for chain nets on species to 17-way tarSyr2 refs #14410
    
• src/hg/makeDb/trackDb/gibbon/nomLeu3/trackDb.chainNet.ra
  • lines changed 19, context: html, text, full: html, text
    adding overrides for chain nets on species to 17-way tarSyr2 refs #14410
    
• src/hg/makeDb/trackDb/gibbon/nomLeu3/trackDb.ra
  • lines changed 5, context: html, text, full: html, text
    adding overrides for chain nets on species to 17-way tarSyr2 refs #14410
    
• src/hg/makeDb/trackDb/gorilla/gorGor3/trackDb.chainNet.ra
  • lines changed 56, context: html, text, full: html, text
    adding overrides for chain nets on species to 17-way tarSyr2 refs #14410
    
• src/hg/makeDb/trackDb/human/hg38/hg38Patch2.html
  • lines changed 8, context: html, text, full: html, text
    Made minor revisions to description page; refs #14167
    
• src/hg/makeDb/trackDb/human/hg38/hg38Patch2.ra
  • lines changed 8, context: html, text, full: html, text
    added search rule for hg38 patch2 names refs #14167
    
• src/hg/makeDb/trackDb/human/hg38/wgEncodeReg.ra
  • lines changed 1, context: html, text, full: html, text
    Change priority to improve ordering in supertrack
    
• src/hg/makeDb/trackDb/marmoset/calJac3/trackDb.chainNet.ra
  • lines changed 110, context: html, text, full: html, text
    adding overrides for chain nets on species to 17-way tarSyr2 refs #14410
    
• src/hg/makeDb/trackDb/mouseLemur/micMur1/trackDb.chainNet.ra
  • lines changed 39, context: html, text, full: html, text
    adding overrides for chain nets on species to 17-way tarSyr2 refs #14410
    
• src/hg/makeDb/trackDb/mouseLemur/micMur1/trackDb.ra
  • lines changed 11, context: html, text, full: html, text
    correcting long standing error in otherDb MicMur1 instead of otherDb micMur1 refs #14410
    
• src/hg/makeDb/trackDb/orangutan/ponAbe2/trackDb.chainNet.ra
  • lines changed 101, context: html, text, full: html, text
    adding overrides for chain nets on species to 17-way tarSyr2 refs #14410
    
• src/hg/makeDb/trackDb/orangutan/ponAbe2/trackDb.ra
  • lines changed 6, context: html, text, full: html, text
    adding overrides for chain nets on species to 17-way tarSyr2 refs #14410
    
• src/hg/makeDb/trackDb/rhesus/rheMac3/trackDb.chainNet.ra
  • lines changed 66, context: html, text, full: html, text
    adding overrides for chain nets on species to 17-way tarSyr2 refs #14410
    
• src/hg/makeDb/trackDb/rhesus/rheMac3/trackDb.ra
  • lines changed 3, context: html, text, full: html, text
    adding overrides for chain nets on species to 17-way tarSyr2 refs #14410
    
• src/hg/makeDb/trackDb/saiBol/saiBol1/trackDb.chainNet.ra
  • lines changed 24, context: html, text, full: html, text
    adding overrides for chain nets on species to 17-way tarSyr2 refs #14410
    
• src/hg/makeDb/trackDb/saiBol/saiBol1/trackDb.ra
  • lines changed 5, context: html, text, full: html, text
    adding overrides for chain nets on species to 17-way tarSyr2 refs #14410
    
• src/hg/makeDb/trackDb/tarsier/tarSyr2/trackDb.ra
  • lines changed 6, context: html, text, full: html, text
    add search rule for gold table refs #14410
    
  • lines changed 2, context: html, text, full: html, text
    correcting long standing error in otherDb MicMur1 instead of otherDb micMur1 refs #14410
    
• src/hg/makeDb/trackDb/trackDb.chainNet.ra
  • lines changed 1, context: html, text, full: html, text
    correcting long standing error in otherDb MicMur1 instead of otherDb micMur1 refs #14410
    
• src/hg/utils/checkUrlsInTable/checkUrlsInTable.c
  • lines changed 6, context: html, text, full: html, text
    Code review with Jonathan.
    
• src/hg/utils/genePredToBigGenePred/genePredToBigGenePred.c
  • lines changed 1, context: html, text, full: html, text
    tweak the usage message for genePredToBigGenePred in response to #13861
    
• src/inc/fieldedTable.h
  • lines changed 9, context: html, text, full: html, text
    Adding several routines that work across a column into library including one to see if column is entirely numeric, another to figure out how wide it is, and a third to sort on a column.
    
• src/lib/basicBed.c
  • lines changed 2, context: html, text, full: html, text
    take out check to find zero sized blocks in bed12's.
    
• src/lib/fieldedTable.c
  • lines changed 98, context: html, text, full: html, text
    Adding several routines that work across a column into library including one to see if column is entirely numeric, another to figure out how wide it is, and a third to sort on a column.
    
• src/lib/udc.c
  • lines changed 4, context: html, text, full: html, text
    Use MAXNAMLEN instead of NAME_MAX for portability to BSD-based systems like Mac OS X. refs #14899
    
  • lines changed 2, context: html, text, full: html, text
    only do cool UDC long directory hashing if USE_SSL=1
    
• src/utils/gitTools/gilt
  • lines changed 3, context: html, text, full: html, text
    use bash redirection instead of /dev/stderr in case of cron job operations refs #14821
    
• src/utils/gitTools/gitFiles
  • lines changed 3, context: html, text, full: html, text
    use bash redirection instead of /dev/stderr in case of cron job operations refs #14821
    
• src/utils/qa/weeklybld/buildBeta.csh
  • lines changed 3, context: html, text, full: html, text
    correcting make beta to be in src/ instead of just src/hg/ refs #14768
    
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    v313 preview2 refs #14887
    
• src/utils/qa/weeklybld/buildWithUseCases
  • lines changed 2, context: html, text, full: html, text
    can not echo to /dev/stderr from within a cron job use bash redirect instead refs #14821
    

• lines changed: 3722
• files changed: 91