All File Changes

v249_preview2 to v249_base (2011-03-22 to 2011-03-29) v249

• src/blat/makefile
  • lines changed 2, context: html, text, full: html, text
    fix up makefiles to grok DESTDIR, add blat,gfServer, and gfClient to userApps #3152
• src/gfClient/makefile
  • lines changed 2, context: html, text, full: html, text
    fix up makefiles to grok DESTDIR, add blat,gfServer, and gfClient to userApps #3152
• src/gfServer/makefile
  • lines changed 2, context: html, text, full: html, text
    fix up makefiles to grok DESTDIR, add blat,gfServer, and gfClient to userApps #3152
• src/hg/encode/DAFs/2.0/gisChiaPet.daf
  • lines changed 7, context: html, text, full: html, text
    Added a stanza for Signal track
• src/hg/encode/encodeExp/encodeExp.c
  • lines changed 80, context: html, text, full: html, text
    Changes to support add/revoke accessions (temp experiments)
  • lines changed 12, context: html, text, full: html, text
    Added useful functions to mdb, including encode specific ones. Fixed encodeExp retreival by mdb obj.
  • lines changed 8, context: html, text, full: html, text
    Clarified a message to Kate
• src/hg/encode/encodeExp/tests/expected/addTest.out.ra
  • lines changed 2, context: html, text, full: html, text
    Changes to support add/revoke accessions (temp experiments)
• src/hg/encode/encodeValidate/doEncodeValidate.pl
  • lines changed 32, context: html, text, full: html, text
    taking out interface to docId
  • lines changed 1, context: html, text, full: html, text
    add bedRrbs
• src/hg/encode/hgEncodeVocab/hgEncodeVocab.c
  • lines changed 117, context: html, text, full: html, text
    Made mdb dependent upon cv defines. Made hgEncodeVocab use cv defines.
• src/hg/hgApi/hgApi.c
  • lines changed 5, context: html, text, full: html, text
    Renamed a bunch of mdbCv APIs to cv APIs.
• src/hg/hgFileSearch/hgFileSearch.c
  • lines changed 43, context: html, text, full: html, text
    Fixed bug on name/description search and fleshed out wild card and quoted strings in description search
  • lines changed 46, context: html, text, full: html, text
    Now both name and description searches match each word, accept wildcards and respect quotes
  • lines changed 21, context: html, text, full: html, text
    Corrected the about message at the bottom of the page.
  • lines changed 47, context: html, text, full: html, text
    Addressed a bug in description searches and slightly streamlined.
  • lines changed 3, context: html, text, full: html, text
    File search should not advertise support for quoted string search, since new lines, etc. in target tdb->html can result in false negatives.
  • lines changed 13, context: html, text, full: html, text
    Ensure the backgound floret is used but avoid the overhead that hgTracks uses to acheive this.
• src/hg/hgFileUi/hgFileUi.c
  • lines changed 7, context: html, text, full: html, text
    Add navigation link to downloads search
  • lines changed 1, context: html, text, full: html, text
    Katrina prefers 'File Search' to 'Downloads Search'
• src/hg/hgGateway/hgGateway.c
  • lines changed 8, context: html, text, full: html, text
    some more NEW_JQUERY stuff - dead code all trees unless explicitly turned on (redmine 2813)
• src/hg/hgTables/bam.c
  • lines changed 2, context: html, text, full: html, text
    put out a warning message if the number of lines is capped #27
• src/hg/hgTables/gffOut.c
  • lines changed 22, context: html, text, full: html, text
    Bug #2964 (Table Browser: RefGene output in GTF gives error):An unanticipated condition led to an errAbort: rn4 refGene contained a transcript (alternate alignment of NM_001008876) with the coding region annotated as the first base of the first exon. Now, instead of errAborting when a requested codon offset is out of bounds, we don't attempt to print start_codon or stop_codon elements when the entire codon is not contained in the transcript's exons and coding region.
• src/hg/hgTables/usage.c
  • lines changed 2, context: html, text, full: html, text
    removing mention of ENCODE regions (since it's no longer an option)
• src/hg/hgTrackUi/hgTrackUi.c
  • lines changed 2, context: html, text, full: html, text
    add support for supertracks in hubs #3381
• src/hg/hgTracks/bamTrack.c
  • lines changed 29, context: html, text, full: html, text
    Feature #2822, #2823 (VCF customFactory + track handler):Added a new track type, vcfTabix, with handlers in hgTracks and hgc and a customFactory. It is a new bigDataUrl type of track; the remote VCF file must be compressed and indexed by tabix, so like BAM a separate index file is required. If the VCF file has genotypes, then each sample's two haplotypes are graphed in a line, with one line per sample. Otherwise, alleles and counts (if available) are drawn using Belinda's pgSnp methods. The source code has to be compiled with USE_TABIX=1 (which is automatically set for us by common.mk when it finds the local installation) in order for the CGIs to recognize the track type.
• src/hg/hgTracks/hgTracks.c
  • lines changed 1, context: html, text, full: html, text
    some more NEW_JQUERY stuff - dead code all trees unless explicitly turned on (redmine 2813)
  • lines changed 17, context: html, text, full: html, text
    Feature #2822, #2823 (VCF customFactory + track handler):Added a new track type, vcfTabix, with handlers in hgTracks and hgc and a customFactory. It is a new bigDataUrl type of track; the remote VCF file must be compressed and indexed by tabix, so like BAM a separate index file is required. If the VCF file has genotypes, then each sample's two haplotypes are graphed in a line, with one line per sample. Otherwise, alleles and counts (if available) are drawn using Belinda's pgSnp methods. The source code has to be compiled with USE_TABIX=1 (which is automatically set for us by common.mk when it finds the local installation) in order for the CGIs to recognize the track type.
• src/hg/hgTracks/hgTracks.h
  • lines changed 15, context: html, text, full: html, text
    Feature #2822, #2823 (VCF customFactory + track handler):Added a new track type, vcfTabix, with handlers in hgTracks and hgc and a customFactory. It is a new bigDataUrl type of track; the remote VCF file must be compressed and indexed by tabix, so like BAM a separate index file is required. If the VCF file has genotypes, then each sample's two haplotypes are graphed in a line, with one line per sample. Otherwise, alleles and counts (if available) are drawn using Belinda's pgSnp methods. The source code has to be compiled with USE_TABIX=1 (which is automatically set for us by common.mk when it finds the local installation) in order for the CGIs to recognize the track type.
• src/hg/hgTracks/makefile
  • lines changed 1, context: html, text, full: html, text
    Feature #2822, #2823 (VCF customFactory + track handler):Added a new track type, vcfTabix, with handlers in hgTracks and hgc and a customFactory. It is a new bigDataUrl type of track; the remote VCF file must be compressed and indexed by tabix, so like BAM a separate index file is required. If the VCF file has genotypes, then each sample's two haplotypes are graphed in a line, with one line per sample. Otherwise, alleles and counts (if available) are drawn using Belinda's pgSnp methods. The source code has to be compiled with USE_TABIX=1 (which is automatically set for us by common.mk when it finds the local installation) in order for the CGIs to recognize the track type.
• src/hg/hgTracks/simpleTracks.c
  • lines changed 54, context: html, text, full: html, text
    Feature #2822, #2823 (VCF customFactory + track handler):Added a new track type, vcfTabix, with handlers in hgTracks and hgc and a customFactory. It is a new bigDataUrl type of track; the remote VCF file must be compressed and indexed by tabix, so like BAM a separate index file is required. If the VCF file has genotypes, then each sample's two haplotypes are graphed in a line, with one line per sample. Otherwise, alleles and counts (if available) are drawn using Belinda's pgSnp methods. The source code has to be compiled with USE_TABIX=1 (which is automatically set for us by common.mk when it finds the local installation) in order for the CGIs to recognize the track type.
  • lines changed 23, context: html, text, full: html, text
    redmine 1876. Hopefully fixed. Subtracks were going through limitVisibility() before their items were loaded.
• src/hg/hgTracks/vcfTrack.c
  • lines changed 429, context: html, text, full: html, text
    Feature #2822, #2823 (VCF customFactory + track handler):Added a new track type, vcfTabix, with handlers in hgTracks and hgc and a customFactory. It is a new bigDataUrl type of track; the remote VCF file must be compressed and indexed by tabix, so like BAM a separate index file is required. If the VCF file has genotypes, then each sample's two haplotypes are graphed in a line, with one line per sample. Otherwise, alleles and counts (if available) are drawn using Belinda's pgSnp methods. The source code has to be compiled with USE_TABIX=1 (which is automatically set for us by common.mk when it finds the local installation) in order for the CGIs to recognize the track type.
• src/hg/hgc/hgc.c
  • lines changed 8, context: html, text, full: html, text
    Feature #2822, #2823 (VCF customFactory + track handler):Added a new track type, vcfTabix, with handlers in hgTracks and hgc and a customFactory. It is a new bigDataUrl type of track; the remote VCF file must be compressed and indexed by tabix, so like BAM a separate index file is required. If the VCF file has genotypes, then each sample's two haplotypes are graphed in a line, with one line per sample. Otherwise, alleles and counts (if available) are drawn using Belinda's pgSnp methods. The source code has to be compiled with USE_TABIX=1 (which is automatically set for us by common.mk when it finds the local installation) in order for the CGIs to recognize the track type.
  • lines changed 13, context: html, text, full: html, text
    Changed functions for omimGeneClass3 to omimGene2.
• src/hg/hgc/hgc.h
  • lines changed 3, context: html, text, full: html, text
    Feature #2822, #2823 (VCF customFactory + track handler):Added a new track type, vcfTabix, with handlers in hgTracks and hgc and a customFactory. It is a new bigDataUrl type of track; the remote VCF file must be compressed and indexed by tabix, so like BAM a separate index file is required. If the VCF file has genotypes, then each sample's two haplotypes are graphed in a line, with one line per sample. Otherwise, alleles and counts (if available) are drawn using Belinda's pgSnp methods. The source code has to be compiled with USE_TABIX=1 (which is automatically set for us by common.mk when it finds the local installation) in order for the CGIs to recognize the track type.
• src/hg/hgc/makefile
  • lines changed 1, context: html, text, full: html, text
    Feature #2822, #2823 (VCF customFactory + track handler):Added a new track type, vcfTabix, with handlers in hgTracks and hgc and a customFactory. It is a new bigDataUrl type of track; the remote VCF file must be compressed and indexed by tabix, so like BAM a separate index file is required. If the VCF file has genotypes, then each sample's two haplotypes are graphed in a line, with one line per sample. Otherwise, alleles and counts (if available) are drawn using Belinda's pgSnp methods. The source code has to be compiled with USE_TABIX=1 (which is automatically set for us by common.mk when it finds the local installation) in order for the CGIs to recognize the track type.
• src/hg/hgc/peakClusters.c
  • lines changed 26, context: html, text, full: html, text
    Adding link to antibody page for factor in TFBS details. Adding cell letter abbreviation column.
• src/hg/hgc/vcfClick.c
  • lines changed 244, context: html, text, full: html, text
    Feature #2822, #2823 (VCF customFactory + track handler):Added a new track type, vcfTabix, with handlers in hgTracks and hgc and a customFactory. It is a new bigDataUrl type of track; the remote VCF file must be compressed and indexed by tabix, so like BAM a separate index file is required. If the VCF file has genotypes, then each sample's two haplotypes are graphed in a line, with one line per sample. Otherwise, alleles and counts (if available) are drawn using Belinda's pgSnp methods. The source code has to be compiled with USE_TABIX=1 (which is automatically set for us by common.mk when it finds the local installation) in order for the CGIs to recognize the track type.
• src/hg/htdocs/ENCODE/downloads.html
  • lines changed 5, context: html, text, full: html, text
    added RIKEN CAGE, redmine #41
  • lines changed 209, context: html, text, full: html, text
    Added 'files search buttons to downloads pages
• src/hg/htdocs/ENCODE/downloadsMouse.html
  • lines changed 56, context: html, text, full: html, text
    Added 'files search buttons to downloads pages
• src/hg/htdocs/ENCODE/index.html
  • lines changed 3, context: html, text, full: html, text
    Added page of search options for ENCODE files nad tracks. Also made attempt at using CSS instead of our usual tables within tables within tables to make borders to things.
  • lines changed 1, context: html, text, full: html, text
    Added a left menu search item under mouse too.
  • lines changed 1, context: html, text, full: html, text
    made edits to new ENCODE search page and ENCODE portal
• src/hg/htdocs/ENCODE/search.html
  • lines changed 91, context: html, text, full: html, text
    Added page of search options for ENCODE files nad tracks. Also made attempt at using CSS instead of our usual tables within tables within tables to make borders to things.
  • lines changed 1, context: html, text, full: html, text
    Added 'files search buttons to downloads pages
  • lines changed 4, context: html, text, full: html, text
    made edits to new ENCODE search page and ENCODE portal
• src/hg/htdocs/FAQ/FAQblat.html
  • lines changed 1, context: html, text, full: html, text
    changing link to new blat executables
• src/hg/htdocs/goldenPath/help/hgTablesHelp.html
  • lines changed 3, context: html, text, full: html, text
    Removed reference to ENCODE region option, redmine #1583
• src/hg/htdocs/goldenPath/help/hgTracksHelp.html
  • lines changed 11, context: html, text, full: html, text
    Added mail list search tool, redmine #3380
• src/hg/htdocs/makefile
  • lines changed 4, context: html, text, full: html, text
    fix more style directory problems.. this time for the user target...grrr
• src/hg/inc/cv.h
  • lines changed 69, context: html, text, full: html, text
    Split out the cv routines into their own lib file, but have yet to rename any of the APIs
  • lines changed 12, context: html, text, full: html, text
    Renamed a bunch of mdbCv APIs to cv APIs.
  • lines changed 16, context: html, text, full: html, text
    Made mdb dependent upon cv defines. Made hgEncodeVocab use cv defines.
• src/hg/inc/encode/encodeExp.h
  • lines changed 18, context: html, text, full: html, text
    Changes to support add/revoke accessions (temp experiments)
  • lines changed 1, context: html, text, full: html, text
    Added useful functions to mdb, including encode specific ones. Fixed encodeExp retreival by mdb obj.
  • lines changed 4, context: html, text, full: html, text
    Needed to protext NULLs when inserting into encodeExp table.
  • lines changed 1, context: html, text, full: html, text
    Fix inconsistent function name (code review)
• src/hg/inc/jsHelper.h
  • lines changed 2, context: html, text, full: html, text
    some more NEW_JQUERY stuff - dead code all trees unless explicitly turned on (redmine 2813)
• src/hg/inc/mdb.h
  • lines changed 71, context: html, text, full: html, text
    Better management of mdb vars and cv terms string literals in anticilation of splitting out cv lib. Also removed the varType once and for all
  • lines changed 67, context: html, text, full: html, text
    Split out the cv routines into their own lib file, but have yet to rename any of the APIs
  • lines changed 6, context: html, text, full: html, text
    Made mdb dependent upon cv defines. Made hgEncodeVocab use cv defines.
  • lines changed 45, context: html, text, full: html, text
    Added useful functions to mdb, including encode specific ones. Fixed encodeExp retreival by mdb obj.
  • lines changed 4, context: html, text, full: html, text
    Needed to expose mdbVarsFree()
• src/hg/inc/versionInfo.h
  • lines changed 1, context: html, text, full: html, text
    New version number v249
• src/hg/lib/customFactory.c
  • lines changed 60, context: html, text, full: html, text
    Feature #2822, #2823 (VCF customFactory + track handler):Added a new track type, vcfTabix, with handlers in hgTracks and hgc and a customFactory. It is a new bigDataUrl type of track; the remote VCF file must be compressed and indexed by tabix, so like BAM a separate index file is required. If the VCF file has genotypes, then each sample's two haplotypes are graphed in a line, with one line per sample. Otherwise, alleles and counts (if available) are drawn using Belinda's pgSnp methods. The source code has to be compiled with USE_TABIX=1 (which is automatically set for us by common.mk when it finds the local installation) in order for the CGIs to recognize the track type.
• src/hg/lib/cv.c
  • lines changed 238, context: html, text, full: html, text
    Split out the cv routines into their own lib file, but have yet to rename any of the APIs
  • lines changed 22, context: html, text, full: html, text
    Renamed a bunch of mdbCv APIs to cv APIs.
  • lines changed 24, context: html, text, full: html, text
    Made mdb dependent upon cv defines. Made hgEncodeVocab use cv defines.
• src/hg/lib/encode/encodeExp.c
  • lines changed 68, context: html, text, full: html, text
    Changes to support add/revoke accessions (temp experiments)
  • lines changed 1, context: html, text, full: html, text
    Fixed a bug from unremoved older code.
  • lines changed 74, context: html, text, full: html, text
    Added useful functions to mdb, including encode specific ones. Fixed encodeExp retreival by mdb obj.
  • lines changed 44, context: html, text, full: html, text
    Needed to protext NULLs when inserting into encodeExp table.
  • lines changed 1, context: html, text, full: html, text
    Fix inconsistent function name (code review)
• src/hg/lib/fileUi.c
  • lines changed 3, context: html, text, full: html, text
    Reduce limit on number of found files to 1000, because 200 takes too long.
  • lines changed 6, context: html, text, full: html, text
    Renamed a bunch of mdbCv APIs to cv APIs.
• src/hg/lib/hubConnect.c
  • lines changed 4, context: html, text, full: html, text
    fix Apache specific HTML access problems #3381
  • lines changed 29, context: html, text, full: html, text
    add support for supertracks in hubs #3381
• src/hg/lib/hui.c
  • lines changed 1, context: html, text, full: html, text
    Renamed a bunch of mdbCv APIs to cv APIs.
• src/hg/lib/makefile
  • lines changed 1, context: html, text, full: html, text
    Split out the cv routines into their own lib file, but have yet to rename any of the APIs
• src/hg/lib/mdb.c
  • lines changed 162, context: html, text, full: html, text
    Better management of mdb vars and cv terms string literals in anticilation of splitting out cv lib. Also removed the varType once and for all
  • lines changed 228, context: html, text, full: html, text
    Split out the cv routines into their own lib file, but have yet to rename any of the APIs
  • lines changed 13, context: html, text, full: html, text
    Renamed a bunch of mdbCv APIs to cv APIs.
  • lines changed 14, context: html, text, full: html, text
    Minor change to the experimentifier output as requested by Cricket.
  • lines changed 222, context: html, text, full: html, text
    Added useful functions to mdb, including encode specific ones. Fixed encodeExp retreival by mdb obj.
  • lines changed 28, context: html, text, full: html, text
    Needed to expose mdbVarsFree()
• src/hg/lib/searchTracks.c
  • lines changed 11, context: html, text, full: html, text
    Renamed a bunch of mdbCv APIs to cv APIs.
• src/hg/lib/trackDbCustom.c
  • lines changed 2, context: html, text, full: html, text
    Feature #2822, #2823 (VCF customFactory + track handler):Added a new track type, vcfTabix, with handlers in hgTracks and hgc and a customFactory. It is a new bigDataUrl type of track; the remote VCF file must be compressed and indexed by tabix, so like BAM a separate index file is required. If the VCF file has genotypes, then each sample's two haplotypes are graphed in a line, with one line per sample. Otherwise, alleles and counts (if available) are drawn using Belinda's pgSnp methods. The source code has to be compiled with USE_TABIX=1 (which is automatically set for us by common.mk when it finds the local installation) in order for the CGIs to recognize the track type.
  • lines changed 14, context: html, text, full: html, text
    add support for supertracks in hubs #3381
• src/hg/lib/trackHub.c
  • lines changed 101, context: html, text, full: html, text
    add support for supertracks in hubs #3381
• src/hg/lib/web.c
  • lines changed 3, context: html, text, full: html, text
    workaround for qaPushQ and style-sheet versioning
• src/hg/lib/wikiLink.c
  • lines changed 7, context: html, text, full: html, text
    adding server port to returnto string for genomewiki login
• src/hg/makeDb/doc/29mammals.txt
  • lines changed 63, context: html, text, full: html, text
    indicate gwUploadFile command to load all this business
  • lines changed 3, context: html, text, full: html, text
    add note reference to genomewiki instructions for this same procedure
• src/hg/makeDb/doc/danRer5.txt
  • lines changed 133, context: html, text, full: html, text
    Documented U Mass ChIP-Seq tracks build.
• src/hg/makeDb/doc/encodeDccHg19/broadHistoneBernstein.hg19.txt
  • lines changed 25, context: html, text, full: html, text
    Checking in old and newer doc of broad HMM
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeBroadHmm.release1.notes
  • lines changed 62, context: html, text, full: html, text
    Preparing for pushQ entry
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeSydhHistone.release1.notes
  • lines changed 185, context: html, text, full: html, text
    Release 1 notes for Sydh Histone.
• src/hg/makeDb/doc/hg19.txt
  • lines changed 4, context: html, text, full: html, text
    fixed chrmito vs chrM problem for acembly table
  • lines changed 90, context: html, text, full: html, text
    Putting in instructions for making pooled & normalized Caltech RNA signals.
  • lines changed 163, context: html, text, full: html, text
    Added the commands for building the Affy Exon track
• src/hg/makeDb/doc/mm9.txt
  • lines changed 44, context: html, text, full: html, text
    Updated mm9 ikmc track.
  • lines changed 32, context: html, text, full: html, text
    Updated mm9 ikmc build, removed 4 records that have overlapping blocks problem.
• src/hg/makeDb/doc/panTro3.txt
  • lines changed 45, context: html, text, full: html, text
    gap annotations on the multiz12way.maf
  • lines changed 82, context: html, text, full: html, text
    lifting ensGene from panTro2 to panTro3
  • lines changed 93, context: html, text, full: html, text
    maf frames added
  • lines changed 191, context: html, text, full: html, text
    4D predictions made on ensGene
• src/hg/makeDb/schema/all.joiner
  • lines changed 1, context: html, text, full: html, text
    adding affyExonProbe tables to tablesIgnored section
• src/hg/makeDb/trackDb/chimp/panTro3/trackDb.ra
  • lines changed 156, context: html, text, full: html, text
    initial contents of 12-way conservation track
• src/hg/makeDb/trackDb/cv/alpha/cv.ra
  • lines changed 11, context: html, text, full: html, text
    Addressing code review feedback from Katrina
  • lines changed 1, context: html, text, full: html, text
    Getting rid of an incorrect download link, by advice of Katrina
  • lines changed 6, context: html, text, full: html, text
    At the request of Greg Crawford, replaced the specific vendor information for HSMM and HSMMtube with a comment to refer to the cell growth protocol document(s)
  • lines changed 1, context: html, text, full: html, text
    testing to see if I can *now* enter a cell line with a vendor name but not a vendor ID
  • lines changed 1, context: html, text, full: html, text
    Now that it appears I can get away with not having a vendor ID for hsmm, removing the n/a vendor ID for the companion cell line hsmmtube
  • lines changed 9, context: html, text, full: html, text
    Added provisional comments to RA enteries that were updated in commit: f2bfbddbbc73adb2ec00232eaf1fdda4890849cb so that Melissa can review them.
• src/hg/makeDb/trackDb/cv/beta/cv.ra
  • lines changed 30, context: html, text, full: html, text
    Copying changes from alpha to beta after code review
• src/hg/makeDb/trackDb/cv/public/cv.ra
  • lines changed 302, context: html, text, full: html, text
    releasing changes I reviewed on beta/cv.ra to public, redmine #3349
• src/hg/makeDb/trackDb/ensGene.html
  • lines changed 5, context: html, text, full: html, text
    changed longLable of ensGene at the request of Ensembl and added link to a description of their build pipeline
  • lines changed 2, context: html, text, full: html, text
    Added missing 'the'. Also included target attribute so page opens in a new tab.
• src/hg/makeDb/trackDb/human/affyExonArray.html
  • lines changed 2, context: html, text, full: html, text
    edits to the html and long labels of Affy Exon Array
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/makefile
  • lines changed 3, context: html, text, full: html, text
    These old tracks needed metadata lines replaced with mdb table entries
  • lines changed 1, context: html, text, full: html, text
    Moved perhaps the last of the metadata lines from trackDb to metaDb.
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeMapability.ra
  • lines changed 162, context: html, text, full: html, text
    These old tracks needed metadata lines replaced with mdb table entries
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeNhgriBip.ra
  • lines changed 16, context: html, text, full: html, text
    These old tracks needed metadata lines replaced with mdb table entries
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeNhgriNRE.ra
  • lines changed 69, context: html, text, full: html, text
    These old tracks needed metadata lines replaced with mdb table entries
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeUmasshaTfbsValid.ra
  • lines changed 17, context: html, text, full: html, text
    Moved perhaps the last of the metadata lines from trackDb to metaDb.
• src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra
  • lines changed 16, context: html, text, full: html, text
    These old tracks needed metadata lines replaced with mdb table entries
  • lines changed 30, context: html, text, full: html, text
    Moved perhaps the last of the metadata lines from trackDb to metaDb.
  • lines changed 29, context: html, text, full: html, text
    Mistakenly took out metadata lines from beta/public versions. They were already removed from alpha versions.
  • lines changed 185, context: html, text, full: html, text
    Round and round. Split the tracks that are having their metadata lines removed into alpha aand beta,public versions.
• src/hg/makeDb/trackDb/human/hg18/wgEncodeAffyRnaChip.ra
  • lines changed 104, context: html, text, full: html, text
    More metadata lines removed from trackDb but all of these should already have been in the mdb.
• src/hg/makeDb/trackDb/human/hg18/wgEncodeCshlShortRnaSeq.ra
  • lines changed 44, context: html, text, full: html, text
    More metadata lines removed from trackDb but all of these should already have been in the mdb.
  • lines changed 44, context: html, text, full: html, text
    Mistakenly took out metadata lines from beta/public versions. They were already removed from alpha versions.
• src/hg/makeDb/trackDb/human/hg18/wgEncodeDukeAffyExon.ra
  • lines changed 58, context: html, text, full: html, text
    More metadata lines removed from trackDb but all of these should already have been in the mdb.
• src/hg/makeDb/trackDb/human/hg18/wgEncodeGisDnaPet.ra
  • lines changed 6, context: html, text, full: html, text
    More metadata lines removed from trackDb but all of these should already have been in the mdb.
  • lines changed 6, context: html, text, full: html, text
    Mistakenly took out metadata lines from beta/public versions. They were already removed from alpha versions.
• src/hg/makeDb/trackDb/human/hg18/wgEncodeGisRnaSeq.ra
  • lines changed 18, context: html, text, full: html, text
    More metadata lines removed from trackDb but all of these should already have been in the mdb.
  • lines changed 18, context: html, text, full: html, text
    Mistakenly took out metadata lines from beta/public versions. They were already removed from alpha versions.
• src/hg/makeDb/trackDb/human/hg18/wgEncodeHelicosRnaSeq.ra
  • lines changed 2, context: html, text, full: html, text
    More metadata lines removed from trackDb but all of these should already have been in the mdb.
• src/hg/makeDb/trackDb/human/hg18/wgEncodeHudsonalphaCnv.ra
  • lines changed 6, context: html, text, full: html, text
    More metadata lines removed from trackDb but all of these should already have been in the mdb.
  • lines changed 6, context: html, text, full: html, text
    Mistakenly took out metadata lines from beta/public versions. They were already removed from alpha versions.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeBroadHmm.ra
  • lines changed 0, context: html, text, full: html, text
    I had let CRLFs seep in while editing in windows.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlLongRnaSeq.ra
  • lines changed 5357, context: html, text, full: html, text
    Changed which views were for downloads only, introduced dccRep and added origAssembly where missing
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibGenotype.ra
  • lines changed 90, context: html, text, full: html, text
    added dccRep into the metaData
  • lines changed 3, context: html, text, full: html, text
    Changed the fileSortOrder to show more, fixed some metaData errors
  • lines changed 23, context: html, text, full: html, text
    Added the links to the SNP data in the .html files, added information about the dual replicate numbering, added the dual replicate labels in the long labels, removed HsmmRep6 see Redmine 1708
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibMethylRrbs.ra
  • lines changed 212, context: html, text, full: html, text
    Added the expIds, corrected the obtainedBy labs
  • lines changed 107, context: html, text, full: html, text
    Changing metadata and file names according to Flo
  • lines changed 3273, context: html, text, full: html, text
    Renamed many files, changed replicate numbering for 2 files, changed some metaData lines for obtainedBy
  • lines changed 178, context: html, text, full: html, text
    Revoking HsmmRep6
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibTfbs.ra
  • lines changed 4532, context: html, text, full: html, text
    Added 14 submissions with appropriate meta-data. Should fix redmine issues: 3057 and 1494. Also fixed typo's in date format in meta-data.
  • lines changed 47, context: html, text, full: html, text
    Added subId 3815.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhHistone.ra
  • lines changed 163, context: html, text, full: html, text
    Fixed labeling of cell line K562 to ucdavis variant K562b. Updated antibody H3K27me3 -> H3K27me3B. Updated experiment NT2-D1/H3K9ac -> NT2-D1/H3K9acB to be associated with the correct anitbodies.
  • lines changed 99, context: html, text, full: html, text
    Fixed the incorrect labeling of control as std rather than UCD on 4 experiments for the NT2-D1 cell line.
  • lines changed 19, context: html, text, full: html, text
    Fixed controlId's that were NT2_D1/None/Input/UCDavis -> NT2-D1/None/Input/UCDavis
  • lines changed 141, context: html, text, full: html, text
    Added submission 3839, which has the inputs of k562b and U2SO that exist on SYDH TFBS track, but are also used in the SYDH Histone track.
  • lines changed 15, context: html, text, full: html, text
    Fixed replicate naming for inputs in meta-data. Updated the fileSortOrder and sortOrder for the track to have fields that would help users filter experiments.
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/makefile
  • lines changed 1, context: html, text, full: html, text
    staging SUNY GeneSt on beta, redmine #37
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeSunyAlbanyGeneSt.ra
  • lines changed 483, context: html, text, full: html, text
    staging SUNY GeneSt on beta, redmine #37
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/makefile
  • lines changed 1, context: html, text, full: html, text
    releasing RIKEN CAGE, redmine #41
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeRikenCage.ra
  • lines changed 5913, context: html, text, full: html, text
    releasing RIKEN CAGE, redmine #41
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    edits to the html and long labels of Affy Exon Array
  • lines changed 33, context: html, text, full: html, text
    Adding the stanzas for the Affy Exon track, which I'd somehow failed to check in before
  • lines changed 2, context: html, text, full: html, text
    recommiting my changes to the long labels (I think they may have been accidentially clobbered)
  • lines changed 98, context: html, text, full: html, text
    Changes to the multiz46way Chain/Net Composite track species ordering. This isto accommodate David's request that species are ordered phylogenetically by default. As it was, they were ordered alphabetically. I added the alpha-prefix to the labels in the subGroup lists for all three composites. For the actual phylo order I followed the listing in the 46way Conservation track's Multiz Alignments Configuration page (even if it clashed slightly with the hg19_46way.gif image). Hiram says that it was in phylo order when it was released but that somehow it must have been reverted (to alpha order).
  • lines changed 13, context: html, text, full: html, text
    affy exon track: standardizing labels and shortening long labels
  • lines changed 1, context: html, text, full: html, text
    removing release tags for affy Exon track since the track is only on hg19 and it is a new track
  • lines changed 3, context: html, text, full: html, text
    Added danRer7 to Vertebrate ChainNet Composite track. Replaced danRer6.
  • lines changed 147, context: html, text, full: html, text
    Added danRer7 to Vertebrate NET Composite track. Missed the NET table first time through.
• src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra
  • lines changed 1, context: html, text, full: html, text
    Changed the release tags to be in the trackDbFile
  • lines changed 1, context: html, text, full: html, text
    releasing RIKEN CAGE, redmine #41
  • lines changed 1, context: html, text, full: html, text
    staging SUNY GeneSt on beta, redmine #37
• src/hg/makeDb/trackDb/human/hg19/wgEncodeBroadHistone.html
  • lines changed 14, context: html, text, full: html, text
    Added text about pooled replicates as per Katrina and Kate request.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeBroadHmm.html
  • lines changed 3, context: html, text, full: html, text
    Standardized the liftOver note as per Katrina's request.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeBroadHmm.ra
  • lines changed 0, context: html, text, full: html, text
    I had let CRLFs seep in while editing in windows.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlLongRnaSeq.ra
  • lines changed 2573, context: html, text, full: html, text
    Changed which views were for downloads only, introduced dccRep and added origAssembly where missing
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibGenotype.html
  • lines changed 10, context: html, text, full: html, text
    Added the links to the SNP data in the .html files, added information about the dual replicate numbering, added the dual replicate labels in the long labels, removed HsmmRep6 see Redmine 1708
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibGenotype.ra
  • lines changed 1, context: html, text, full: html, text
    Changed the fileSortOrder to show more, fixed some metaData errors
  • lines changed 49, context: html, text, full: html, text
    Added the links to the SNP data in the .html files, added information about the dual replicate numbering, added the dual replicate labels in the long labels, removed HsmmRep6 see Redmine 1708
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethylRrbs.new.ra
  • lines changed 230, context: html, text, full: html, text
    Renamed many files, changed replicate numbering for 2 files, changed some metaData lines for obtainedBy
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibTfbs.ra
  • lines changed 801, context: html, text, full: html, text
    Added 14 submissions with appropriate meta-data. Should fix redmine issues: 3057 and 1494. Also fixed typo's in date format in meta-data.
  • lines changed 20, context: html, text, full: html, text
    Added subId 3815.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSunyAlbanyGeneSt.html
  • lines changed 4, context: html, text, full: html, text
    changing contact hyperlink to display contact name
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhHistone.ra
  • lines changed 50, context: html, text, full: html, text
    Fixed labeling of cell line K562 to ucdavis variant K562b. Updated antibody H3K27me3 -> H3K27me3B. Updated experiment NT2-D1/H3K9ac -> NT2-D1/H3K9acB to be associated with the correct anitbodies.
  • lines changed 15, context: html, text, full: html, text
    Fixed the incorrect labeling of control as std rather than UCD on 4 experiments for the NT2-D1 cell line.
  • lines changed 19, context: html, text, full: html, text
    Added submission 3839, which has the inputs of k562b and U2SO that exist on SYDH TFBS track, but are also used in the SYDH Histone track.
  • lines changed 9, context: html, text, full: html, text
    Removed metadata line and replaced with just subId and dateSubmitted as pipeline now makes tracDb.ra enteries.
  • lines changed 67, context: html, text, full: html, text
    Added comprehensive notes section. Updated downloads page to be fileSortOrder. First pass at short and long labels.
  • lines changed 33, context: html, text, full: html, text
    Fixed shortLabels so that they fit with 17 character limit. Also removed extranous comment line about data being through Jun 2010 freeze.
  • lines changed 2, context: html, text, full: html, text
    Fixed replicate naming for inputs in meta-data. Updated the fileSortOrder and sortOrder for the track to have fields that would help users filter experiments.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUchicagoTfbs.html
  • lines changed 19, context: html, text, full: html, text
    Added Methods header and removed email addresses
• src/hg/makeDb/trackDb/pig/susScr2/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    changed longLable of ensGene at the request of Ensembl and added link to a description of their build pipeline
• src/hg/makeDb/trackDb/sacCer/sacCer2/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    changed longLable of ensGene at the request of Ensembl and added link to a description of their build pipeline
• src/hg/makeDb/trackDb/snp132.html
  • lines changed 24, context: html, text, full: html, text
    Track #1684 (SNPs 132 (dbSNP)): Strawman enhanced descriptions asrequested by Brooke -- hopefully b0b and Jim will provide some input.
• src/hg/makeDb/trackDb/snp132Common.html
  • lines changed 10, context: html, text, full: html, text
    Track #1684 (SNPs 132 (dbSNP)): Strawman enhanced descriptions asrequested by Brooke -- hopefully b0b and Jim will provide some input.
• src/hg/makeDb/trackDb/snp132NonUnique.html
  • lines changed 7, context: html, text, full: html, text
    Track #1684 (SNPs 132 (dbSNP)): Strawman enhanced descriptions asrequested by Brooke -- hopefully b0b and Jim will provide some input.
• src/hg/makeDb/trackDb/snp132Patient.html
  • lines changed 10, context: html, text, full: html, text
    Track #1684 (SNPs 132 (dbSNP)): Strawman enhanced descriptions asrequested by Brooke -- hopefully b0b and Jim will provide some input.
• src/hg/makeDb/trackDb/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    changed longLable of ensGene at the request of Ensembl and added link to a description of their build pipeline
• src/hg/makeDb/trackDb/zebrafish/danRer5/UMassChIP-Seq.html
  • lines changed 31, context: html, text, full: html, text
    Created UMassChIP-Seq.html.
  • lines changed 0, context: html, text, full: html, text
    Created UMassChIP-Seq.html.
• src/hg/makeDb/trackDb/zebrafish/danRer5/UMassChIP-SeqSuper.html
  • lines changed 1, context: html, text, full: html, text
    Created UMassChIP-SeqSuper.html.
• src/hg/makeDb/trackDb/zebrafish/danRer5/UMassInput.html
  • lines changed 1, context: html, text, full: html, text
    Created UMassInput.html.
• src/hg/makeDb/trackDb/zebrafish/danRer5/UMassME1.html
  • lines changed 1, context: html, text, full: html, text
    Created UMassME1.html.
• src/hg/makeDb/trackDb/zebrafish/danRer5/UMassME1Hotspot.html
  • lines changed 1, context: html, text, full: html, text
    Created UMassME1Hotspot.html.
• src/hg/makeDb/trackDb/zebrafish/danRer5/UMassME1Peak.html
  • lines changed 1, context: html, text, full: html, text
    Created UMassME1Peak.html.
• src/hg/makeDb/trackDb/zebrafish/danRer5/UMassME3.html
  • lines changed 1, context: html, text, full: html, text
    Created UMassME3.html.
• src/hg/makeDb/trackDb/zebrafish/danRer5/UMassME3Hotspot.html
  • lines changed 1, context: html, text, full: html, text
    Created UMassME3Hotspot.html.
• src/hg/makeDb/trackDb/zebrafish/danRer5/UMassME3Peak.html
  • lines changed 1, context: html, text, full: html, text
    Created UMassME3Peak.html.
• src/hg/makeDb/trackDb/zebrafish/danRer5/trackDb.ra
  • lines changed 74, context: html, text, full: html, text
    Updated zebrafish/danRer5/trackDb.ra for U Mass ChIP-Seq tracks.
• src/hg/pslPretty/makefile
  • lines changed 1, context: html, text, full: html, text
    fix up makefiles to grok DESTDIR, add blat,gfServer, and gfClient to userApps #3152
• src/hg/pslReps/makefile
  • lines changed 1, context: html, text, full: html, text
    fix up makefiles to grok DESTDIR, add blat,gfServer, and gfClient to userApps #3152
• src/hg/pslSort/makefile
  • lines changed 1, context: html, text, full: html, text
    fix up makefiles to grok DESTDIR, add blat,gfServer, and gfClient to userApps #3152
• src/hg/qaPushQ/formPushQ.html
  • lines changed 2, context: html, text, full: html, text
    oops removing accidental duplicate of qid on edit form
• src/hg/regulate/regClusterTreeCells/regClusterTreeCells.c
  • lines changed 1, context: html, text, full: html, text
    Improving usage message.
• src/hg/regulate/regStartSampleEmbl/annotate.embl
  • lines changed 1512, context: html, text, full: html, text
    Saving file with hand annotations of genes in source tree.
• src/hg/utils/automation/gwUploadFile
  • lines changed 5, context: html, text, full: html, text
    correcting some of the later stderr outputs
• src/hg/utils/bedWeedOverlapping/bedWeedOverlapping.c
  • lines changed 1, context: html, text, full: html, text
    Fixing memory leak in bedWeedOverlapping.
• src/inc/basicBed.h
  • lines changed 4, context: html, text, full: html, text
    Adding utility to calculate average bigWig value for a bed file.
• src/inc/cheapcgi.h
  • lines changed 3, context: html, text, full: html, text
    adding server port to returnto string for genomewiki login
• src/inc/common.h
  • lines changed 6, context: html, text, full: html, text
    Added respect for quotes in a couple of places.
  • lines changed 1, context: html, text, full: html, text
    Little more robust handling of one case of respect quotes.
• src/inc/linefile.h
  • lines changed 2, context: html, text, full: html, text
    Code review feedback from Mark: use MayOpen naming convention, solineFileOnTabix -> lineFileTabixMayOpen. I still can't bring myself to remove the calls to warn, because I want the CGIs to get those using the webAbort error handlers in conjunction w/errCatch etc. There are tons of calls to warn() in our lib code, which can be redirected using the errAbort handler stack if desired.
• src/inc/net.h
  • lines changed 1, context: html, text, full: html, text
    fixing FTP UTC time converted to localtime for udc, removed 1 debug comment, expanded comment about ftp time being UTC
• src/inc/vcf.h
  • lines changed 1, context: html, text, full: html, text
    Fixing copy-paste misnomer found by Mark.
  • lines changed 50, context: html, text, full: html, text
    Feature #2822, #2823 (VCF customFactory + track handler):Added a new track type, vcfTabix, with handlers in hgTracks and hgc and a customFactory. It is a new bigDataUrl type of track; the remote VCF file must be compressed and indexed by tabix, so like BAM a separate index file is required. If the VCF file has genotypes, then each sample's two haplotypes are graphed in a line, with one line per sample. Otherwise, alleles and counts (if available) are drawn using Belinda's pgSnp methods. The source code has to be compiled with USE_TABIX=1 (which is automatically set for us by common.mk when it finds the local installation) in order for the CGIs to recognize the track type.
• src/lib/basicBed.c
  • lines changed 30, context: html, text, full: html, text
    Adding utility to calculate average bigWig value for a bed file.
• src/lib/cheapcgi.c
  • lines changed 6, context: html, text, full: html, text
    adding server port to returnto string for genomewiki login
  • lines changed 5, context: html, text, full: html, text
    a default of port 80 if it isn't defined
• src/lib/common.c
  • lines changed 39, context: html, text, full: html, text
    Added respect for quotes in a couple of places.
  • lines changed 7, context: html, text, full: html, text
    Little more robust handling of one case of respect quotes.
  • lines changed 5, context: html, text, full: html, text
    Fixed bug that Kate found.
• src/lib/linefile.c
  • lines changed 5, context: html, text, full: html, text
    Code review feedback from Mark: use MayOpen naming convention, solineFileOnTabix -> lineFileTabixMayOpen. I still can't bring myself to remove the calls to warn, because I want the CGIs to get those using the webAbort error handlers in conjunction w/errCatch etc. There are tons of calls to warn() in our lib code, which can be redirected using the errAbort handler stack if desired.
  • lines changed 2, context: html, text, full: html, text
    Feature #2822, #2823 (VCF customFactory + track handler):Added a new track type, vcfTabix, with handlers in hgTracks and hgc and a customFactory. It is a new bigDataUrl type of track; the remote VCF file must be compressed and indexed by tabix, so like BAM a separate index file is required. If the VCF file has genotypes, then each sample's two haplotypes are graphed in a line, with one line per sample. Otherwise, alleles and counts (if available) are drawn using Belinda's pgSnp methods. The source code has to be compiled with USE_TABIX=1 (which is automatically set for us by common.mk when it finds the local installation) in order for the CGIs to recognize the track type.
• src/lib/net.c
  • lines changed 96, context: html, text, full: html, text
    adding non-blocking tcp connect to deal with long several minutes default delay
  • lines changed 2, context: html, text, full: html, text
    fixing FTP UTC time converted to localtime for udc, removed 1 debug comment, expanded comment about ftp time being UTC
• src/lib/tests/expected/vcfParse1kGNoGenotypes.out
  • lines changed 1, context: html, text, full: html, text
    Tweak to vcfParseTest: better handling of ranges with 0 items;include the range in output message.
• src/lib/tests/expected/vcfParse1kGWithGenotypes.out
  • lines changed 1, context: html, text, full: html, text
    Tweak to vcfParseTest: better handling of ranges with 0 items;include the range in output message.
• src/lib/tests/expected/vcfParseOldV3.out
  • lines changed 44, context: html, text, full: html, text
    Feature #2822, #2823 (VCF customFactory + track handler):Added a new track type, vcfTabix, with handlers in hgTracks and hgc and a customFactory. It is a new bigDataUrl type of track; the remote VCF file must be compressed and indexed by tabix, so like BAM a separate index file is required. If the VCF file has genotypes, then each sample's two haplotypes are graphed in a line, with one line per sample. Otherwise, alleles and counts (if available) are drawn using Belinda's pgSnp methods. The source code has to be compiled with USE_TABIX=1 (which is automatically set for us by common.mk when it finds the local installation) in order for the CGIs to recognize the track type.
• src/lib/tests/input/20091110_pilot1_vcf_merged_call_sets_YRI.2and3_way.vcf.gz
  • lines changed 0, context: html, text, full: html, text
    Feature #2822, #2823 (VCF customFactory + track handler):Added a new track type, vcfTabix, with handlers in hgTracks and hgc and a customFactory. It is a new bigDataUrl type of track; the remote VCF file must be compressed and indexed by tabix, so like BAM a separate index file is required. If the VCF file has genotypes, then each sample's two haplotypes are graphed in a line, with one line per sample. Otherwise, alleles and counts (if available) are drawn using Belinda's pgSnp methods. The source code has to be compiled with USE_TABIX=1 (which is automatically set for us by common.mk when it finds the local installation) in order for the CGIs to recognize the track type.
• src/lib/tests/input/20091110_pilot1_vcf_merged_call_sets_YRI.2and3_way.vcf.gz.tbi
  • lines changed 0, context: html, text, full: html, text
    Feature #2822, #2823 (VCF customFactory + track handler):Added a new track type, vcfTabix, with handlers in hgTracks and hgc and a customFactory. It is a new bigDataUrl type of track; the remote VCF file must be compressed and indexed by tabix, so like BAM a separate index file is required. If the VCF file has genotypes, then each sample's two haplotypes are graphed in a line, with one line per sample. Otherwise, alleles and counts (if available) are drawn using Belinda's pgSnp methods. The source code has to be compiled with USE_TABIX=1 (which is automatically set for us by common.mk when it finds the local installation) in order for the CGIs to recognize the track type.
• src/lib/tests/makefile
  • lines changed 13, context: html, text, full: html, text
    Feature #2822, #2823 (VCF customFactory + track handler):Added a new track type, vcfTabix, with handlers in hgTracks and hgc and a customFactory. It is a new bigDataUrl type of track; the remote VCF file must be compressed and indexed by tabix, so like BAM a separate index file is required. If the VCF file has genotypes, then each sample's two haplotypes are graphed in a line, with one line per sample. Otherwise, alleles and counts (if available) are drawn using Belinda's pgSnp methods. The source code has to be compiled with USE_TABIX=1 (which is automatically set for us by common.mk when it finds the local installation) in order for the CGIs to recognize the track type.
• src/lib/tests/tabixFetch.c
  • lines changed 4, context: html, text, full: html, text
    Code review feedback from Mark: use MayOpen naming convention, solineFileOnTabix -> lineFileTabixMayOpen. I still can't bring myself to remove the calls to warn, because I want the CGIs to get those using the webAbort error handlers in conjunction w/errCatch etc. There are tons of calls to warn() in our lib code, which can be redirected using the errAbort handler stack if desired.
• src/lib/tests/vcfParseTest.c
  • lines changed 4, context: html, text, full: html, text
    Tweak to vcfParseTest: better handling of ranges with 0 items;include the range in output message.
  • lines changed 2, context: html, text, full: html, text
    Replacing atoi with sqlUnsigned as suggested by Mark.
  • lines changed 1, context: html, text, full: html, text
    Feature #2822, #2823 (VCF customFactory + track handler):Added a new track type, vcfTabix, with handlers in hgTracks and hgc and a customFactory. It is a new bigDataUrl type of track; the remote VCF file must be compressed and indexed by tabix, so like BAM a separate index file is required. If the VCF file has genotypes, then each sample's two haplotypes are graphed in a line, with one line per sample. Otherwise, alleles and counts (if available) are drawn using Belinda's pgSnp methods. The source code has to be compiled with USE_TABIX=1 (which is automatically set for us by common.mk when it finds the local installation) in order for the CGIs to recognize the track type.
• src/lib/udc.c
  • lines changed 11, context: html, text, full: html, text
    fixing FTP UTC time converted to localtime for udc, removed 1 debug comment, expanded comment about ftp time being UTC
  • lines changed 1, context: html, text, full: html, text
    fixed bug
• src/lib/vcf.c
  • lines changed 3, context: html, text, full: html, text
    Tweak to vcfParseTest: better handling of ranges with 0 items;include the range in output message.
  • lines changed 103, context: html, text, full: html, text
    Feature #2822, #2823 (VCF customFactory + track handler):Added a new track type, vcfTabix, with handlers in hgTracks and hgc and a customFactory. It is a new bigDataUrl type of track; the remote VCF file must be compressed and indexed by tabix, so like BAM a separate index file is required. If the VCF file has genotypes, then each sample's two haplotypes are graphed in a line, with one line per sample. Otherwise, alleles and counts (if available) are drawn using Belinda's pgSnp methods. The source code has to be compiled with USE_TABIX=1 (which is automatically set for us by common.mk when it finds the local installation) in order for the CGIs to recognize the track type.
• src/makefile
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    adding paraSync to utils built
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    fix up makefiles to grok DESTDIR, add blat,gfServer, and gfClient to userApps #3152
• src/utils/bedGeneParts/bedGeneParts.c
  • lines changed 156, context: html, text, full: html, text
    Utility to extract coordinates for promoters, introns, first exon of bed seems to work.
• src/utils/bedGeneParts/firstExon.expected
  • lines changed 9, context: html, text, full: html, text
    Utility to extract coordinates for promoters, introns, first exon of bed seems to work.
• src/utils/bedGeneParts/introns.expected
  • lines changed 7, context: html, text, full: html, text
    Utility to extract coordinates for promoters, introns, first exon of bed seems to work.
• src/utils/bedGeneParts/makefile
  • lines changed 26, context: html, text, full: html, text
    Utility to extract coordinates for promoters, introns, first exon of bed seems to work.
• src/utils/bedGeneParts/promoter.expected
  • lines changed 9, context: html, text, full: html, text
    Utility to extract coordinates for promoters, introns, first exon of bed seems to work.
• src/utils/bigWigAverageOverBed/bigWigAverageOverBed.c
  • lines changed 282, context: html, text, full: html, text
    Adding utility to calculate average bigWig value for a bed file.
• src/utils/bigWigAverageOverBed/makefile
  • lines changed 18, context: html, text, full: html, text
    Adding utility to calculate average bigWig value for a bed file.
• src/utils/bigWigMerge/bigWigMerge.c
  • lines changed 226, context: html, text, full: html, text
    Big wig merge utility seems to work.
  • lines changed 56, context: html, text, full: html, text
    Adding utility to calculate average bigWig value for a bed file.
• src/utils/bigWigMerge/makefile
  • lines changed 18, context: html, text, full: html, text
    Big wig merge utility seems to work.
• src/utils/colTransform/colTransform.c
  • lines changed 61, context: html, text, full: html, text
    Utility to add or multiply a column of a tab or space separated file by a constant seems to work.
• src/utils/colTransform/makefile
  • lines changed 18, context: html, text, full: html, text
    Utility to add or multiply a column of a tab or space separated file by a constant seems to work.
• src/utils/faPolyASizes/makefile
  • lines changed 2, context: html, text, full: html, text
    fix up makefiles to grok DESTDIR, add blat,gfServer, and gfClient to userApps #3152
• src/utils/qa/alertBqueue.csh
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    removed some old names from debug list
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 3, context: html, text, full: html, text
    v249 final build

• lines changed: 33944
• files changed: 267