All File Changes

v256_preview to v256_preview2 (2011-08-16 to 2011-08-23) v256

• python/lib/ucscgenomics/cvfile/CvFile.py
  • lines changed 1, context: html, text, full: html, text
    added commandline functionality to mkGeoPkg and trackInfo. also changed library files to now point at the correct package.
  • lines changed 76, context: html, text, full: html, text
    mkGeoPkg/trackInfo incremental update. cvValidate added duplicate key detection.
  • lines changed 220, context: html, text, full: html, text
    new release of cv validator
• python/lib/ucscgenomics/rafile/RaFile.py
  • lines changed 11, context: html, text, full: html, text
    temporary commit for adding additional bigWigs to cshllong
  • lines changed 1, context: html, text, full: html, text
    added commandline functionality to mkGeoPkg and trackInfo. also changed library files to now point at the correct package.
  • lines changed 15, context: html, text, full: html, text
    mkGeoPkg/trackInfo incremental update. cvValidate added duplicate key detection.
• python/lib/ucscgenomics/softfile/SoftFile.py
  • lines changed 2, context: html, text, full: html, text
    small but in soft file, work on mkGeoPkg for micro array submissions (still not functional) and added a readme
  • lines changed 1, context: html, text, full: html, text
    added commandline functionality to mkGeoPkg and trackInfo. also changed library files to now point at the correct package.
  • lines changed 2, context: html, text, full: html, text
    mkGeoPkg/trackInfo incremental update. cvValidate added duplicate key detection.
• python/programs/cvValidate/cvValidate
  • lines changed 1, context: html, text, full: html, text
    mkGeoPkg/trackInfo incremental update. cvValidate added duplicate key detection.
• python/programs/mkGeoPkg/README
  • lines changed 24, context: html, text, full: html, text
    small but in soft file, work on mkGeoPkg for micro array submissions (still not functional) and added a readme
• python/programs/mkGeoPkg/mkGeoPkg
  • lines changed 33, context: html, text, full: html, text
    small but in soft file, work on mkGeoPkg for micro array submissions (still not functional) and added a readme
  • lines changed 58, context: html, text, full: html, text
    temporary commit for adding additional bigWigs to cshllong
  • lines changed 66, context: html, text, full: html, text
    slight reworking in preparation for new module integration
  • lines changed 2, context: html, text, full: html, text
    temporary changes while switching branch
  • lines changed 154, context: html, text, full: html, text
    added commandline functionality to mkGeoPkg and trackInfo. also changed library files to now point at the correct package.
  • lines changed 77, context: html, text, full: html, text
    mkGeoPkg/trackInfo incremental update. cvValidate added duplicate key detection.
• python/programs/mkGeoPkg/trackInfo
  • lines changed 286, context: html, text, full: html, text
    small but in soft file, work on mkGeoPkg for micro array submissions (still not functional) and added a readme
  • lines changed 2, context: html, text, full: html, text
    fixed a minor bug in trackInfo
  • lines changed 2, context: html, text, full: html, text
    bugfix to trackInfo now displays missing files correctly
  • lines changed 0, context: html, text, full: html, text
    removed form feeds in trackInfo
  • lines changed 243, context: html, text, full: html, text
    added commandline functionality to mkGeoPkg and trackInfo. also changed library files to now point at the correct package.
  • lines changed 21, context: html, text, full: html, text
    mkGeoPkg/trackInfo incremental update. cvValidate added duplicate key detection.
• src/hg/encode/encodeMkFilesList/encodeMkFilesList
  • lines changed 1, context: html, text, full: html, text
    changed error message
  • lines changed 5, context: html, text, full: html, text
    changed how mkfiles generates list of files in directory by processing ls
  • lines changed 5, context: html, text, full: html, text
    decided to lock the shared variable just in case
• src/hg/encode/encodeMkGeoPkg/encodeAddGeoAccessions
  • lines changed 0, context: html, text, full: html, text
    small but in soft file, work on mkGeoPkg for micro array submissions (still not functional) and added a readme
• src/hg/encode/qaDateUnrestrictedCheck/makefile
  • lines changed 27, context: html, text, full: html, text
    added in first version of qaDateUnrestrictedCheck, no comments, basic usage statement, and functionality only. Referenced in redmine #4331
• src/hg/encode/qaDateUnrestrictedCheck/qaDateUnrestrictedCheck
  • lines changed 100, context: html, text, full: html, text
    added in first version of qaDateUnrestrictedCheck, no comments, basic usage statement, and functionality only. Referenced in redmine #4331
• src/hg/encode/validateFiles/validateFiles.c
  • lines changed 1, context: html, text, full: html, text
    Changes related to change source filenames around: bamUdc.ch -> bamFile.ch and bamFile.ch -> hgBam.ch
• src/hg/hgApi/hgApi.c
  • lines changed 5, context: html, text, full: html, text
    Added support for cv terms that are searchable='wildList'. This type of searching allows comma dilimied lists and '%' wild card.
• src/hg/hgGene/hgGene.c
  • lines changed 2, context: html, text, full: html, text
    Feature #4916 hgGene needs a "data last updated" line
• src/hg/hgHubConnect/hgHubConnect.c
  • lines changed 20, context: html, text, full: html, text
    various changes concerning the soft-reset button for #4815
  • lines changed 1, context: html, text, full: html, text
    cleaning up the library to remove a dependency on the cart that used to be necessary when private hubs were saved in the trash, rather than the hubStatus table. This fixes up an ifdef that Tim did to fix some bug with right-click in v255
  • lines changed 23, context: html, text, full: html, text
    check to see if hub is okay after adding a myHub #4679
  • lines changed 2, context: html, text, full: html, text
    add a note about the data not being QA'ed by UCSC #3260
  • lines changed 6, context: html, text, full: html, text
    add the ability to put the hgHubConnect contact email address in hg.conf (by request of the Lowe lab)
• src/hg/hgTables/asFilter.c
  • lines changed 2, context: html, text, full: html, text
    Feature #3707 (VCF+tabix support in hgTables):Basic hgTables support for VCF, modeled after BAM code. Tested all fields, selected fields, bed output; filter, intersection, schema on 3 flavors of vcfTabix: ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/release/20101123/interim_phase1_release/ALL.chr17.phase1.projectConsensus.genotypes.vcf.gz ftp://ftp-trace.ncbi.nlm.nih.gov/1000genomes/ftp/release/20100804/AFR.dindel.20100804.sites.vcf.gz ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606/VCF/v4.0/ByChromosomeNoGeno/00-All.vcf.gz
• src/hg/hgTables/asObj.c
  • lines changed 5, context: html, text, full: html, text
    Feature #3707 (VCF+tabix support in hgTables):Basic hgTables support for VCF, modeled after BAM code. Tested all fields, selected fields, bed output; filter, intersection, schema on 3 flavors of vcfTabix: ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/release/20101123/interim_phase1_release/ALL.chr17.phase1.projectConsensus.genotypes.vcf.gz ftp://ftp-trace.ncbi.nlm.nih.gov/1000genomes/ftp/release/20100804/AFR.dindel.20100804.sites.vcf.gz ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606/VCF/v4.0/ByChromosomeNoGeno/00-All.vcf.gz
• src/hg/hgTables/bam.c
  • lines changed 1, context: html, text, full: html, text
    Changes related to change source filenames around: bamUdc.ch -> bamFile.ch and bamFile.ch -> hgBam.ch
  • lines changed 19, context: html, text, full: html, text
    Feature #3707 (VCF+tabix support in hgTables):Basic hgTables support for VCF, modeled after BAM code. Tested all fields, selected fields, bed output; filter, intersection, schema on 3 flavors of vcfTabix: ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/release/20101123/interim_phase1_release/ALL.chr17.phase1.projectConsensus.genotypes.vcf.gz ftp://ftp-trace.ncbi.nlm.nih.gov/1000genomes/ftp/release/20100804/AFR.dindel.20100804.sites.vcf.gz ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606/VCF/v4.0/ByChromosomeNoGeno/00-All.vcf.gz
• src/hg/hgTables/bedList.c
  • lines changed 2, context: html, text, full: html, text
    Feature #3707 (VCF+tabix support in hgTables):Basic hgTables support for VCF, modeled after BAM code. Tested all fields, selected fields, bed output; filter, intersection, schema on 3 flavors of vcfTabix: ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/release/20101123/interim_phase1_release/ALL.chr17.phase1.projectConsensus.genotypes.vcf.gz ftp://ftp-trace.ncbi.nlm.nih.gov/1000genomes/ftp/release/20100804/AFR.dindel.20100804.sites.vcf.gz ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606/VCF/v4.0/ByChromosomeNoGeno/00-All.vcf.gz
• src/hg/hgTables/filterFields.c
  • lines changed 25, context: html, text, full: html, text
    Feature #3707 (VCF+tabix support in hgTables):Basic hgTables support for VCF, modeled after BAM code. Tested all fields, selected fields, bed output; filter, intersection, schema on 3 flavors of vcfTabix: ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/release/20101123/interim_phase1_release/ALL.chr17.phase1.projectConsensus.genotypes.vcf.gz ftp://ftp-trace.ncbi.nlm.nih.gov/1000genomes/ftp/release/20100804/AFR.dindel.20100804.sites.vcf.gz ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606/VCF/v4.0/ByChromosomeNoGeno/00-All.vcf.gz
• src/hg/hgTables/hgTables.c
  • lines changed 15, context: html, text, full: html, text
    Feature #3707 (VCF+tabix support in hgTables):Basic hgTables support for VCF, modeled after BAM code. Tested all fields, selected fields, bed output; filter, intersection, schema on 3 flavors of vcfTabix: ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/release/20101123/interim_phase1_release/ALL.chr17.phase1.projectConsensus.genotypes.vcf.gz ftp://ftp-trace.ncbi.nlm.nih.gov/1000genomes/ftp/release/20100804/AFR.dindel.20100804.sites.vcf.gz ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606/VCF/v4.0/ByChromosomeNoGeno/00-All.vcf.gz
• src/hg/hgTables/hgTables.h
  • lines changed 34, context: html, text, full: html, text
    Feature #3707 (VCF+tabix support in hgTables):Basic hgTables support for VCF, modeled after BAM code. Tested all fields, selected fields, bed output; filter, intersection, schema on 3 flavors of vcfTabix: ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/release/20101123/interim_phase1_release/ALL.chr17.phase1.projectConsensus.genotypes.vcf.gz ftp://ftp-trace.ncbi.nlm.nih.gov/1000genomes/ftp/release/20100804/AFR.dindel.20100804.sites.vcf.gz ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606/VCF/v4.0/ByChromosomeNoGeno/00-All.vcf.gz
• src/hg/hgTables/identifiers.c
  • lines changed 7, context: html, text, full: html, text
    Feature #3707 (VCF+tabix support in hgTables):Basic hgTables support for VCF, modeled after BAM code. Tested all fields, selected fields, bed output; filter, intersection, schema on 3 flavors of vcfTabix: ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/release/20101123/interim_phase1_release/ALL.chr17.phase1.projectConsensus.genotypes.vcf.gz ftp://ftp-trace.ncbi.nlm.nih.gov/1000genomes/ftp/release/20100804/AFR.dindel.20100804.sites.vcf.gz ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606/VCF/v4.0/ByChromosomeNoGeno/00-All.vcf.gz
• src/hg/hgTables/joining.c
  • lines changed 12, context: html, text, full: html, text
    Feature #3707 (VCF+tabix support in hgTables):Basic hgTables support for VCF, modeled after BAM code. Tested all fields, selected fields, bed output; filter, intersection, schema on 3 flavors of vcfTabix: ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/release/20101123/interim_phase1_release/ALL.chr17.phase1.projectConsensus.genotypes.vcf.gz ftp://ftp-trace.ncbi.nlm.nih.gov/1000genomes/ftp/release/20100804/AFR.dindel.20100804.sites.vcf.gz ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606/VCF/v4.0/ByChromosomeNoGeno/00-All.vcf.gz
• src/hg/hgTables/mainPage.c
  • lines changed 5, context: html, text, full: html, text
    Feature #3707 (VCF+tabix support in hgTables):Basic hgTables support for VCF, modeled after BAM code. Tested all fields, selected fields, bed output; filter, intersection, schema on 3 flavors of vcfTabix: ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/release/20101123/interim_phase1_release/ALL.chr17.phase1.projectConsensus.genotypes.vcf.gz ftp://ftp-trace.ncbi.nlm.nih.gov/1000genomes/ftp/release/20100804/AFR.dindel.20100804.sites.vcf.gz ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606/VCF/v4.0/ByChromosomeNoGeno/00-All.vcf.gz
• src/hg/hgTables/makefile
  • lines changed 1, context: html, text, full: html, text
    Feature #3707 (VCF+tabix support in hgTables):Basic hgTables support for VCF, modeled after BAM code. Tested all fields, selected fields, bed output; filter, intersection, schema on 3 flavors of vcfTabix: ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/release/20101123/interim_phase1_release/ALL.chr17.phase1.projectConsensus.genotypes.vcf.gz ftp://ftp-trace.ncbi.nlm.nih.gov/1000genomes/ftp/release/20100804/AFR.dindel.20100804.sites.vcf.gz ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606/VCF/v4.0/ByChromosomeNoGeno/00-All.vcf.gz
• src/hg/hgTables/schema.c
  • lines changed 4, context: html, text, full: html, text
    Feature #3707 (VCF+tabix support in hgTables):Basic hgTables support for VCF, modeled after BAM code. Tested all fields, selected fields, bed output; filter, intersection, schema on 3 flavors of vcfTabix: ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/release/20101123/interim_phase1_release/ALL.chr17.phase1.projectConsensus.genotypes.vcf.gz ftp://ftp-trace.ncbi.nlm.nih.gov/1000genomes/ftp/release/20100804/AFR.dindel.20100804.sites.vcf.gz ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606/VCF/v4.0/ByChromosomeNoGeno/00-All.vcf.gz
• src/hg/hgTables/vcf.c
  • lines changed 492, context: html, text, full: html, text
    Feature #3707 (VCF+tabix support in hgTables):Basic hgTables support for VCF, modeled after BAM code. Tested all fields, selected fields, bed output; filter, intersection, schema on 3 flavors of vcfTabix: ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/release/20101123/interim_phase1_release/ALL.chr17.phase1.projectConsensus.genotypes.vcf.gz ftp://ftp-trace.ncbi.nlm.nih.gov/1000genomes/ftp/release/20100804/AFR.dindel.20100804.sites.vcf.gz ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606/VCF/v4.0/ByChromosomeNoGeno/00-All.vcf.gz
• src/hg/hgTrackUi/hgTrackUi.c
  • lines changed 1, context: html, text, full: html, text
    cleaning up the library to remove a dependency on the cart that used to be necessary when private hubs were saved in the trash, rather than the hubStatus table. This fixes up an ifdef that Tim did to fix some bug with right-click in v255
• src/hg/hgTracks/bamTrack.c
  • lines changed 1, context: html, text, full: html, text
    Changes related to change source filenames around: bamUdc.ch -> bamFile.ch and bamFile.ch -> hgBam.ch
• src/hg/hgTracks/hgTracks.c
  • lines changed 19, context: html, text, full: html, text
    various changes concerning the soft-reset button for #4815
  • lines changed 5, context: html, text, full: html, text
    Code that is ifdef'd out for >1x dragScroll.
  • lines changed 3, context: html, text, full: html, text
    Larry and I have added page/image refresh when it is dirty. This is for solving the main back-button issue, where js/ajax changes to the image are lost when using back-button.
  • lines changed 1, context: html, text, full: html, text
    abandon attempt at in-place update when user hits back button b/c it wasn't restoring track order; use boolean type values in the dirty hidden
  • lines changed 5, context: html, text, full: html, text
    The reload on dirty page can be called earlier for FF and Chrome, but IE still relies upon the slower approach of full load then reload.
  • lines changed 23, context: html, text, full: html, text
    move excludeVars so it can be used in multiple CGIs
• src/hg/hgTracks/hgTracks.h
  • lines changed 3, context: html, text, full: html, text
    turn on SUPPORT_CONTENT_TYPE; unused in most trees (see redmine 4888)
• src/hg/hgTracks/imageV2.h
  • lines changed 6, context: html, text, full: html, text
    Code that is ifdef'd out for >1x dragScroll.
• src/hg/hgTracks/mainMain.c
  • lines changed 20, context: html, text, full: html, text
    move excludeVars so it can be used in multiple CGIs
• src/hg/hgTracks/makefile
  • lines changed 2, context: html, text, full: html, text
    Adding CFLAGS to hgTracks' linking.
• src/hg/hgTracks/renderMain.c
  • lines changed 22, context: html, text, full: html, text
    support call as a CGI using the cart (see redmine 4888)
• src/hg/hgTracks/simpleTracks.c
  • lines changed 9, context: html, text, full: html, text
    Code that is ifdef'd out for >1x dragScroll.
• src/hg/hgTracks/variation.c
  • lines changed 12, context: html, text, full: html, text
    Code that is ifdef'd out for >1x dragScroll.
• src/hg/hgTracks/vcfTrack.c
  • lines changed 5, context: html, text, full: html, text
    Feature #3711 (VCF haplotype sorting display): For now, limit the numberof variants on either side of the center variant to 20 instead of 50 -- I happened to land in a small region that had many variants that seemed to have no linkage whatsoever in 1000 Genomes phase 1 interim VCF, e.g. chr1:1,225,165-1,225,869 would take 42 seconds to cluster and draw! Limiting to 20 reduces that ~0.5s (also paired w/performance improvements, but it's mostly the number of distinct haplotypes that we pass into hacTreeFromItems). Also, a rounding overflow (transforming pixels to gtHapOrder index) was sporadically causing apache-only SEGVs; check that range! :)
• src/hg/hgc/bamClick.c
  • lines changed 2, context: html, text, full: html, text
    Changes related to change source filenames around: bamUdc.ch -> bamFile.ch and bamFile.ch -> hgBam.ch
• src/hg/hgc/hgc.c
  • lines changed 23, context: html, text, full: html, text
    now showing geneName from ensemblToGeneName table for ensGene items
  • lines changed 31, context: html, text, full: html, text
    now showing correctly protein coding vs not for Ensembl genes
  • lines changed 1, context: html, text, full: html, text
    correct casing on title
  • lines changed 1, context: html, text, full: html, text
    cleaning up the library to remove a dependency on the cart that used to be necessary when private hubs were saved in the trash, rather than the hubStatus table. This fixes up an ifdef that Tim did to fix some bug with right-click in v255
• src/hg/hgc/lowelab.c
  • lines changed 43, context: html, text, full: html, text
    change arCOG code to link to arCOGs browser instead of local table
  • lines changed 2, context: html, text, full: html, text
    Fixing compile-breaker: boolean TRUE and FALSE need to be uppercased.
• src/hg/htdocs/ENCODE/downloads.html
  • lines changed 10, context: html, text, full: html, text
    added HAIB Genotype, redmine #1708 and cleaned up some bad html
  • lines changed 160, context: html, text, full: html, text
    changed the indenting so it is easier to read and less prone to copy and paste errors
• src/hg/htdocs/ENCODE/downloadsMouse.html
  • lines changed 0, context: html, text, full: html, text
    changed the indenting so it is easier to read and less prone to copy and paste errors
• src/hg/htdocs/FAQ/FAQformat.html
  • lines changed 4, context: html, text, full: html, text
    fixing spelling errors in ENCODE data formats, redmine #4563
• src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html
  • lines changed 19, context: html, text, full: html, text
    Added # before color values to be html 4 compliant and fix display issue in FF/Win
  • lines changed 2, context: html, text, full: html, text
    made data plural
• src/hg/htdocs/style/HGStyle.css
  • lines changed 2, context: html, text, full: html, text
    added style deswignation to let us fix table borders in description pages that have looked rather ugly since the html 3->4 transition
• src/hg/htdocs/style/hgHubConnect.css
  • lines changed 2, context: html, text, full: html, text
    various changes concerning the soft-reset button for #4815
• src/hg/inc/bamFile.h
  • lines changed 52, context: html, text, full: html, text
    Changes related to change source filenames around: bamUdc.ch -> bamFile.ch and bamFile.ch -> hgBam.ch
• src/hg/inc/cv.h
  • lines changed 2, context: html, text, full: html, text
    Added support for cv terms that are searchable='wildList'. This type of searching allows comma dilimied lists and '%' wild card.
• src/hg/inc/hgBam.h
  • lines changed 53, context: html, text, full: html, text
    Changes related to change source filenames around: bamUdc.ch -> bamFile.ch and bamFile.ch -> hgBam.ch
  • lines changed 11, context: html, text, full: html, text
    removed open, fetch, exists functions to make way for removing udcFUSE stuff
  • lines changed 4, context: html, text, full: html, text
    More udcFUSE stripping but also forget to remove the bamOpen function which has been moved to src/inc/bamFile.h
• src/hg/inc/hubConnect.h
  • lines changed 7, context: html, text, full: html, text
    various changes concerning the soft-reset button for #4815
  • lines changed 7, context: html, text, full: html, text
    cleaning up the library to remove a dependency on the cart that used to be necessary when private hubs were saved in the trash, rather than the hubStatus table. This fixes up an ifdef that Tim did to fix some bug with right-click in v255
  • lines changed 2, context: html, text, full: html, text
    check to see if hub is okay after adding a myHub #4679
• src/hg/inc/hui.h
  • lines changed 2, context: html, text, full: html, text
    dateUnrestricted should no longer be calculated off of dateSubmitted. It should also no longer be seen in hgc or hgTables when it is in the past.
• src/hg/js/ajax.js
  • lines changed 9, context: html, text, full: html, text
    modify ajax error to encourage user to retry
• src/hg/js/hgTracks.js
  • lines changed 8, context: html, text, full: html, text
    hide contextmenu when initiating a drag-select or drag-scroll
  • lines changed 99, context: html, text, full: html, text
    Larry and I have added page/image refresh when it is dirty. This is for solving the main back-button issue, where js/ajax changes to the image are lost when using back-button.
  • lines changed 9, context: html, text, full: html, text
    abandon attempt at in-place update when user hits back button b/c it wasn't restoring track order; use boolean type values in the dirty hidden
  • lines changed 4, context: html, text, full: html, text
    working version of jQuery.jStore code (currently not-used, but we may use this in the future)
  • lines changed 2, context: html, text, full: html, text
    use markAsDirtyPage the the track group toggling code
  • lines changed 5, context: html, text, full: html, text
    add markAsDirtyPage calls when hiding tracks
  • lines changed 7, context: html, text, full: html, text
    comments about hgTracks object
  • lines changed 8, context: html, text, full: html, text
    For shift-dragZoom, switching the cursor to crosshair when shift key is down.
  • lines changed 1, context: html, text, full: html, text
    The reload on dirty page can be called earlier for FF and Chrome, but IE still relies upon the slower approach of full load then reload.
  • lines changed 6, context: html, text, full: html, text
    always call updateTiming in handleUpdateTrackMap (i.e. even when only updating a single track)
• src/hg/js/jquery.contextmenu.js
  • lines changed 2, context: html, text, full: html, text
    return new menu rather than the container from the constructor
• src/hg/js/jquery.jstore.js
  • lines changed 56, context: html, text, full: html, text
    plugin to allow local storage (see redmine 4952)
  • lines changed 1825, context: html, text, full: html, text
    add most recent version (downloaded from http://jquery-jstore.googlecode.com/svn-history/r38/trunk/src/jquery.jstore.js)
  • lines changed 1824, context: html, text, full: html, text
    backout new version because it was broken (had reference to undefined Class object)
• src/hg/js/utils.js
  • lines changed 2, context: html, text, full: html, text
    Added support for cv terms that are searchable='wildList'. This type of searching allows comma dilimied lists and '%' wild card.
• src/hg/lib/bamFile.c
  • lines changed 308, context: html, text, full: html, text
    Changes related to change source filenames around: bamUdc.ch -> bamFile.ch and bamFile.ch -> hgBam.ch
• src/hg/lib/customFactory.c
  • lines changed 1, context: html, text, full: html, text
    Changes related to change source filenames around: bamUdc.ch -> bamFile.ch and bamFile.ch -> hgBam.ch
  • lines changed 1, context: html, text, full: html, text
    Feature #3707 (VCF+tabix support in hgTables):Basic hgTables support for VCF, modeled after BAM code. Tested all fields, selected fields, bed output; filter, intersection, schema on 3 flavors of vcfTabix: ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/release/20101123/interim_phase1_release/ALL.chr17.phase1.projectConsensus.genotypes.vcf.gz ftp://ftp-trace.ncbi.nlm.nih.gov/1000genomes/ftp/release/20100804/AFR.dindel.20100804.sites.vcf.gz ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606/VCF/v4.0/ByChromosomeNoGeno/00-All.vcf.gz
• src/hg/lib/cv.c
  • lines changed 5, context: html, text, full: html, text
    Added support for cv terms that are searchable='wildList'. This type of searching allows comma dilimied lists and '%' wild card.
• src/hg/lib/hdb.c
  • lines changed 5, context: html, text, full: html, text
    cleaning up the library to remove a dependency on the cart that used to be necessary when private hubs were saved in the trash, rather than the hubStatus table. This fixes up an ifdef that Tim did to fix some bug with right-click in v255
• src/hg/lib/hgBam.c
  • lines changed 308, context: html, text, full: html, text
    Changes related to change source filenames around: bamUdc.ch -> bamFile.ch and bamFile.ch -> hgBam.ch
  • lines changed 40, context: html, text, full: html, text
    removed open, fetch, exists functions to make way for removing udcFUSE stuff
  • lines changed 2, context: html, text, full: html, text
    More udcFUSE stripping but also forget to remove the bamOpen function which has been moved to src/inc/bamFile.h
• src/hg/lib/hubConnect.c
  • lines changed 21, context: html, text, full: html, text
    various changes concerning the soft-reset button for #4815
  • lines changed 11, context: html, text, full: html, text
    cleaning up the library to remove a dependency on the cart that used to be necessary when private hubs were saved in the trash, rather than the hubStatus table. This fixes up an ifdef that Tim did to fix some bug with right-click in v255
  • lines changed 10, context: html, text, full: html, text
    check to see if hub is okay after adding a myHub #4679
• src/hg/lib/hui.c
  • lines changed 24, context: html, text, full: html, text
    dateUnrestricted should no longer be calculated off of dateSubmitted. It should also no longer be seen in hgc or hgTables when it is in the past.
  • lines changed 1, context: html, text, full: html, text
    Extra careful on that dateUnrestricted.
• src/hg/lib/makefile
  • lines changed 1, context: html, text, full: html, text
    Changes related to change source filenames around: bamUdc.ch -> bamFile.ch and bamFile.ch -> hgBam.ch
• src/hg/lib/mdb.c
  • lines changed 36, context: html, text, full: html, text
    Added support for cv terms that are searchable='wildList'. This type of searching allows comma dilimied lists and '%' wild card.
• src/hg/lib/omimAvRepl.sql
  • lines changed 1, context: html, text, full: html, text
    Added description col.
• src/hg/lib/omimPhenotype.sql
  • lines changed 1, context: html, text, full: html, text
    Corrected a typo.
• src/hg/lib/search.c
  • lines changed 12, context: html, text, full: html, text
    Added support for cv terms that are searchable='wildList'. This type of searching allows comma dilimied lists and '%' wild card.
• src/hg/lib/trackHub.c
  • lines changed 1, context: html, text, full: html, text
    Changes related to change source filenames around: bamUdc.ch -> bamFile.ch and bamFile.ch -> hgBam.ch
• src/hg/makeDb/doc/anoCar2.txt
  • lines changed 84, context: html, text, full: html, text
    added cpgIsland track per user request
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeSunyAlbanyGeneSt.release2.notes
  • lines changed 154, context: html, text, full: html, text
    updated notes for sydh tfbs release 1and added notes for gene ST release 2
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeSunyRipSeq.release1.notes
  • lines changed 75, context: html, text, full: html, text
    removed the double-slash
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeSydhTfbs.release1.notes
  • lines changed 1210, context: html, text, full: html, text
    updated notes for sydh tfbs release 1and added notes for gene ST release 2
• src/hg/makeDb/doc/hg19.txt
  • lines changed 81, context: html, text, full: html, text
    add the deCODE recomb lift over track from hg18
• src/hg/makeDb/doc/makeEnsembl.txt
  • lines changed 43, context: html, text, full: html, text
    add the susScr2 lift from susScr1
• src/hg/makeDb/doc/ucscGenes/hg19.ucscGenes13.csh
  • lines changed 9, context: html, text, full: html, text
    To address Redmine issue #411, created two new tables knownGeneTxMrna and knownGeneTxPep. These files contain respectively the mRNA sequence that would be produced by transcribing the exons in each UCSC Gene gene prediction, and translating those sequences. They differ from knownGeneMrna and knownGenePep in that those files contain copies of the RefSeq mRNA and RefPep protein for transcripts that are derived from RefSeq. These are verbatim copies of the sequence, including regions that don't align to the genome. This has led to confusion, including TCGA losing a fair bit of time in a mis-assumption that these sequences were direct transcripts of the gene predictions. So, to address the issue, we're adding direct transcripts of the gene predictions, and (still) looking for the appropriate place to document which sequences are which
  • lines changed 14, context: html, text, full: html, text
    Updated the proteins database referenced
• src/hg/makeDb/schema/all.joiner
  • lines changed 24, context: html, text, full: html, text
    adding ensemblToGeneName and ensemblSource tables to ensGene checks and all assemblies that have ensGene
  • lines changed 34, context: html, text, full: html, text
    proper list of wgs assemblies and all new Ensembl gene definitions
  • lines changed 1, context: html, text, full: html, text
    adding susScr2 for ensGene
• src/hg/makeDb/trackDb/chimp/panTro2/trackDb.chainNet.ra
  • lines changed 3, context: html, text, full: html, text
    added an override to override the top level override that was makeing the chain values in panTro2 show incorrectly
• src/hg/makeDb/trackDb/chimp/panTro3/cons12way.html
  • lines changed 24, context: html, text, full: html, text
    Corrected the funky table borders using css. Corrected phylogenetic order of species in two places.
  • lines changed 6, context: html, text, full: html, text
    Corrected list of species to be shown by default according to communication from Jim. Will also be update trackDb to reflect this.
• src/hg/makeDb/trackDb/chimp/panTro3/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    Added default off line per Jim's request for these 3 species to not show on default.
  • lines changed 2, context: html, text, full: html, text
    changed order of species so that they appear in correct phylo order in track controls
• src/hg/makeDb/trackDb/cv/alpha/cv.ra
  • lines changed 12, context: html, text, full: html, text
    It turns out that there were several cases of duplicate tags, i.e. two distinct stanzas with the same tag, and the validator wasn't catching this. Just resolved the duplicate tags
  • lines changed 10, context: html, text, full: html, text
    (1) Removed a comment indicating that two cell lines have the same tag, when this problem was fixed last week and the two cell lines no longer have the same tag. (2) Accepted several provisional view stanzas. (3) Accepted a provisional change on the t-rex cell line
  • lines changed 2, context: html, text, full: html, text
    Fixed vendorId for Colo829 and Ishikawa
  • lines changed 2, context: html, text, full: html, text
    Added vendor names
  • lines changed 1, context: html, text, full: html, text
    Changed Blood to Lymphatic for the HMVEC-dLy-Ad line, ly means Lymphatic and Bl means Blood
  • lines changed 1, context: html, text, full: html, text
    changed tags for pbdefetal from PBDEF to PBDEFETAL
  • lines changed 61, context: html, text, full: html, text
    Adding cell lines
  • lines changed 20, context: html, text, full: html, text
    Adding another cell line
  • lines changed 16, context: html, text, full: html, text
    Adding derivedFrom term
  • lines changed 3, context: html, text, full: html, text
    Expanded FSHD description and Added crossrefsfor NH-A and Astrocy in description
  • lines changed 1, context: html, text, full: html, text
    Noting partial shared donor of PanIslets and PanIsletD
  • lines changed 1, context: html, text, full: html, text
    Adding NHBERA protocol
  • lines changed 29, context: html, text, full: html, text
    Fixes to antibody registration
  • lines changed 32, context: html, text, full: html, text
    More fixes for antibodies
  • lines changed 2, context: html, text, full: html, text
    Adding validation doc type
  • lines changed 2, context: html, text, full: html, text
    Adding more validation details
  • lines changed 2, context: html, text, full: html, text
    Changing the regEx for md5sum to accept bai
  • lines changed 2, context: html, text, full: html, text
    Final changes to get a clean validate of the mdb, changed the regEx for md5sum, dropped ripTgtProtein, changed DIFF_7d to Myocyte
  • lines changed 4, context: html, text, full: html, text
    Merge branch 'cvQA'
  • lines changed 14, context: html, text, full: html, text
    Accepted provisional changes
  • lines changed 45, context: html, text, full: html, text
    Fixing carriage returns and commenting out antibodies without validation
  • lines changed 60, context: html, text, full: html, text
    Adding antibodies back in- documentation not required for mouse
  • lines changed 8, context: html, text, full: html, text
    Added support for cv terms that are searchable='wildList'. This type of searching allows comma dilimied lists and '%' wild card.
• src/hg/makeDb/trackDb/cv/beta/cv.ra
  • lines changed 74, context: html, text, full: html, text
    Copied cvMaven branch changes into the beta cvQA branch on beta. What should be different is that some tags have been modified so that all tags are unique
• src/hg/makeDb/trackDb/human/decode.rmap.ra
  • lines changed 165, context: html, text, full: html, text
    moving deCODE Recomb up one level to get both hg18 and hg19 in one definition
  • lines changed 1, context: html, text, full: html, text
    adjust color for female track
• src/hg/makeDb/trackDb/human/decodeRmap.html
  • lines changed 46, context: html, text, full: html, text
    moving deCODE Recomb up one level to get both hg18 and hg19 in one definition
• src/hg/makeDb/trackDb/human/hg18/decode.rmap.ra
  • lines changed 164, context: html, text, full: html, text
    moving deCODE Recomb up one level to get both hg18 and hg19 in one definition
• src/hg/makeDb/trackDb/human/hg18/decodeRmap.html
  • lines changed 46, context: html, text, full: html, text
    moving deCODE Recomb up one level to get both hg18 and hg19 in one definition
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeChromatinMap.ra
  • lines changed 9, context: html, text, full: html, text
    revoked colliding files
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeRikenCage.ra
  • lines changed 9, context: html, text, full: html, text
    Removing RawData3 and ripTgtProtien, the information was redundant and is giving errors for the validator
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeSunyalbanyRnaGeneChip.ra
  • lines changed 8, context: html, text, full: html, text
    Removing RawData3 and ripTgtProtien, the information was redundant and is giving errors for the validator
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeYaleChIPseq.ra
  • lines changed 127, context: html, text, full: html, text
    made the K562b to K62 transition
• src/hg/makeDb/trackDb/human/hg18/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    moving deCODE Recomb up one level to get both hg18 and hg19 in one definition
• src/hg/makeDb/trackDb/human/hg18/wgEncodeHudsonalphaMethyl27.html
  • lines changed 2, context: html, text, full: html, text
    fixing broken link, redmine #5020
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeBroadHistone.ra
  • lines changed 74, context: html, text, full: html, text
    last time I changed date unrestricteds, i didnt change alpha again after the revert. so I'm doing it now, so when release 2 comes along, we don't have weirdo metadata inconsistencies
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCaltechRnaSeq.ra
  • lines changed 13, context: html, text, full: html, text
    Final changes to get a clean validate of the mdb, changed the regEx for md5sum, dropped ripTgtProtein, changed DIFF_7d to Myocyte
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGencodeV3.ra
  • lines changed 4, context: html, text, full: html, text
    added md5sums
  • lines changed 7, context: html, text, full: html, text
    added dcc accession and expId
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGisRnaPet.ra
  • lines changed 207, context: html, text, full: html, text
    Added seqPlatform, changed some resubmission dates and subIds, swapped two labExpIds
  • lines changed 10, context: html, text, full: html, text
    Changeing long label errors and bed12 to bed
  • lines changed 25, context: html, text, full: html, text
    added expids and dcc accessions
  • lines changed 247, context: html, text, full: html, text
    changed date unrestricted and date submitted for items in hg18 and hg19
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSunyAlbanyGeneSt.ra
  • lines changed 169, context: html, text, full: html, text
    converted the whole shebang to V2
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSunyAlbanyTiling.ra
  • lines changed 9, context: html, text, full: html, text
    Final changes to get a clean validate of the mdb, changed the regEx for md5sum, dropped ripTgtProtein, changed DIFF_7d to Myocyte
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSunySwitchgear.ra
  • lines changed 3, context: html, text, full: html, text
    Final changes to get a clean validate of the mdb, changed the regEx for md5sum, dropped ripTgtProtein, changed DIFF_7d to Myocyte
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhTfbs.ra
  • lines changed 37, context: html, text, full: html, text
    added in missing expId's and accessions for uw and sydh tfbs
  • lines changed 19, context: html, text, full: html, text
    forgot to change the actual values in metaDb
  • lines changed 32, context: html, text, full: html, text
    fixed some control errros ans revoked md5sum colliding files
  • lines changed 3, context: html, text, full: html, text
    revoked an experiment's views for which both alignment replicates were bad
  • lines changed 25, context: html, text, full: html, text
    revoked all objects for colliding experiments
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUncBsuProt.ra
  • lines changed 75, context: html, text, full: html, text
    loaded last 4 submission for unc bsu prot
  • lines changed 5, context: html, text, full: html, text
    added in md5sums for new files
  • lines changed 78, context: html, text, full: html, text
    removed lines for mistakenly added entries from metaDb
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwHistone.ra
  • lines changed 149, context: html, text, full: html, text
    added in missing expId's and accessions for uw and sydh tfbs
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwTfbs.ra
  • lines changed 329, context: html, text, full: html, text
    added in missing expId's and accessions for uw and sydh tfbs
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/makefile
  • lines changed 1, context: html, text, full: html, text
    staging SUNY Rip-seq on hgwbeta, redmine #1708
  • lines changed 1, context: html, text, full: html, text
    staging track on beta, redmine #141
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeSunyRipSeq.ra
  • lines changed 1158, context: html, text, full: html, text
    staging SUNY Rip-seq on hgwbeta, redmine #1708
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeUncBsuProt.ra
  • lines changed 224, context: html, text, full: html, text
    staging track on beta, redmine #141
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/makefile
  • lines changed 1, context: html, text, full: html, text
    releasing HAIB Genotype, redmine #1708
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeBroadHistone.ra
  • lines changed 77, context: html, text, full: html, text
    releasing metadata changes to dateUnrestricted because of publication
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeHaibGenotype.ra
  • lines changed 2207, context: html, text, full: html, text
    releasing HAIB Genotype, redmine #1708
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 3, context: html, text, full: html, text
    add pennantIcon for hg18 to decodeRmap
• src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra
  • lines changed 2, context: html, text, full: html, text
    started release2 for unc bsu prot
  • lines changed 1, context: html, text, full: html, text
    error in typing t>d
  • lines changed 1, context: html, text, full: html, text
    staging SUNY Rip-seq on hgwbeta, redmine #1708
  • lines changed 2, context: html, text, full: html, text
    reversed release 2 changes
  • lines changed 2, context: html, text, full: html, text
    changes for suny genest in trackDb for V2ness
  • lines changed 1, context: html, text, full: html, text
    fixed spelling error
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlLongRnaSeq.html
  • lines changed 1, context: html, text, full: html, text
    Changed a url
  • lines changed 6, context: html, text, full: html, text
    Fixing Jacobs issues in track 43 note 40, adding html text, setting to dense
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlLongRnaSeq.ra
  • lines changed 2, context: html, text, full: html, text
    Fixing Jacobs issues in track 43 note 40, adding html text, setting to dense
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV3.html
  • lines changed 4, context: html, text, full: html, text
    added ftp link to gencove v3
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGisRnaPet.ra
  • lines changed 6, context: html, text, full: html, text
    Changeing long label errors and bed12 to bed
  • lines changed 1, context: html, text, full: html, text
    hadn't meant to check in that file, I fixed an errant e in cloneed so that it would make
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethylRrbs.new.ra
  • lines changed 6, context: html, text, full: html, text
    Added a track back in, Rep 3 HSMM
• src/hg/makeDb/trackDb/human/hg19/wgEncodeProtGenoSuper.html
  • lines changed 1, context: html, text, full: html, text
    Renamed the display heading as indicated by Jacob
  • lines changed 10, context: html, text, full: html, text
    Addressing pre-QA feedback from Redmine ticket # 4944, issue # 4
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSunyAlbanyGeneSt.new.ra
  • lines changed 278, context: html, text, full: html, text
    changes for suny genest in trackDb for V2ness
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSuper.ra
  • lines changed 7, context: html, text, full: html, text
    Added the proteogenomics supertrack
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUncBsuProt.html
  • lines changed 3, context: html, text, full: html, text
    loaded last 4 submission for unc bsu prot
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUncBsuProt.new.ra
  • lines changed 99, context: html, text, full: html, text
    started release2 for unc bsu prot
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUncBsuProt.ra
  • lines changed 21, context: html, text, full: html, text
    loaded last 4 submission for unc bsu prot
  • lines changed 19, context: html, text, full: html, text
    moved release2 stuff into release 1
  • lines changed 1, context: html, text, full: html, text
    fixing composite longLabel, redmine #141
• src/hg/makeDb/trackDb/human/omimGene2.html
  • lines changed 2, context: html, text, full: html, text
    Updated table name from mim2gene to omim2gene.
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    moving deCODE Recomb up one level to get both hg18 and hg19 in one definition
• src/hg/protein/pbCalDist/pbCalDist.c
  • lines changed 1, context: html, text, full: html, text
    Added amino acids U (selenocysteine), O (pyrrolysine) and J (leucine OR isoleucine)
  • lines changed 3, context: html, text, full: html, text
    (1) In response to loads of warning messages that U is an invalid amino acid, when actually it's not, I updated the expected amino acid alphabet in many places. I added U (selenocysteine), O (pyrrolysine) and J (a wildcard indicating either leucine or isoleucine). In many places, I replaced a hardcoded amino acid alphabet size with the strlen of the string of expected amino acids. And in one place, I replaced a hardcoded protein database name with a command line argument, and changed the UCSC Genes script accordingly
• src/hg/protein/pbCalDistGlobal/pbCalDistGlobal.c
  • lines changed 4, context: html, text, full: html, text
    (1) In response to loads of warning messages that U is an invalid amino acid, when actually it's not, I updated the expected amino acid alphabet in many places. I added U (selenocysteine), O (pyrrolysine) and J (a wildcard indicating either leucine or isoleucine). In many places, I replaced a hardcoded amino acid alphabet size with the strlen of the string of expected amino acids. And in one place, I replaced a hardcoded protein database name with a command line argument, and changed the UCSC Genes script accordingly
• src/hg/protein/pbCalResStd/pbCalResStd.c
  • lines changed 14, context: html, text, full: html, text
    (1) In response to loads of warning messages that U is an invalid amino acid, when actually it's not, I updated the expected amino acid alphabet in many places. I added U (selenocysteine), O (pyrrolysine) and J (a wildcard indicating either leucine or isoleucine). In many places, I replaced a hardcoded amino acid alphabet size with the strlen of the string of expected amino acids. And in one place, I replaced a hardcoded protein database name with a command line argument, and changed the UCSC Genes script accordingly
• src/hg/protein/pbCalResStdGlobal/pbCalResStdGlobal.c
  • lines changed 3, context: html, text, full: html, text
    (1) In response to loads of warning messages that U is an invalid amino acid, when actually it's not, I updated the expected amino acid alphabet in many places. I added U (selenocysteine), O (pyrrolysine) and J (a wildcard indicating either leucine or isoleucine). In many places, I replaced a hardcoded amino acid alphabet size with the strlen of the string of expected amino acids. And in one place, I replaced a hardcoded protein database name with a command line argument, and changed the UCSC Genes script accordingly
• src/hg/protein/pbGlobal/pbGlobal.c
  • lines changed 1, context: html, text, full: html, text
    (1) In response to loads of warning messages that U is an invalid amino acid, when actually it's not, I updated the expected amino acid alphabet in many places. I added U (selenocysteine), O (pyrrolysine) and J (a wildcard indicating either leucine or isoleucine). In many places, I replaced a hardcoded amino acid alphabet size with the strlen of the string of expected amino acids. And in one place, I replaced a hardcoded protein database name with a command line argument, and changed the UCSC Genes script accordingly
• src/hg/protein/pbTracks/pbTracks.c
  • lines changed 1, context: html, text, full: html, text
    (1) In response to loads of warning messages that U is an invalid amino acid, when actually it's not, I updated the expected amino acid alphabet in many places. I added U (selenocysteine), O (pyrrolysine) and J (a wildcard indicating either leucine or isoleucine). In many places, I replaced a hardcoded amino acid alphabet size with the strlen of the string of expected amino acids. And in one place, I replaced a hardcoded protein database name with a command line argument, and changed the UCSC Genes script accordingly
• src/hg/txGene/txGeneProtAndRna/txGeneProtAndRna.c
  • lines changed 31, context: html, text, full: html, text
    To address Redmine issue #411, created two new tables knownGeneTxMrna and knownGeneTxPep. These files contain respectively the mRNA sequence that would be produced by transcribing the exons in each UCSC Gene gene prediction, and translating those sequences. They differ from knownGeneMrna and knownGenePep in that those files contain copies of the RefSeq mRNA and RefPep protein for transcripts that are derived from RefSeq. These are verbatim copies of the sequence, including regions that don't align to the genome. This has led to confusion, including TCGA losing a fair bit of time in a mis-assumption that these sequences were direct transcripts of the gene predictions. So, to address the issue, we're adding direct transcripts of the gene predictions, and (still) looking for the appropriate place to document which sequences are which
  • lines changed 2, context: html, text, full: html, text
    Initializing repProtSeq
• src/hg/txGene/txGeneXref/txGeneXref.c
  • lines changed 40, context: html, text, full: html, text
    Addressed Redmine Bug # 2712, which concerns entries in the kgXref table for which the gene symbol and the description are inconsistent. This bug occurs when the gene symbol and the description are being pulled out of the genbank records for the sequences used as evidence (i.e. when there's no RefSeq record to rely on). It happens because the gene symbol and description are derived from separate queries, which are periodically inconsistent. To resolve this, I added some logic to the code to first try to get the gene symbol AND description from GenBank records that have both; failing that, get the gene symbol, and get the GenBank record separately
• src/hg/utils/automation/doEnsGeneUpdate.pl
  • lines changed 6, context: html, text, full: html, text
    add in the business to create the ensemblToGeneName translation table
  • lines changed 5, context: html, text, full: html, text
    now adding ensemblSource table for coding status
• src/hg/utils/automation/ensemblInfo.pl
  • lines changed 62, context: html, text, full: html, text
    now adding ensemblSource table for coding status
• src/hg/utils/automation/ensemblToGeneName.pl
  • lines changed 52, context: html, text, full: html, text
    initial contents to transform infoOut.txt to ensemblToGeneName.tab reference
  • lines changed 52, context: html, text, full: html, text
    has become the generic ensemblInfo.pl
• src/hg/utils/automation/makefile
  • lines changed 1, context: html, text, full: html, text
    adding ensemblToGeneName.pl to the scripts list
  • lines changed 1, context: html, text, full: html, text
    ensemblToGeneName becomes the generic ensemblInfo
• src/inc/bamFile.h
  • lines changed 132, context: html, text, full: html, text
    Changes related to change source filenames around: bamUdc.ch -> bamFile.ch and bamFile.ch -> hgBam.ch
  • lines changed 4, context: html, text, full: html, text
    deleted anything udcFUSE-related
  • lines changed 8, context: html, text, full: html, text
    made a spinoff function of bamFetch() that also handles an already-open bam file/index for cases where fetch is done within a loop
  • lines changed 11, context: html, text, full: html, text
    Fix for compiling without USE_BAM: bamFile.h needs to define bam_index_t.
• src/inc/bamUdc.h
  • lines changed 132, context: html, text, full: html, text
    Changes related to change source filenames around: bamUdc.ch -> bamFile.ch and bamFile.ch -> hgBam.ch
• src/inc/common.mk
  • lines changed 2, context: html, text, full: html, text
    If environment variable CFLAGS is set, don't override it in common.mk. Now we can compile and link for gprof using CFLAGS=-pg.
• src/inc/vcf.h
  • lines changed 1, context: html, text, full: html, text
    Feature #3707 (VCF+tabix support in hgTables):Basic hgTables support for VCF, modeled after BAM code. Tested all fields, selected fields, bed output; filter, intersection, schema on 3 flavors of vcfTabix: ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/release/20101123/interim_phase1_release/ALL.chr17.phase1.projectConsensus.genotypes.vcf.gz ftp://ftp-trace.ncbi.nlm.nih.gov/1000genomes/ftp/release/20100804/AFR.dindel.20100804.sites.vcf.gz ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606/VCF/v4.0/ByChromosomeNoGeno/00-All.vcf.gz
• src/lib/bamFile.c
  • lines changed 693, context: html, text, full: html, text
    Changes related to change source filenames around: bamUdc.ch -> bamFile.ch and bamFile.ch -> hgBam.ch
  • lines changed 116, context: html, text, full: html, text
    deleted anything udcFUSE-related
  • lines changed 29, context: html, text, full: html, text
    made a spinoff function of bamFetch() that also handles an already-open bam file/index for cases where fetch is done within a loop
• src/lib/bamUdc.c
  • lines changed 693, context: html, text, full: html, text
    Changes related to change source filenames around: bamUdc.ch -> bamFile.ch and bamFile.ch -> hgBam.ch
• src/lib/hacTree.c
  • lines changed 24, context: html, text, full: html, text
    Feature #3711 (VCF haplotype sorting display): Performance improvements.1. lib/hacTree.c: instead of doing a zillion incremental memcpy's to drop nodes, build up a set of nodes to delete and then do the minimal memmove's afterwards. Use memmove per memcpy's man page, which says not to use memcpy if regions overlap! 2. lib/vcf.c: avoid unnecessary calls to vcfFilePooledStr from inner loops. Also, if ref is all nucleotides (not symbolic as for SV's), use it to set chromEnd. It may still be overwritten if the END keyword is used in the info column.
• src/lib/makefile
  • lines changed 1, context: html, text, full: html, text
    Changes related to change source filenames around: bamUdc.ch -> bamFile.ch and bamFile.ch -> hgBam.ch
• src/lib/tests/expected/hacTreeTest.out
  • lines changed 55, context: html, text, full: html, text
    Oops, forgot that one of my changes to hacTree (when merging root intoa node, preserve the order of its kids -- was inadvertently swapping left kid to right when merging right kid) would require a change to the expected output file. It's just an internal reordering in the tree, doesn't change levels.
• src/lib/vcf.c
  • lines changed 20, context: html, text, full: html, text
    Feature #3711 (VCF haplotype sorting display): Performance improvements.1. lib/hacTree.c: instead of doing a zillion incremental memcpy's to drop nodes, build up a set of nodes to delete and then do the minimal memmove's afterwards. Use memmove per memcpy's man page, which says not to use memcpy if regions overlap! 2. lib/vcf.c: avoid unnecessary calls to vcfFilePooledStr from inner loops. Also, if ref is all nucleotides (not symbolic as for SV's), use it to set chromEnd. It may still be overwritten if the END keyword is used in the info column.
  • lines changed 1, context: html, text, full: html, text
    Sheesh, forgot a .h file for last-minute tweak. At least I haven't pushed yet! :)
  • lines changed 13, context: html, text, full: html, text
    Feature #3707 (VCF+tabix support in hgTables):Basic hgTables support for VCF, modeled after BAM code. Tested all fields, selected fields, bed output; filter, intersection, schema on 3 flavors of vcfTabix: ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/release/20101123/interim_phase1_release/ALL.chr17.phase1.projectConsensus.genotypes.vcf.gz ftp://ftp-trace.ncbi.nlm.nih.gov/1000genomes/ftp/release/20100804/AFR.dindel.20100804.sites.vcf.gz ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606/VCF/v4.0/ByChromosomeNoGeno/00-All.vcf.gz
• src/product/ex.hg.conf
  • lines changed 6, context: html, text, full: html, text
    add the ability to put the hgHubConnect contact email address in hg.conf (by request of the Lowe lab)
• src/utils/omim/buildOmimTracks.csh
  • lines changed 167, context: html, text, full: html, text
    Created buildOmimTracks.csh
• src/utils/omim/checkOmim.sh
  • lines changed 129, context: html, text, full: html, text
    Created checkOmim.sh
• src/utils/qa/alertBqueue.csh
  • lines changed 2, context: html, text, full: html, text
    removed redundant line
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    v256 preview2

• lines changed: 18292
• files changed: 269