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 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
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
- 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
- src/hg/lib/omimPhenotype.sql
- 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 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 20, context: html, text, full: html, text
Adding another cell line
- 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 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 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
- 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 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
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
- src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlLongRnaSeq.html
- 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
- 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
- src/utils/qa/alertBqueue.csh
- src/utils/qa/weeklybld/buildEnv.csh
- lines changed: 18292
- files changed: 269