All File Changes
v296_base to v297_preview (2014-02-24 to 2014-03-03) v297
- src/hg/encode3/encodeDataWarehouse/oneShot/edwFakeEncode2Submit/hg19_encode2_date.tab
- lines changed 20834, context: html, text, full: html, text
eplaced hg19_encode2_date.tab and mm9_encode2_date.tab with hg19_encode2_meta.tab and mm9_encode2_meta.tab.Added hg19_group_lab.tab and mm9_group_lab.tab which
is column 6 and column 2 extracted from the meta.lab files.
- src/hg/encode3/encodeDataWarehouse/oneShot/edwFakeEncode2Submit/hg19_encode2_meta.tab
- lines changed 20785, context: html, text, full: html, text
eplaced hg19_encode2_date.tab and mm9_encode2_date.tab with hg19_encode2_meta.tab and mm9_encode2_meta.tab.Added hg19_group_lab.tab and mm9_group_lab.tab which
is column 6 and column 2 extracted from the meta.lab files.
- src/hg/encode3/encodeDataWarehouse/oneShot/edwFakeEncode2Submit/hg19_group_lab.tab
- lines changed 70, context: html, text, full: html, text
eplaced hg19_encode2_date.tab and mm9_encode2_date.tab with hg19_encode2_meta.tab and mm9_encode2_meta.tab.Added hg19_group_lab.tab and mm9_group_lab.tab which
is column 6 and column 2 extracted from the meta.lab files.
- src/hg/encode3/encodeDataWarehouse/oneShot/edwFakeEncode2Submit/mm9_encode2_date.tab
- lines changed 4696, context: html, text, full: html, text
eplaced hg19_encode2_date.tab and mm9_encode2_date.tab with hg19_encode2_meta.tab and mm9_encode2_meta.tab.Added hg19_group_lab.tab and mm9_group_lab.tab which
is column 6 and column 2 extracted from the meta.lab files.
- src/hg/encode3/encodeDataWarehouse/oneShot/edwFakeEncode2Submit/mm9_encode2_meta.tab
- lines changed 4677, context: html, text, full: html, text
eplaced hg19_encode2_date.tab and mm9_encode2_date.tab with hg19_encode2_meta.tab and mm9_encode2_meta.tab.Added hg19_group_lab.tab and mm9_group_lab.tab which
is column 6 and column 2 extracted from the meta.lab files.
- src/hg/encode3/encodeDataWarehouse/oneShot/edwFakeEncode2Submit/mm9_group_lab.tab
- lines changed 22, context: html, text, full: html, text
eplaced hg19_encode2_date.tab and mm9_encode2_date.tab with hg19_encode2_meta.tab and mm9_encode2_meta.tab.Added hg19_group_lab.tab and mm9_group_lab.tab which
is column 6 and column 2 extracted from the meta.lab files.
- src/hg/encode3/validateManifest/VERSION.TXT
- lines changed 2, context: html, text, full: html, text
adding support for phage phiX174 to bam validation by adding the sequence to the chrom.sizes and hg19.2bit that are in the encode3 vm package
- src/hg/hgMirror/hgMirror
- lines changed 1, context: html, text, full: html, text
only showing active assemblies in hgMirror, refs #11957
- lines changed 1, context: html, text, full: html, text
adding description html to default mirror files, refs #11957
- lines changed 5, context: html, text, full: html, text
grey out checkboxes if table is already downloaded, refs #11957, note 161
- lines changed 4, context: html, text, full: html, text
fixing missing var, refs #11957
- lines changed 12, context: html, text, full: html, text
better greying out, refs #11957
- src/hg/hgTables/gffOut.c
- lines changed 16, context: html, text, full: html, text
Fixes #12737. Had to be more careful about custom tracks and hubs etc. This should now work on a wide variety of file types
- src/hg/hgTables/hgTables.h
- lines changed 3, context: html, text, full: html, text
Fixing a couple bugs uncovered by MLQ #12777: first, the intersectionbutton was appearing even for tables that don't pass canIntersect().
Second, canIntersect() was returning false for VCF instead of true.
So the intersect button appeared for VCF tracks, but the user's
intersection settings were ignored. Now intersection works for VCF.
refs #12777
- src/hg/hgTables/intersect.c
- lines changed 3, context: html, text, full: html, text
Fixing a couple bugs uncovered by MLQ #12777: first, the intersectionbutton was appearing even for tables that don't pass canIntersect().
Second, canIntersect() was returning false for VCF instead of true.
So the intersect button appeared for VCF tracks, but the user's
intersection settings were ignored. Now intersection works for VCF.
refs #12777
- src/hg/hgTables/mainPage.c
- lines changed 1, context: html, text, full: html, text
Fixing a couple bugs uncovered by MLQ #12777: first, the intersectionbutton was appearing even for tables that don't pass canIntersect().
Second, canIntersect() was returning false for VCF instead of true.
So the intersect button appeared for VCF tracks, but the user's
intersection settings were ignored. Now intersection works for VCF.
refs #12777
- src/hg/hgTracks/hgTracks.c
- lines changed 2, context: html, text, full: html, text
patch to fix build on OSX which has no malloc.h refs #12656
- src/hg/htdocs/goldenPath/help/oligoMatch.html
- lines changed 2, context: html, text, full: html, text
Fixed spacing error (redmine #11681)
- src/hg/htdocs/goldenPath/newsarch.html
- lines changed 21, context: html, text, full: html, text
Adding section about new training intake survey refs #12753.
- src/hg/htdocs/indexNews.html
- lines changed 58, context: html, text, full: html, text
Adding section about new training intake survey refs #12753.
- src/hg/htdocs/training.html
- lines changed 22, context: html, text, full: html, text
Adding blurb about workshop survey. refs #12681
- lines changed 1, context: html, text, full: html, text
Minor revision. refs #12681
- lines changed 7, context: html, text, full: html, text
added box around trainng announcement and fixed link to bit.ly. refs #12753
- lines changed 18, context: html, text, full: html, text
Made a few edits to training annoucement at top of page.
- lines changed 18, context: html, text, full: html, text
Fixed merge conflict after making a few edits to training announcement at top of page.
- lines changed 1, context: html, text, full: html, text
Small edit to headline after discussions with Bob, Ann, and Donna. refs #12753
- src/hg/inc/customPp.h
- lines changed 3, context: html, text, full: html, text
Improved error messages for bigData custom track common mistakes likemissing bigDataUrl setting or trying to upload a bigData file instead
of making a track line with a public URL. I added a new "factory"
to customFactory.c that produces no tracks, only error messages about
directly uploaded bigData files.
refs #12747
- src/hg/lib/bioCycMapDesc.sql
- lines changed 1, context: html, text, full: html, text
a bunch of changes to SQL files to accomodate a change from TYPE=ISAM toENGINE=ISAM.
- src/hg/lib/bioCycPathway.sql
- lines changed 1, context: html, text, full: html, text
a bunch of changes to SQL files to accomodate a change from TYPE=ISAM toENGINE=ISAM.
- src/hg/lib/customFactory.c
- lines changed 161, context: html, text, full: html, text
Improved error messages for bigData custom track common mistakes likemissing bigDataUrl setting or trying to upload a bigData file instead
of making a track line with a public URL. I added a new "factory"
to customFactory.c that produces no tracks, only error messages about
directly uploaded bigData files.
refs #12747
- lines changed 2, context: html, text, full: html, text
patch to fix build on OSX which has no malloc.h refs #12656
- src/hg/lib/customPp.c
- lines changed 9, context: html, text, full: html, text
Improved error messages for bigData custom track common mistakes likemissing bigDataUrl setting or trying to upload a bigData file instead
of making a track line with a public URL. I added a new "factory"
to customFactory.c that produces no tracks, only error messages about
directly uploaded bigData files.
refs #12747
- src/hg/lib/customTrack.c
- lines changed 42, context: html, text, full: html, text
Improved error messages for bigData custom track common mistakes likemissing bigDataUrl setting or trying to upload a bigData file instead
of making a track line with a public URL. I added a new "factory"
to customFactory.c that produces no tracks, only error messages about
directly uploaded bigData files.
refs #12747
- src/hg/lib/gpFx.c
- lines changed 4, context: html, text, full: html, text
Fixed coord-arithmetic bug that caused crash for user in MLQ #12778.refs #12778
- src/hg/lib/kgAlias.sql
- lines changed 1, context: html, text, full: html, text
a bunch of changes to SQL files to accomodate a change from TYPE=ISAM toENGINE=ISAM.
- src/hg/lib/kgProtAlias.sql
- lines changed 1, context: html, text, full: html, text
a bunch of changes to SQL files to accomodate a change from TYPE=ISAM toENGINE=ISAM.
- src/hg/lib/knownGene.sql
- lines changed 1, context: html, text, full: html, text
a bunch of changes to SQL files to accomodate a change from TYPE=ISAM toENGINE=ISAM.
- src/hg/lib/pfamXref.sql
- lines changed 1, context: html, text, full: html, text
a bunch of changes to SQL files to accomodate a change from TYPE=ISAM toENGINE=ISAM.
- src/hg/lib/spSecondaryID.sql
- lines changed 1, context: html, text, full: html, text
a bunch of changes to SQL files to accomodate a change from TYPE=ISAM toENGINE=ISAM.
- src/hg/lib/spXref3.sql
- lines changed 1, context: html, text, full: html, text
a bunch of changes to SQL files to accomodate a change from TYPE=ISAM toENGINE=ISAM.
- src/hg/lib/trackHub.c
- lines changed 6, context: html, text, full: html, text
Use vcfTabixFileMayOpen instead of vcfFileMayOpen so that we alsocheck the tabix index file.
- src/hg/makeDb/doc/bosTau7.txt
- lines changed 12, context: html, text, full: html, text
Brian L found that hgc crashed on snp138 in cow & pig. That wascaused by invalid table contents due to a bug in the script
collectNcbiFuncAnnotations.pl. Fixed the bug, removed a bogus
warning, and re-ran the script for cow, pig, chicken and dog.
refs #12490
- lines changed 3, context: html, text, full: html, text
Working on farm animal QTL tracks - makedoc entries likely to get updated before this is finished. refs #10954
- src/hg/makeDb/doc/canFam3.txt
- lines changed 11, context: html, text, full: html, text
Brian L found that hgc crashed on snp138 in cow & pig. That wascaused by invalid table contents due to a bug in the script
collectNcbiFuncAnnotations.pl. Fixed the bug, removed a bogus
warning, and re-ran the script for cow, pig, chicken and dog.
refs #12490
- src/hg/makeDb/doc/galGal4.txt
- lines changed 15, context: html, text, full: html, text
Brian L found that hgc crashed on snp138 in cow & pig. That wascaused by invalid table contents due to a bug in the script
collectNcbiFuncAnnotations.pl. Fixed the bug, removed a bogus
warning, and re-ran the script for cow, pig, chicken and dog.
refs #12490
- lines changed 1, context: html, text, full: html, text
Working on farm animal QTL tracks - makedoc entries likely to get updated before this is finished. refs #10954
- src/hg/makeDb/doc/go.txt
- src/hg/makeDb/doc/hg19.txt
- lines changed 28, context: html, text, full: html, text
update cosmic to v68 refs #10158
- src/hg/makeDb/doc/hg38.txt
- lines changed 40, context: html, text, full: html, text
load ncbiAltSequence PSL mappings with sequence display refs #11681
- lines changed 22, context: html, text, full: html, text
added centromeres to cytoBandIdeo
- lines changed 27, context: html, text, full: html, text
lifted exoniphy to hg38 for UCSC genes build process
- lines changed 110, context: html, text, full: html, text
starting rat lastz refs #11681
- src/hg/makeDb/doc/oviAri3.txt
- lines changed 6, context: html, text, full: html, text
Working on farm animal QTL tracks - makedoc entries likely to get updated before this is finished. refs #10954
- src/hg/makeDb/doc/proteins/140122.txt
- lines changed 17, context: html, text, full: html, text
finished the build of protein140122 database
- src/hg/makeDb/doc/susScr3.txt
- lines changed 13, context: html, text, full: html, text
Brian L found that hgc crashed on snp138 in cow & pig. That wascaused by invalid table contents due to a bug in the script
collectNcbiFuncAnnotations.pl. Fixed the bug, removed a bogus
warning, and re-ran the script for cow, pig, chicken and dog.
refs #12490
- lines changed 2, context: html, text, full: html, text
Working on farm animal QTL tracks - makedoc entries likely to get updated before this is finished. refs #10954
- src/hg/makeDb/doc/uniProt/sp140122.txt
- lines changed 13, context: html, text, full: html, text
finished build of sp140122 database
- src/hg/makeDb/genbank/src/ccds/ccdsMkTables.c
- lines changed 2, context: html, text, full: html, text
generate an error when building CCDS tables and no entries in imported CCDS database match criteria
- src/hg/makeDb/schema/all.joiner
- lines changed 28, context: html, text, full: html, text
Added hg38 to GENCODE V19 sections (redmine #11681)
- src/hg/makeDb/trackDb/chainSelf.html
- lines changed 38, context: html, text, full: html, text
For hg38, made changes to description pages (and other relevant pages when necessary) (redmine #11681)
- src/hg/makeDb/trackDb/dog/canFam3/trackDb.chainNet.ra
- lines changed 2, context: html, text, full: html, text
While adding hg38 entries, noticed other problems; fixed chain/net entries in .ra files (redmine #11681)
- src/hg/makeDb/trackDb/dog/canFam3/trackDb.ra
- lines changed 2, context: html, text, full: html, text
While adding hg38 entries, noticed other problems; fixed chain/net entries in .ra files (redmine #11681)
- src/hg/makeDb/trackDb/dog/trackDb.chainNet.ra
- lines changed 4, context: html, text, full: html, text
While adding hg38 entries, noticed other problems; fixed chain/net entries in .ra files (redmine #11681)
- src/hg/makeDb/trackDb/drosophila/trackDb.ra
- lines changed 4, context: html, text, full: html, text
Removing shortCircuit setting to get it equal to zero. refs #10504
- src/hg/makeDb/trackDb/human/chainSelf.html
- lines changed 38, context: html, text, full: html, text
For hg38, made changes to description pages (and other relevant pages when necessary) (redmine #11681)
- src/hg/makeDb/trackDb/human/hg18/wgEncodeBuOrchid.html
- lines changed 4, context: html, text, full: html, text
Commented out html tags based on hgTablesTest robot errors; running hgTablesTest robot again to see if errors go away (redmine #12656)
- lines changed 3, context: html, text, full: html, text
Accidentally commented out the description section header (redmine #12656)
- lines changed 22, context: html, text, full: html, text
Made some html formatting corrections based on more errors in the hgTablesTest log (redmine #12656)
- src/hg/makeDb/trackDb/human/hg19/chainSelf.html
- lines changed 3, context: html, text, full: html, text
For hg38, made changes to description pages (and other relevant pages when necessary) (redmine #11681)
- src/hg/makeDb/trackDb/human/hg19/wgEncodeBuOrchid.html
- lines changed 4, context: html, text, full: html, text
Commented out html tags based on hgTablesTest robot errors; running hgTablesTest robot again to see if errors go away (redmine #12656)
- lines changed 3, context: html, text, full: html, text
Accidentally commented out the description section header (redmine #12656)
- lines changed 23, context: html, text, full: html, text
Made some html formatting corrections based on more errors in the hgTablesTest log (redmine #12656)
- src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeSuper.html
- lines changed 1, context: html, text, full: html, text
Updated a URL for hg38 GENCODE; updated for other similar tracks as well (redmine #11681)
- src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV11.html
- lines changed 1, context: html, text, full: html, text
Updated a URL for hg38 GENCODE; updated for other similar tracks as well (redmine #11681)
- src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV12.html
- lines changed 1, context: html, text, full: html, text
Updated a URL for hg38 GENCODE; updated for other similar tracks as well (redmine #11681)
- src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV13.html
- lines changed 1, context: html, text, full: html, text
Updated a URL for hg38 GENCODE; updated for other similar tracks as well (redmine #11681)
- src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV14.html
- lines changed 1, context: html, text, full: html, text
Updated a URL for hg38 GENCODE; updated for other similar tracks as well (redmine #11681)
- src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV15.html
- lines changed 1, context: html, text, full: html, text
Updated a URL for hg38 GENCODE; updated for other similar tracks as well (redmine #11681)
- src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV16.html
- lines changed 1, context: html, text, full: html, text
Updated a URL for hg38 GENCODE; updated for other similar tracks as well (redmine #11681)
- src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV17.html
- lines changed 1, context: html, text, full: html, text
Updated a URL for hg38 GENCODE; updated for other similar tracks as well (redmine #11681)
- src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV18.html
- lines changed 1, context: html, text, full: html, text
Updated a URL for hg38 GENCODE; updated for other similar tracks as well (redmine #11681)
- src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV18.ra
- lines changed 1, context: html, text, full: html, text
Readding priority to sort Gencode V19 to top (V18 to on dev) note 68 refs #7343
- src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV19.html
- lines changed 1, context: html, text, full: html, text
Updated a URL for hg38 GENCODE; updated for other similar tracks as well (redmine #11681)
- src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV19.ra
- lines changed 1, context: html, text, full: html, text
Readding priority to sort Gencode V19 to top (V18 to on dev) note 68 refs #7343
- src/hg/makeDb/trackDb/human/hg38/altSequence.html
- lines changed 86, context: html, text, full: html, text
new organization for the Alt Map track refs #11681
- lines changed 95, context: html, text, full: html, text
updating documents to Alt Map sequence refs #11681
- src/hg/makeDb/trackDb/human/hg38/description.html
- lines changed 10, context: html, text, full: html, text
For hg38, made changes to description pages (and other relevant pages when necessary) (redmine #11681)
- lines changed 1, context: html, text, full: html, text
updating documents to Alt Map sequence refs #11681
- src/hg/makeDb/trackDb/human/hg38/gap.html
- lines changed 3, context: html, text, full: html, text
For hg38, made changes to description pages (and other relevant pages when necessary) (redmine #11681)
- src/hg/makeDb/trackDb/human/hg38/scaffolds.html
- lines changed 7, context: html, text, full: html, text
For hg38, made changes to description pages (and other relevant pages when necessary) (redmine #11681)
- src/hg/makeDb/trackDb/human/hg38/trackDb.ra
- lines changed 57, context: html, text, full: html, text
new arrangement of the Alt Map track refs #11681
- lines changed 2, context: html, text, full: html, text
correct tablename for Alt Map table name refs #11681
- lines changed 2, context: html, text, full: html, text
default priority for UCSC Genes and hide centromeres refs #11681
- src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV19.html
- lines changed 335, context: html, text, full: html, text
add HTML page for gencode in hg38
- lines changed 1, context: html, text, full: html, text
Updated a URL for hg38 GENCODE; updated for other similar tracks as well (redmine #11681)
- src/hg/makeDb/trackDb/mouse/mm10/wgEncodeGencodeSuper.html
- lines changed 1, context: html, text, full: html, text
Updated a URL for hg38 GENCODE; updated for other similar tracks as well (redmine #11681)
- src/hg/makeDb/trackDb/mouse/mm10/wgEncodeGencodeVM2.html
- lines changed 1, context: html, text, full: html, text
Updated a URL for hg38 GENCODE; updated for other similar tracks as well (redmine #11681)
- lines changed 2, context: html, text, full: html, text
Making small corrections on description page, refs #12701
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/beta/wgEncodeSydhHist.ra
- lines changed 6, context: html, text, full: html, text
Adding meta data about revoked files for mm9 SydhHist H3k27ac files refs# 10465
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/public/wgEncodeSydhHist.ra
- lines changed 6, context: html, text, full: html, text
Adding meta data about revoked files for mm9 SydhHist H3k27ac files refs# 10465
- src/hg/makeDb/trackDb/orfeomeMrna.html
- lines changed 1, context: html, text, full: html, text
For hg38, made changes to description pages (and other relevant pages when necessary) (redmine #11681)
- src/hg/makeDb/trackDb/refGene.html
- lines changed 1, context: html, text, full: html, text
For hg38, made changes to description pages (and other relevant pages when necessary) (redmine #11681)
- lines changed 7, context: html, text, full: html, text
Made minor corrections; modified references (redmine #11681)
- src/hg/makeDb/trackDb/refGene.new.html
- lines changed 1, context: html, text, full: html, text
For hg38, made changes to description pages (and other relevant pages when necessary) (redmine #11681)
- lines changed 9, context: html, text, full: html, text
Made minor corrections; modified references (redmine #11681)
- src/hg/makeDb/trackDb/rhesus/rheMac3/trackDb.chainNet.ra
- lines changed 9, context: html, text, full: html, text
While adding hg38 entries, noticed other problems; fixed chain/net entries in .ra files (redmine #11681)
- src/hg/makeDb/trackDb/rhesus/rheMac3/trackDb.ra
- lines changed 1, context: html, text, full: html, text
While adding hg38 entries, noticed other problems; fixed chain/net entries in .ra files (redmine #11681)
- src/hg/makeDb/trackDb/rhesus/trackDb.chainNet.ra
- lines changed 8, context: html, text, full: html, text
While adding hg38 entries, noticed other problems; fixed chain/net entries in .ra files (redmine #11681)
- src/hg/makeDb/trackDb/trackDb.chainNet.ra
- lines changed 51, context: html, text, full: html, text
felCat5 chain net now on hg19 refs #12744
- src/hg/makeDb/trackDb/ucscToINSDC.html
- lines changed 5, context: html, text, full: html, text
For hg38, made changes to description pages (and other relevant pages when necessary) (redmine #11681)
- src/hg/makeDb/trackDb/xenoEst.html
- lines changed 26, context: html, text, full: html, text
For hg38, made changes to description pages (and other relevant pages when necessary) (redmine #11681)
- src/hg/protein/spToDb/spDb.sql
- lines changed 1, context: html, text, full: html, text
another change of TYPE=ISAM to ENGINE=ISAM
- src/hg/utils/automation/EnsGeneAutomate.pm
- lines changed 210, context: html, text, full: html, text
v75 release definitions refs #12796
- src/hg/utils/automation/collectNcbiFuncAnnotations.pl
- lines changed 3, context: html, text, full: html, text
Brian L found that hgc crashed on snp138 in cow & pig. That wascaused by invalid table contents due to a bug in the script
collectNcbiFuncAnnotations.pl. Fixed the bug, removed a bogus
warning, and re-ran the script for cow, pig, chicken and dog.
refs #12490
- src/hg/utils/automation/loadCosmic.pl
- lines changed 4, context: html, text, full: html, text
cosmic download site has changed the format of their file names refs #10158
- src/inc/linefile.h
- lines changed 2, context: html, text, full: html, text
Improved error messages for bigData custom track common mistakes likemissing bigDataUrl setting or trying to upload a bigData file instead
of making a track line with a public URL. I added a new "factory"
to customFactory.c that produces no tracks, only error messages about
directly uploaded bigData files.
refs #12747
- src/lib/linefile.c
- lines changed 1, context: html, text, full: html, text
Improved error messages for bigData custom track common mistakes likemissing bigDataUrl setting or trying to upload a bigData file instead
of making a track line with a public URL. I added a new "factory"
to customFactory.c that produces no tracks, only error messages about
directly uploaded bigData files.
refs #12747
- src/utils/qa/weeklybld/buildEnv.csh
- lines changed 2, context: html, text, full: html, text
preview1 v297 refs #12656
- lines changed: 53007
- files changed: 118