All File Changes
v317_preview2 to v317_base (2015-05-25 to 2015-06-01) v317
- src/hg/hgGene/hgGene.c
- lines changed 2, context: html, text, full: html, text
use #define for constant refs #15407
- src/hg/hgTrackUi/hgTrackUi.c
- lines changed 8, context: html, text, full: html, text
support setting transMap track default item labeling in trackDb (#15440)
- src/hg/hgTracks/chainTrack.c
- lines changed 2, context: html, text, full: html, text
fix score filter on chains refs #15143
- src/hg/hgTracks/transMapTracks.c
- lines changed 37, context: html, text, full: html, text
support setting transMap track default item labeling in trackDb (#15440)
- src/hg/hgc/hgc.c
- lines changed 1, context: html, text, full: html, text
print link to other genome assembly on snake tracks that are not assembly hubs
- src/hg/htdocs/goldenPath/help/hgIntegratorHelp.html
- lines changed 56, context: html, text, full: html, text
Moving the 'quick-reference' contents of hgIntegratorHelp.html to
hgIntegrator.jsx so Matt can write a proper user's guide in
hgIntegratorHelp.html. Also, now we don't need to fetch html
from the server and use React's dangerouslySetInnerHTML.
refs #14579 note 65
- src/hg/htdocs/goldenPath/help/trackDb/trackDbDoc.html
- lines changed 47, context: html, text, full: html, text
1. Get version from doc. 2. Fix err messages. refs #10015
- src/hg/htdocs/goldenPath/help/trackDb/trackDbDoc.js
- lines changed 9, context: html, text, full: html, text
1. Get version from doc. 2. Fix err messages. refs #10015
- lines changed 1, context: html, text, full: html, text
Fix test on doc type. Commit v0 version. refs #10015
- src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.html
- lines changed 44, context: html, text, full: html, text
1. Get version from doc. 2. Fix err messages. refs #10015
- src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.v0.html
- lines changed 785, context: html, text, full: html, text
Fix test on doc type. Commit v0 version. refs #10015
- src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
- lines changed 90, context: html, text, full: html, text
1. Get version from doc. 2. Fix err messages. refs #10015
- src/hg/htdocs/goldenPath/newsarch.html
- lines changed 31, context: html, text, full: html, text
Adding announcement for new mm10 UCSC Genes track, refs #15145
- lines changed 2, context: html, text, full: html, text
Correcting typo in annnouncement, refs #15145
- src/hg/htdocs/indexNews.html
- lines changed 37, context: html, text, full: html, text
Adding announcement for new mm10 UCSC Genes track, refs #15145
- lines changed 2, context: html, text, full: html, text
Correcting typo in annnouncement, refs #15145
- src/hg/inc/hgBam.h
- src/hg/inc/trackHub.h
- lines changed 34, context: html, text, full: html, text
1. Add -test option to use genome-test spec file. 2. Remove unneeded errCatch (from code review). 3. Simplify code org (delibify unshared code); bye to lib/trackHubCheck.c. refs #10015
- src/hg/inc/transMapStuff.h
- lines changed 10, context: html, text, full: html, text
support setting transMap track default item labeling in trackDb (#15440)
- src/hg/inc/versionInfo.h
- src/hg/js/model/hgIntegrator/hgIntegratorModel.js
- lines changed 5, context: html, text, full: html, text
Moving the 'quick-reference' contents of hgIntegratorHelp.html to
hgIntegrator.jsx so Matt can write a proper user's guide in
hgIntegratorHelp.html. Also, now we don't need to fetch html
from the server and use React's dangerouslySetInnerHTML.
refs #14579 note 65
- src/hg/js/react/hgIntegrator/hgIntegrator.jsx
- lines changed 84, context: html, text, full: html, text
Moving the 'quick-reference' contents of hgIntegratorHelp.html to
hgIntegrator.jsx so Matt can write a proper user's guide in
hgIntegratorHelp.html. Also, now we don't need to fetch html
from the server and use React's dangerouslySetInnerHTML.
refs #14579 note 65
- src/hg/js/react/lib/Modal.jsx
- lines changed 8, context: html, text, full: html, text
Fixed wacky scrolling behavior in pop-up dialog (Modal).
refs #14579 note 68
- lines changed 6, context: html, text, full: html, text
When pop-up/Modal closes, return to the original page scroll height
in case the user has scrolled way down while viewing the Modal.
refs #14579 note 54
- src/hg/lib/makefile
- lines changed 1, context: html, text, full: html, text
1. Add -test option to use genome-test spec file. 2. Remove unneeded errCatch (from code review). 3. Simplify code org (delibify unshared code); bye to lib/trackHubCheck.c. refs #10015
- src/hg/lib/tests/expected/annoGrator/bigBedToTabOut.txt
- lines changed 1, context: html, text, full: html, text
Updating hg/lib/tests annoGrator files for some recent(ish) changes: full source name in header,
wiggle chrom shown by default in addition to start and end, and wiggle average shown instead of
comma-sep list in tab-sep output.
refs #14579
- src/hg/lib/tests/expected/annoGrator/pgSnpDbToTabOut.txt
- lines changed 1, context: html, text, full: html, text
Updating hg/lib/tests annoGrator files for some recent(ish) changes: full source name in header,
wiggle chrom shown by default in addition to start and end, and wiggle average shown instead of
comma-sep list in tab-sep output.
refs #14579
- src/hg/lib/tests/expected/annoGrator/pgSnpKgDbToGpFx.txt
- lines changed 1, context: html, text, full: html, text
Updating hg/lib/tests annoGrator files for some recent(ish) changes: full source name in header,
wiggle chrom shown by default in addition to start and end, and wiggle average shown instead of
comma-sep list in tab-sep output.
refs #14579
- src/hg/lib/tests/expected/annoGrator/pgSnpKgDbToTabOutShort.txt
- lines changed 1, context: html, text, full: html, text
Updating hg/lib/tests annoGrator files for some recent(ish) changes: full source name in header,
wiggle chrom shown by default in addition to start and end, and wiggle average shown instead of
comma-sep list in tab-sep output.
refs #14579
- src/hg/lib/tests/expected/annoGrator/snpBigWigToTabOut.txt
- lines changed 288, context: html, text, full: html, text
Updating hg/lib/tests annoGrator files for some recent(ish) changes: full source name in header,
wiggle chrom shown by default in addition to start and end, and wiggle average shown instead of
comma-sep list in tab-sep output.
refs #14579
- src/hg/lib/tests/expected/annoGrator/snpConsDbToTabOutShort.txt
- lines changed 38, context: html, text, full: html, text
Updating hg/lib/tests annoGrator files for some recent(ish) changes: full source name in header,
wiggle chrom shown by default in addition to start and end, and wiggle average shown instead of
comma-sep list in tab-sep output.
refs #14579
- src/hg/lib/tests/expected/annoGrator/vcfEx1.txt
- lines changed 1, context: html, text, full: html, text
Updating hg/lib/tests annoGrator files for some recent(ish) changes: full source name in header,
wiggle chrom shown by default in addition to start and end, and wiggle average shown instead of
comma-sep list in tab-sep output.
refs #14579
- src/hg/lib/tests/expected/annoGrator/vcfEx2.txt
- lines changed 1, context: html, text, full: html, text
Updating hg/lib/tests annoGrator files for some recent(ish) changes: full source name in header,
wiggle chrom shown by default in addition to start and end, and wiggle average shown instead of
comma-sep list in tab-sep output.
refs #14579
- src/hg/lib/trackHubCheck.c
- lines changed 494, context: html, text, full: html, text
1. Add -test option to use genome-test spec file. 2. Remove unneeded errCatch (from code review). 3. Simplify code org (delibify unshared code); bye to lib/trackHubCheck.c. refs #10015
- src/hg/lib/web.c
- lines changed 2, context: html, text, full: html, text
Don't restrict hgIntegrator to private hosts anymore -- we're going to release it!
refs #14579
- src/hg/makeDb/genbank/etc/align.dbs
- lines changed 1, context: html, text, full: html, text
Added micMur2 - Mouse lemur refs #15292
- src/hg/makeDb/genbank/etc/genbank.conf
- lines changed 1, context: html, text, full: html, text
fixup bisBis1 config refs #15388
- src/hg/makeDb/genbank/etc/hgwdev.dbs
- lines changed 2, context: html, text, full: html, text
Added micMur2 - Mouse lemur refs #15292
- src/hg/makeDb/schema/all.joiner
- lines changed 1, context: html, text, full: html, text
ignore augustusGene table nothing to check refs #13088
- src/hg/makeDb/trackDb/human/chainNetMicMur1.ra
- lines changed 15, context: html, text, full: html, text
turn of micMur2 chainNet for alpha target leave micMur1 as beta public refs #15292
- src/hg/makeDb/trackDb/human/chainNetMicMur2.ra
- lines changed 15, context: html, text, full: html, text
turn of micMur2 chainNet for alpha target leave micMur1 as beta public refs #15292
- src/hg/makeDb/trackDb/human/chainNetPrimate.ra
- lines changed 15, context: html, text, full: html, text
turn of micMur2 chainNet for alpha target leave micMur1 as beta public refs #15292
- src/hg/makeDb/trackDb/human/hg19/trackDb.ra
- lines changed 2, context: html, text, full: html, text
turn of micMur2 chainNet for alpha target leave micMur1 as beta public refs #15292
- src/hg/makeDb/trackDb/human/hg38/hg38Patch3.html
- lines changed 3, context: html, text, full: html, text
Made slight modification to description page; modified release tags for Patch 2 & 3; refs #15143
- src/hg/makeDb/trackDb/human/hg38/trackDb.ra
- lines changed 2, context: html, text, full: html, text
Made slight modification to description page; modified release tags for Patch 2 & 3; refs #15143
- lines changed 2, context: html, text, full: html, text
Edited release tags for Patch 2 & 3; refs #15143
- src/hg/makeDb/trackDb/loadTracks
- lines changed 1, context: html, text, full: html, text
fixed undefined variable when -local is not specified
- src/hg/makeDb/trackDb/tarsier/tarSyr2/trackDb.ra
- lines changed 1, context: html, text, full: html, text
Change based on CR, refs #15403
- src/hg/makeDb/trackDb/trackDb.chainNet.ra
- lines changed 51, context: html, text, full: html, text
turn of micMur2 chainNet for alpha target leave micMur1 as beta public refs #15292
- src/hg/makeDb/trackDb/trackDb.ra
- lines changed 7, context: html, text, full: html, text
add search rule for augustusGene track refs #13088
- src/hg/utils/automation/doAugustus.pl
- lines changed 14, context: html, text, full: html, text
auto detect UTR option and manage no partBundles correctly refs #13088
- src/hg/utils/automation/doBlastzChainNet.pl
- lines changed 1, context: html, text, full: html, text
correct symlink for synNet downloads refs #14560
- src/hg/utils/hubCheck/hubCheck.c
- lines changed 562, context: html, text, full: html, text
1. Add -test option to use genome-test spec file. 2. Remove unneeded errCatch (from code review). 3. Simplify code org (delibify unshared code); bye to lib/trackHubCheck.c. refs #10015
- lines changed 97, context: html, text, full: html, text
1. Get version from doc. 2. Fix err messages. refs #10015
- lines changed 9, context: html, text, full: html, text
Fix to handling of deprecated settings. refs #10015
- src/lib/annoFormatTab.c
- lines changed 18, context: html, text, full: html, text
In order to make it more clear that wiggle values are averaged now,
print out wiggle's value column as "valueAverage" in the header.
refs #14579 note 61
- src/utils/bedToBigBed/tests/makefile
- lines changed 1, context: html, text, full: html, text
fixup expected failing command so its failure code will not bother make refs #15417
- src/utils/qa/weeklybld/buildEnv.csh
- lines changed: 2959
- files changed: 58