All File Changes
v279_preview2 to v279_base (2013-02-05 to 2013-02-12) v279
- src/hg/hgVarAnnogrator/hgVarAnnogrator.c
- lines changed 4, context: html, text, full: html, text
Encapsulating hgVarAnnogrator.js into a single global object (hgva)with public methods for page events.
- src/hg/hgc/bigBedClick.c
- lines changed 8, context: html, text, full: html, text
Passing an item's coords as the range to bigBedIntervalQuery worksfor retrieving the item -- except when the item is an insertion (length=0).
In that case, the search range must be expanded to 2 bases, one base
to the left of an item and one base to the right, so starts and ends
will overlap.
- src/hg/htdocs/goldenPath/credits.html
- lines changed 1, context: html, text, full: html, text
Updated a link per Brooke's code review (redmine #10108)
- src/hg/htdocs/goldenPath/newsarch.html
- lines changed 2, context: html, text, full: html, text
Fixed two small errors in 28 assemblies list (RM #8887#note-104).
- src/hg/htdocs/goldenPath/pubs.html
- lines changed 6, context: html, text, full: html, text
Added Zerbino et al. pub.
- src/hg/htdocs/indexNews.html
- lines changed 47, context: html, text, full: html, text
Adding entry for Denisova tracks.
- src/hg/inc/versionInfo.h
- src/hg/js/hgVarAnnogrator.js
- lines changed 197, context: html, text, full: html, text
Encapsulating hgVarAnnogrator.js into a single global object (hgva)with public methods for page events.
- src/hg/makeDb/doc/hg17.txt
- lines changed 14, context: html, text, full: html, text
Track #9401 (need DGV update): reloaded in order to pick up missing IDs. Still waiting for missing Iafrate items in hg18.
- src/hg/makeDb/doc/hg18.txt
- lines changed 16, context: html, text, full: html, text
Track #9401 (need DGV update): reloaded in order to pick up missing IDs. Still waiting for missing Iafrate items in hg18.
- src/hg/makeDb/doc/hg19.txt
- lines changed 17, context: html, text, full: html, text
Track #9401 (need DGV update): reloaded in order to pick up missing IDs. Still waiting for missing Iafrate items in hg18.
- src/hg/makeDb/hgLoadOut/hgLoadOut.c
- lines changed 21, context: html, text, full: html, text
Rm run with custom libraries that have no class/family indication end up with an empty string for the 11th word in the line, recognize that word as digits only or (digits) only and assume there is no class/family indication
- src/hg/makeDb/trackDb/cat/felCat4/description.html
- src/hg/makeDb/trackDb/cat/felCat4/gold.html
- lines changed 0, context: html, text, full: html, text
Removed an extra blank space from the end of one of the links
- src/hg/makeDb/trackDb/cv/alpha/cv.ra
- lines changed 1, context: html, text, full: html, text
Changing link for Vendor URL for item CREB1_(9198) from pdf to html page, Cron Job reported timing out, and pdf was failing to load on test.
- src/hg/makeDb/trackDb/cv/beta/cv.ra
- lines changed 1, context: html, text, full: html, text
Copying alpha/cv.ra to beta and public: Changing link for Vendor URL for item CREB1_(9198) from pdf to html page, Cron Job reported timing out, and pdf was failing to load on test.
- src/hg/makeDb/trackDb/cv/public/cv.ra
- lines changed 1, context: html, text, full: html, text
Copying alpha/cv.ra to beta and public: Changing link for Vendor URL for item CREB1_(9198) from pdf to html page, Cron Job reported timing out, and pdf was failing to load on test.
- src/hg/makeDb/trackDb/human/hg19/trackDb.denisova.ra
- lines changed 1, context: html, text, full: html, text
Adding maxWindowToDraw to a couple very dense VCF tracks after Pauline found that chr1 load runs out of mem (#8886 note 47).
- src/hg/makeDb/trackDb/human/hg19/trackDb.ra
- lines changed 1, context: html, text, full: html, text
Adding maxWindowToDraw to a couple very dense VCF tracks after Pauline found that chr1 load runs out of mem (#8886 note 47).
- lines changed 2, context: html, text, full: html, text
Removed commented-out lines for canFam2.ra inclusion per Brooke's code review (redmine #10108)
- src/hg/makeDb/trackDb/human/trackDb.ra
- lines changed 0, context: html, text, full: html, text
Trimming of trailing whitespace in e9a3d621 caused hgTrackDb to fail -- putting it back.
- src/hg/makeDb/trackDb/tagTypes.tab
- lines changed 1, context: html, text, full: html, text
Adding maxWindowToDraw to a couple very dense VCF tracks after Pauline found that chr1 load runs out of mem (#8886 note 47).
- src/hg/utils/automation/ensGene/felCat5.ensGene.ra
- lines changed 2, context: html, text, full: html, text
CR#10114 feedback - removed extra comment string on db specification.
- src/hg/utils/automation/ensGene/melGal1.ensGene.ra
- lines changed 4, context: html, text, full: html, text
Track #9407 Ensembl Genes v70 update add lift MT over to chrM task inside process step
- src/inc/common.h
- lines changed 8, context: html, text, full: html, text
Should have been checked in with common.c. Added slSortMerge and slSortMergeUniq at Angie's request.
- src/inc/localmem.h
- lines changed 4, context: html, text, full: html, text
Dropped lmFlushZ function at Angie's request. It added little value over lmCleanup/lmInit.
- src/inc/vcf.h
- lines changed 14, context: html, text, full: html, text
Some changes requested by Angie in code review, along with a bug fix. Next checkin will break out the vcfBits routines into separate .c/.h files
- lines changed 110, context: html, text, full: html, text
Split vcfBits.c/.h off from vcf.c/.h. No code changes made.
- src/inc/vcfBits.h
- lines changed 120, context: html, text, full: html, text
Split vcfBits.c/.h off from vcf.c/.h. No code changes made.
- lines changed 7, context: html, text, full: html, text
Updated the file comment in vcfBits.c/.h. No code change.
- src/lib/bigBed.c
- lines changed 1, context: html, text, full: html, text
For #8886 (Denisova tracks) Pauline found that some data tables appearedempty in the Table Browser. Turns out that insertion items (length=0) were
dropped by bigbedIntervalQuery because it required a positive rangeIntersection.
Fix: instead, compare start and end coords of search range and item.
Note: In order to catch an insertion item, the search range has to encompass
the item (>=1 base to left and >=1 base to right).
- src/lib/common.c
- lines changed 18, context: html, text, full: html, text
Added slSortMerge and slSortMergeUniq at Angie's request. These functions are little more than wrappers for slSort and slUniqify but are still valuable additions.
- src/lib/elmTree.c
- lines changed 39, context: html, text, full: html, text
Name changes to clarify code, made at Angie's request. No functional changes here.
- src/lib/localmem.c
- lines changed 12, context: html, text, full: html, text
Dropped lmFlushZ function at Angie's request. It added little value over lmCleanup/lmInit.
- src/lib/makefile
- lines changed 1, context: html, text, full: html, text
Split vcfBits.c/.h off from vcf.c/.h. No code changes made.
- src/lib/vcf.c
- lines changed 59, context: html, text, full: html, text
Some changes requested by Angie in code review, along with a bug fix. Next checkin will break out the vcfBits routines into separate .c/.h files
- lines changed 450, context: html, text, full: html, text
Split vcfBits.c/.h off from vcf.c/.h. No code changes made.
- src/lib/vcfBits.c
- lines changed 463, context: html, text, full: html, text
Split vcfBits.c/.h off from vcf.c/.h. No code changes made.
- lines changed 7, context: html, text, full: html, text
Updated the file comment in vcfBits.c/.h. No code change.
- src/utils/qa/getRRdumpfile.csh
- lines changed 1, context: html, text, full: html, text
adjusted getRRdumpfile.csh and getRRtableStatus.csh to accommodate rrnfs1
- src/utils/qa/getRRtableStatus.csh
- lines changed 1, context: html, text, full: html, text
adjusted getRRdumpfile.csh and getRRtableStatus.csh to accommodate rrnfs1
- src/utils/qa/joinerBatchKeys.csh
- lines changed 1, context: html, text, full: html, text
Edited the 'pick-n-choose' line to reflect all the new databases added since the last time the script was run
- src/utils/qa/weeklybld/buildEnv.csh
- lines changed: 1672
- files changed: 45