Commits for angie
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v290_base to v291_preview (2013-09-30 to 2013-10-07) v291
- Code review feedback from Brian - use trackDb instead of hardcoding accessory URL.refs #11763
- src/hg/makeDb/trackDb/human/trackDb.ra - lines changed 1, context: html, text, full: html, text
- src/hg/makeDb/trackDb/tagTypes.tab - lines changed 1, context: html, text, full: html, text
- Adding details pages for snp138* tracks. refs #11438
- src/hg/makeDb/trackDb/human/hg19/snp138.html - lines changed 36, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg19/snp138Flagged.html - lines changed 29, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg19/snp138FlaggedMention.html - lines changed 4, context: html, text, full: html, text
- src/hg/makeDb/trackDb/snp138.html - lines changed 31, context: html, text, full: html, text
- src/hg/makeDb/trackDb/snp138.shared.html - lines changed 460, context: html, text, full: html, text
- src/hg/makeDb/trackDb/snp138Common.html - lines changed 28, context: html, text, full: html, text
- src/hg/makeDb/trackDb/snp138Mult.html - lines changed 25, context: html, text, full: html, text
- Make annoAssemblySeqSize cache sequence sizes, because twoBitSeqSizedoes a seek and read, and some annoStreams check sequence size pretty often.
- src/lib/annoAssembly.c - lines changed 18, context: html, text, full: html, text
- In annoStreamerSetRegion, if we're given (chrom, 0, 0), treat that as(chrom, 0, chromSize).
- When reading a VCF file without a tabix index, make sure we stopafter regionEnd (if there is one).
- src/lib/annoStreamVcf.c - lines changed 16, context: html, text, full: html, text
- Fix for crash found by Jonathan in http://redmine.soe.ucsc.edu/issues/11775#note-60 ;more careful error-checking and corner-case handling in getTxCoords.
When CDS starts out of frame, we were getting early truncation of
coding sequence, leading to some strange characters in output; the
ideal fix would be to take exonFrames into account, but for now we can
just bail if coding sequence ends before the variant hits it. Also
fixing a couple bone-headed incorrect invocations of slAddTail, and
making sure that an exon's splice_region_variant is listed with an
exon number, not an intron number.
refs #11775, #11771
- Fixing corner case: if we hit the end of rowBuf in nextRowFromBuffer,then discover in asdDoQueryChunking that we don't need to query again,
then we need to reset rowBuf because when we return to nextRowFromBuffer,
we check rowBuf->size which should be 0. We could also check self->eof,
but I think it's cleaner to have the correct rowBuf state.
- src/hg/lib/annoStreamDb.c - lines changed 3, context: html, text, full: html, text
- Adding search specs for snp138 tracks (thx Luvina!) refs #11438
- src/hg/makeDb/trackDb/human/hg19/trackDb.ra - lines changed 1, context: html, text, full: html, text
- src/hg/makeDb/trackDb/trackDb.ra - lines changed 32, context: html, text, full: html, text
- Adding percentages to reports of hits and misses so we don't have to manually calculate those.
- src/hg/makeDb/schema/joinerCheck/joinerCheck.c - lines changed 10, context: html, text, full: html, text
- mysql 5.6 doesn't accept TYPE= anymore, we must use ENGINE=.
- src/hg/lib/rgdQtlLink.sql - lines changed 1, context: html, text, full: html, text
- Steve found a joinerCheck error about a duplicate ID in rn4.rgdQtl.Comments in doc/rn4.txt indicated that the dupe should have been
resolved, but somehow the database tables on hgwdev did not reflect
the fix. So I followed the same steps in rn4.txt to fix the dupe,
and the joinerCheck error is resolved on hgwdev.
- src/hg/makeDb/doc/rn4.txt - lines changed 3, context: html, text, full: html, text
- Resolving various joinerCheck errors found by Steve.
- src/hg/makeDb/schema/all.joiner - lines changed 35, context: html, text, full: html, text
- When user selects Artificial Example Variants, force genome-wide searchbecause the example variants often fall outside of the cart position range.
refs #11110
- Fixing incorrect comment found by Brian L. refs #11200
- f8bcbbee didn't go far enough to completely fix #11787 -- I forgot toaccount for changing chromosomes.
fixes #11787
refs #11775
- src/lib/annoStreamVcf.c - lines changed 5, context: html, text, full: html, text
- Refining a 10-year-old kludge for a few tracks that have thickStart=thickEnd=0,but want thick items. There aren't many, but they include wgRna in hg18 and hg19,
and hg18.ncRna. Without this additional check for item start != 0, it's possible
for the kludge to falsely trigger on items that have thickStart=thickEnd=chromStart
when chromStart just happens to be 0, for example in DGV. Of the remaining tracks
that need this kludge, none seem to have chromStart=0, so this seems to take care of
both new and old tracks. In the long term, it would be best for all tables to
just have thickStart=chromStart and thickEnd=chromEnd if they want thick items.
fixes #11870
- src/hg/hgTracks/simpleTracks.c - lines changed 1, context: html, text, full: html, text
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