Commits for angie
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v260_preview2 to v260_base (2011-11-22 to 2011-12-06) v260
- Feature #3711 (VCF haplotype-sorting display): reduce min height to 4, because there can be as few as 4 haplotypes to sort.
- Feature #3711 (VCF haplotype-sorting display): Fixed a silly boundary& rounding error in pixel loop. Also, use lower case for alternate
allele in cluster mouseovers so the relationship to blue and red pixels
is more clear.
- src/hg/hgTracks/vcfTrack.c - lines changed 7, context: html, text, full: html, text
- Tweak to make less editing work in the future: derive dated directoryname from output of date command instead of search & replace.
- src/hg/makeDb/doc/hg19.txt - lines changed 3, context: html, text, full: html, text
- Feature #2822 (VCF customFactory): Fixing typo caught by Brooke.
- src/hg/htdocs/goldenPath/help/vcf.html - lines changed 2, context: html, text, full: html, text
- oops, forgot cartSaveSession() in VCF details page's little form to anchor haplotype sorting to this variant.
- MLQ #6136: adding support for VCF 3.3 header line formats.
- Feature #3710 (vcfTabix UI options): added section headers forhaplo-sorting display and filters; added some explanatory text at
the beginning of the haplo-sorting section.
- Fix for buffer overflow case found by Brooke, in vcfToPgSnp allele-abbreviating code.
- src/hg/hgTracks/vcfTrack.c - lines changed 1, context: html, text, full: html, text
- Feature #3707 (VCF+tabix support in hgTables): Brooke reported out-of-memconditions in notes 11 & 12. Fix: add an optional threshold on the number
of records to retrieve in vcfTabixFileMayOpen.
- src/hg/hgTracks/vcfTrack.c - lines changed 1, context: html, text, full: html, text
- src/hg/lib/customFactory.c - lines changed 1, context: html, text, full: html, text
- Feature #3707 (VCF in hgTables): when calling vcf.c's addFilteredBedsOnRegion ina loop, apply maxOut cumulatively, instead of separately for each region.
Unfortunately, some higher-level code calls vcfGetFilteredBedsOnRegions with
one region at a time, so it doesn't know it's running in a loop. The check for
maxOut needs to move up to top-level (e.g. doSummaryStats), or VCF needs its own
top-level routines, or a true genome-wide query needs to be possible in hgTables.
- Feature #3707 (VCF in hgTables): Brooke pointed out the annoyance ofVCF custom track's hyperlinks output setting vis to full when it was
already pack. Turns out that the canPack info for all custom tracks
was being discarded due to use of hTrackOpenVis which looks for
trackDb in database. We usually already have the tdb anyway, so when
it's available, look at tdb->canPack and set vis only if the track is
currently hidden.
Also, while looking into a timeout case that Brooke identified, I noticed
that hgTables wasn't calling knetUdc so it was using samtools & tabix's
knetfile library instead of our own -- fixed.
- src/hg/hgTables/hgTables.c - lines changed 48, context: html, text, full: html, text
- Oops, forgot to run 'make test' before committing, and overlookeda test program...
- src/lib/tests/vcfParseTest.c - lines changed 1, context: html, text, full: html, text
- Feature #3711 (VCF haplo-sorting display): Implemented Richard Durbin'ssuggestions as new defaults:
1. Instead of ref=blue, alt=red, simply ignore ref and draw only alt, in black.
Draw top & bottom bounds of variants in extra pixel rows.
2. Draw the tree using open triangles instead of open rectangles.
- src/hg/hgTracks/vcfTrack.c - lines changed 164, context: html, text, full: html, text
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