Commits for angie
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v260_base to v261_preview (2011-12-06 to 2011-12-13) v261
- Feature #6172 (ISCA track tweaks): per ISCA's requests, change"Structural variant cluster" to "Variant region", add link to dbVar's
variant page, and add link to dbVar's page for the ISCA study (nstd37).
- src/hg/makeDb/trackDb/human/iscaComposite.html - lines changed 3, context: html, text, full: html, text
- Feature #6172 (ISCA track tweaks): per ISCA's request, appendabbreviated variant origin to display names.
- src/hg/hgTracks/gvfTrack.c - lines changed 28, context: html, text, full: html, text
- Feature #3711 (VCF haplo-sorting display): David requested that non-leafbranches always appear as rectangles. Now the triangular vs. rectangular
option applies only to leaf clusters.
- src/hg/hgTracks/vcfTrack.c - lines changed 10, context: html, text, full: html, text
- Feature #3711 (VCF haplo-sorting display): minor tweaks to horizontalendpoints of clustering tree lines, so that they join up in PS/PDF
instead of leaving a little gap.
- src/hg/hgTracks/vcfTrack.c - lines changed 6, context: html, text, full: html, text
- Doc #5529 (VCF+tabix doc): updated for recent enhancements (see #3711).Also reworked some parts to be more clear & accurate.
- src/hg/htdocs/goldenPath/help/hgVcfTrackHelp.html - lines changed 53, context: html, text, full: html, text
- Feature #3710 (vcfTabix UI): describe QUAL using the same words as in hgc, as Katrina suggests.
- Feature #6172 (ISCA track tweaks): refinements suggested by b0b;also spotted the opportunity to link to the Human Phenotype Ontology
browser, helpful when the Phenotype is something like "Craniosynostosis".
- src/hg/hgTracks/gvfTrack.c - lines changed 1, context: html, text, full: html, text
- Updating local default version of tabix to 0.2.5.
- Thanks Brian for catching the "need to warn here" loose end in code review --now there is an actual warning. I also updated bam.c to have the same
maxOut improvements as vcf.c.
Unfortunately, we still have the problem that several layers of code will
have to be modified in order to have genome-wide maxOut instead of per-region,
for non-wiggle data types.
- Track #1656 (GWAS Catalog): bi-monthly update. The initSample columnneeds to be a longblob not varchar because there are a couple very
long descriptions -- no change to the C code fortunately because it's
just a char * either way.
- src/hg/inc/gwasCatalog.h - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
- src/hg/lib/gwasCatalog.as - lines changed 1, context: html, text, full: html, text
- src/hg/lib/gwasCatalog.sql - lines changed 1, context: html, text, full: html, text
- src/hg/makeDb/doc/hg18.txt - lines changed 11, context: html, text, full: html, text
- src/hg/makeDb/doc/hg19.txt - lines changed 7, context: html, text, full: html, text
- Feature #3707 (VCF+tabix in hgTables): the filter page was not showingthe "Limit data output to [100,000]" option for BAM and VCF custom tracks.
- src/hg/hgTables/filterFields.c - lines changed 1, context: html, text, full: html, text
- Fixing some dumb non-reentrant code that caused a race condition whenmultiple VCF tracks are translating VCF to pgSnp in different threads.
This led to a sporadic error reported by Greg and caught in a session
by Brooke in #2823 (VCF track handler, notes 12 & 14).
- More informative error message for debugging.
- src/hg/hgTracks/simpleTracks.c - lines changed 6, context: html, text, full: html, text
- Feature #2823 (VCF+tabix track handler): found & fixed more non-reentrant code that can lead to race conditions when multiple VCF
tracks are loaded in parallel. More than 1000 tries have been
successful compared to 5 or 6 failures per 1000 tries before.
- src/hg/hgTracks/vcfTrack.c - lines changed 38, context: html, text, full: html, text
- Feature #5019 (VCF support in track hubs): Pauline found that next/previtem arrows were appearing for VCF tracks in hubs, but they don't work.
Brian pointed out that the hgTracks handler can disable the inherited
settings that enable the arrows. Done. Not sure why the arrows appeared
only for hub VCF tracks, not VCF custom tracks.
- src/hg/hgTracks/vcfTrack.c - lines changed 4, context: html, text, full: html, text
- Feature #3707 (VCF in hgTables): Brooke pointed out that the headerline that shows the selected fields should appear just before the data
rows (note 25). I had put it up top to invalidate the VCF header, but
that was silly. Instead, put an informational comment up top explaining
that the output is not valid VCF, and put the selected-columns header
line where it belongs.
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