Commits for angie
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v258_base to v259_preview (2011-10-10 to 2011-10-25) v259
- Bug #5591 (dup. GO id's in joining query w/knownGene, kgXref):1. Band-aid: remove successive duplicates from joined output.
It would be better to prevent duplicate queries upstream, but
significantly more work.
2. Got rid of unnecessary duplication of code (joinedTablesTabOut
and joinedTablesTabOutFile) that would have required the same fix
in two places.
- src/hg/hgTables/joining.c - lines changed 60, context: html, text, full: html, text
- Fixing stricter compiler warning (warning: format not a string literal and no format arguments)
- src/hg/lib/hubConnect.c - lines changed 1, context: html, text, full: html, text
- Removing unwanted double-quote at end of line that is pulled in by loosened regex.
- Feature #3710 (vcfTabix UI options): added filtering on minor allelefrequency (actually, 1 - major allele frequency), if INFO column
contains the AF tag, or AC and AN tags.
Also, in vcfTrack.c, fixed a bug in multi-allele abbreviation code
in vcfFileToPgSnp.
- src/hg/hgTracks/vcfTrack.c - lines changed 102, context: html, text, full: html, text
- Track #34 (dbVar / ISCA): Added iscaRetrospective subtracks to hg19,including two new subtracks (likely benign & likely pathogenic) for
categories that were not present when I loaded data into hg18.
- src/hg/makeDb/doc/hg19.txt - lines changed 74, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/trackDb.ra - lines changed 29, context: html, text, full: html, text
- Track #34 (dbVar / ISCA): Removed "Retrospective" from the track namesbecause prospective data are included now. Reloaded both hg18 and hg19
isca* with both "submitted" (on this assembly) and "remapped" (from some
other assembly) files from dbVar. Changed subtrack order to match ISCA
custom tracks' order.
- src/hg/makeDb/doc/hg18.txt - lines changed 43, context: html, text, full: html, text
- src/hg/makeDb/doc/hg19.txt - lines changed 28, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/trackDb.ra - lines changed 56, context: html, text, full: html, text
- Track #34 (dbVar/ISCA): forgot to rename .html when renaming tracks, thanks b0b for catching!
- src/hg/makeDb/trackDb/human/iscaComposite.html - lines changed 123, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/iscaRetrospectiveComposite.html - lines changed 123, context: html, text, full: html, text
- Registered track handlers for snp135 tables, to make sure they're in the next release.
- src/hg/hgTracks/simpleTracks.c - lines changed 4, context: html, text, full: html, text
- Track #1702 (DGV update): Loaded DGV's beta data in new file format into hg19.This is just a dry run to check out the new format, no need to QA until their
data integration is complete.
- src/hg/makeDb/doc/hg19.txt - lines changed 66, context: html, text, full: html, text
- Code review advice from Tim about how to properly use ClosestToHome.
- src/hg/hgTracks/vcfTrack.c - lines changed 39, context: html, text, full: html, text
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