Commits for angie
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v243_base to v244_preview (2010-11-02 to 2010-11-16) v244
- Work in progress for Track #683: moving almost all of Belinda'sGenome Variants hgwdev-only subtracks into the main Genome Variants.
Also updating some reference links and adding subtrack matrix settings.
- src/hg/makeDb/trackDb/human/hg18/pgSnp.html - lines changed 160, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg18/trackDb.ra - lines changed 15, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/trackDb.ra - lines changed 270, context: html, text, full: html, text
- Removed a bit of pubmed link cruft.
- src/hg/makeDb/trackDb/human/hg18/pgSnp.html - lines changed 6, context: html, text, full: html, text
- Bug found by Fan: in our zeal to detect "term:offset" (e.g. "chr1:2385495")search terms, we were mangling IDs like "RGD:2138". Solution: don't support
single-base offsets except for sequences named in chromInfo
(hgOfficialChromName).
- Work in progress for #559: split snp131 into 3 subtracks:Common: uniquely mapped SNPs found by HapMap and/or 1000 Genomes;
Misc: uniquely mapped SNPs;
Non-unique: SNPs that map to more than one genomic location.
Currently I'm only using the validation codes by-hapmap and
by-1000genomes to separate Common and Misc; however, I really
should add a filter on allele frequency because the dbSNP doc
implies that some by-hapmap SNPs only found a single allele,
which would mean they validated that it's not a common SNP.
We don't get allele freq data from dbSNP; would need to fetch
new db dump files etc. It would be great to include allele
freq data in the SNPs track if we go to the trouble, and Jim
has suggested adding a clinically associated bit (although
that bit can be triggered by the most tangential of associations,
like region endpoints in OMIM). Spot-checking other validation
codes, none of them seem reliable enough to use as a basis for
Common. E.g. cluster might be from earlier+later version of same
submitter's bulk submission.
- src/hg/hgTracks/simpleTracks.c - lines changed 1, context: html, text, full: html, text
- src/hg/makeDb/doc/hg19.txt - lines changed 61, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/trackDb.ra - lines changed 51, context: html, text, full: html, text
- Better bug fix for b509f936321e0d635a785f48ee0638744fbc3b8d:chop up a copy, not the original search term, when it looks like
a chrom:offset or chrom:start-end term. Merely restoring the
original for searching left the original term chopped for
error-reporting, which meant a truncated term in the message
when a term couldn't be found, as Fan noticed.
- Oops, lost pgYoruban2 (which will remain hgwdev-only) when merging mypgSnp human/trackDb.ra changes with Belinda's.
- src/hg/makeDb/trackDb/human/trackDb.ra - lines changed 8, context: html, text, full: html, text
- Track #683: Moving the new pgIrish from pgSnpHgwdev to pgSnp.
- src/hg/makeDb/trackDb/human/hg18/pgSnp.html - lines changed 18, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/trackDb.ra - lines changed 15, context: html, text, full: html, text
- Prevent pgSnpRecognizer from returning before calling customPpReuse(as Brooke noticed, this caused the first line to be lost for types
with recognizers that run after pgSnp).
- src/hg/lib/customFactory.c - lines changed 5, context: html, text, full: html, text
- Track #1702 (DGV update): done in hg18 and hg19.
- src/hg/makeDb/doc/hg18.txt - lines changed 11, context: html, text, full: html, text
- src/hg/makeDb/doc/hg19.txt - lines changed 8, context: html, text, full: html, text
- Track #1702 (DGV update): need to update hg17 too (minimal changes).
- src/hg/makeDb/doc/hg17.txt - lines changed 14, context: html, text, full: html, text
- Track #1702 (DGV update): add release alpha definition for dataVersion v9 -> v10.
- src/hg/makeDb/trackDb/human/trackDb.ra - lines changed 17, context: html, text, full: html, text
- Tweaks for successfully parsing dbSNP human 132 data.
- src/hg/snp/snpLoad/snpNcbiToUcsc.c - lines changed 7, context: html, text, full: html, text
- Revert "Tweaks for successfully parsing dbSNP human 132 data."
This reverts commit 2deaf8fc3e14d917fda89a30aa15809a7dc4d08e.
- src/hg/snp/snpLoad/snpNcbiToUcsc.c - lines changed 7, context: html, text, full: html, text
- Track #1684 (SNPs 132 (dbSNP)): Tweaks for successfully parsinghuman b132 data.
- src/hg/snp/snpLoad/snpNcbiToUcsc.c - lines changed 7, context: html, text, full: html, text
- Track #1684 (SNPs 132 (dbSNP)): work in progress: basic tables areloaded (snp132, snp132Exceptions, snp132ExceptionDesc, snp132Seq).
Still need to build ortho alleles, snp132CodingDbSnp; still
need to split up snp132 into subsets which will end up either as
subtracks or individual tracks, TBD; and still need to add new
columns for allele frequency & bitfields (or at least the clinically
assoc'd bit).
- src/hg/hgTracks/simpleTracks.c - lines changed 1, context: html, text, full: html, text
- src/hg/makeDb/doc/hg19.txt - lines changed 429, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg19/trackDb.ra - lines changed 11, context: html, text, full: html, text
- src/hg/makeDb/trackDb/tagTypes.tab - lines changed 1, context: html, text, full: html, text
- src/hg/makeDb/trackDb/trackDb.ra - lines changed 12, context: html, text, full: html, text
- Track #1570 (search using OMIM id used in URL): added support forsingleSearch=omimGeneAcc, or any searchName (which defaults to
searchTable if not defined in trackDb.ra). May not be strictly
necessary for OMIM because as Fan found OMIM numeric IDs already
get unique semiShortCircuit hits, but we expect this to be useful
for track-specific links to us in general.
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