Commits for angie
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v256_base to v257_preview (2011-08-29 to 2011-09-06) v257
- Feature #2821 (VCF parser): Fun with flawed input. This file's rows have6 keywords in the format column, but most genotype columns have only 5
pieces of data:
ftp://ftp-trace.ncbi.nlm.nih.gov/1000genomes/ftp/release/20100804/supporting/AFR.BI_withr2.20100804.genotypes.vcf.gz
This causes many vcfFileErr calls in vcfParseGenotypes. Turned out that
vcfFileErr was not stopping after the specified # of errors; and that the
warnings are so verbose that I don't think we really need to display them
in hgTracks and hgc. So they are now ignored, and we don't segv on missing
genotype info.
- src/hg/hgTracks/vcfTrack.c - lines changed 9, context: html, text, full: html, text
- Feature #3711 (VCF haplotype-sorting display): Changing appearance ofcluster tree in the left label area. I was drawing trees as I had seen
in microarray & other clustering tools, but David wants something more
compatible with the species-tree view... I'll just quote David here:
It has to look like a legitmate species tree, exactly like the ones on
the details page of the vertebrate conservation track. The only
difference here is that some leaf objects are fatter than other, and it
is not clear where one leaf begins and the other ends.
You need to
1. always draw the branch all the way to the right side (leaf level) so
all the leaves are at the leaf level.
2. The vertical bar representing the "footprint" of each leaf (i.e. the
span of the rows of that cluster) needs to terminate at least 1 or 2
pixels before the edge of the cluster of rows for a given leaf, so there
is white space between clusters. (Or put a colored or bold or vertical
mark at the edge of a cluster of rows.)
- src/hg/hgTracks/vcfTrack.c - lines changed 23, context: html, text, full: html, text
- Feature #2823 (VCF track handler): on details page, display allele andgenotype frequencies as percents. When genotypes are given, display
Hardy-Weinberg equilibrium genotype probabilities for comparison.
- Use safecpy instead of safef when there is no formatting to do, so we avoidstrict compiler warnings about variable used as format string.
- src/hg/lib/hubConnect.c - lines changed 1, context: html, text, full: html, text
- Track #5133 (dbSNP 134):Generated all track tables, added trackDb entries and html based on snp132.
Registered track handlers in hgTracks.c -- really this should become a track
type so CGI tweaks aren't required every time.
Processing pipeline updates:
- doDbSnp.pl: dbSNP split allele frequency data into two tables
(SNPAlleleFreq and SNPAlleleFreq_TGP) in human 134, so now we need to
download SNPAlleleFreq_TGP and integrate it with SNPAlleleFreq. I added
a new script for the integration: snpAddTGPAlleleFreq.pl.
Also, when db has a par table, extract its rows and pass to snpNcbiToUcsc.
- snpNcbiToUcsc: loosened some regex's, increased MAX_SNPID
Also, dbSNP is still assigning weight=3 to alleles that map uniquely to
X PAR and Y PAR. In 132 I fixed this with awk; now handled internally.
- snpMaskSingle: instead of printing reports of differing observed alleles
at the same position to stderr, optionally save them to a file because
there are thousands of them.
Clicking around the new tracks, I already see some possible cases of missing
frequency data, so it's possible that I'll have to get updated frequency info
from dbSNP and re-run.
- src/hg/hgTracks/simpleTracks.c - lines changed 7, context: html, text, full: html, text
- src/hg/makeDb/doc/hg19.txt - lines changed 378, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg19/trackDb.ra - lines changed 45, context: html, text, full: html, text
- src/hg/makeDb/trackDb/snp134.html - lines changed 36, context: html, text, full: html, text
- src/hg/makeDb/trackDb/snp134.shared.html - lines changed 360, context: html, text, full: html, text
- src/hg/makeDb/trackDb/snp134Common.html - lines changed 28, context: html, text, full: html, text
- src/hg/makeDb/trackDb/snp134Flagged.html - lines changed 29, context: html, text, full: html, text
- src/hg/makeDb/trackDb/snp134Mult.html - lines changed 25, context: html, text, full: html, text
- src/hg/makeDb/trackDb/trackDb.ra - lines changed 55, context: html, text, full: html, text
- src/hg/snp/snpLoad/snpNcbiToUcsc.c - lines changed 21, context: html, text, full: html, text
- src/hg/snp/snpMask/snpMaskSingle.c - lines changed 17, context: html, text, full: html, text
- src/hg/utils/automation/doDbSnp.pl - lines changed 39, context: html, text, full: html, text
- src/hg/utils/automation/snpAddTGPAlleleFreq.pl - lines changed 221, context: html, text, full: html, text
- Track #1656 (GWAS Catalog): monthly update on hgwdev.
- src/hg/makeDb/doc/hg18.txt - lines changed 16, context: html, text, full: html, text
- src/hg/makeDb/doc/hg19.txt - lines changed 16, context: html, text, full: html, text
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