Commits for angie
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v248_base to v249_preview (2011-03-08 to 2011-03-15) v249
- Track #1684 (SNPs 132 (dbSNP)): regenerated snp132 with updatedsnpNcbiToUcsc's -par option. Tweaked singly-mapped PAR SNPs' weights
to 1 (dbSNP agrees they should be 1 not 3 and plans to fix).
Regenerated subset tracks snp132{Common,Patient,NonUnique}.
- src/hg/makeDb/doc/hg19.txt - lines changed 51, context: html, text, full: html, text
- Build a more accurate description in regexMatchSubstrMaybeCase.
- Recurse to tests in the clean target.
- src/hg/utils/refSeqGet/makefile - lines changed 1, context: html, text, full: html, text
- Feature #2821 (VCF parser): works on a 1000 Genomes pilot release VCF+tabix file with genotypes.[Note: this is a squash of 6 commits, developed off in my vcf branch.]
- src/oneShot/vcfParseTest/makefile - lines changed 18, context: html, text, full: html, text
- src/oneShot/vcfParseTest/vcfParseTest.c - lines changed 56, context: html, text, full: html, text
- Bug #3150 (blat is crashing): The gfPepTile logic assumes that aaValcontains either -1 or 0 to 19. Previously, aaVal['X'] was -1. Then
in 1b5e64c4, 'X' was added to dnautil.c's aminoAcidTable and therefore
to aaVal, with aaVal['X'] = 20. One of the peptide test sequences
ends with "XXXXX", which caused gfPepTile to produce an out-of-range
tile, leading to a SEGV in gfStraightFindHits. Fix: if aaVal[] is > 19,
treat as if -1.
- src/jkOwnLib/genoFind.c - lines changed 1, context: html, text, full: html, text
- Extended hgTrackDb's new #insert syntax: optionally it may be precededby a conditional on the database, e.g.
<!-- #if (db==hg19) #insert file="human/hg19/specialNote.html" -->
- src/hg/makeDb/hgTrackDb/hgTrackDb.c - lines changed 28, context: html, text, full: html, text
- src/hg/makeDb/trackDb/README - lines changed 3, context: html, text, full: html, text
- Track #1684 (SNPs 132 (dbSNP)): At Brooke's suggestion, added a noteto the #Weight section about the tweaking of weights in the PAR region.
- src/hg/makeDb/trackDb/human/hg19/snp132ParTweak.html - lines changed 13, context: html, text, full: html, text
- src/hg/makeDb/trackDb/snp132.shared.html - lines changed 1, context: html, text, full: html, text
- Feature/Bug #3148 (DGV description page refs): fixing bug found by b0b:the filter on PubMed references was set to "include" by default, but all
checkboxes were empty by default. Fix: if the checkbox group variable is
not defined in the cart, then set all checkboxes.
- src/hg/hgTrackUi/hgTrackUi.c - lines changed 6, context: html, text, full: html, text
- While working on something else, I realized that when cartRemove iscalled on a list variable, it should remove the list's multShadow
variable in addition to all values, because the list variable is no
longer defined in the cart. If the multShadow is left around, it will
look like the variable is in the cart, set to empty.
- Track #34 (dbVar for human): new track type gvf needs to be made packable in trackDbCustom.c. I forget this every time I make a new track type.
- src/hg/lib/trackDbCustom.c - lines changed 1, context: html, text, full: html, text
- Track #34 (dbVar for human): Hooked up next/prev exon methodfor simple bed tracks, which simply hops to right edge/left edge
of items hanging off the end of the window.
- src/hg/hgTracks/bedTrack.c - lines changed 28, context: html, text, full: html, text
- Mark rightly pointed out that these programs I used for quick testingshould go in lib/tests with proper testcases, not in oneShot/.
Test cases coming up...
- src/lib/tests/tabixFetch.c - lines changed 114, context: html, text, full: html, text
- src/lib/tests/vcfParseTest.c - lines changed 56, context: html, text, full: html, text
- src/oneShot/tabixFetch/makefile - lines changed 18, context: html, text, full: html, text
- src/oneShot/tabixFetch/tabixFetch.c - lines changed 114, context: html, text, full: html, text
- src/oneShot/vcfParseTest/makefile - lines changed 18, context: html, text, full: html, text
- src/oneShot/vcfParseTest/vcfParseTest.c - lines changed 56, context: html, text, full: html, text
- Feature #2820 (tabix), #2821 (VCF parser): added basic test cases for VCF andtabix -- thanks Mark for the prod.
- src/lib/tests/expected/tabixFetch1kGNoGenotypes.out - lines changed 6, context: html, text, full: html, text
- src/lib/tests/expected/tabixFetch1kGWithGenotypes.out - lines changed 7, context: html, text, full: html, text
- src/lib/tests/expected/vcfParse1kGNoGenotypes.out - lines changed 7, context: html, text, full: html, text
- src/lib/tests/expected/vcfParse1kGWithGenotypes.out - lines changed 8, context: html, text, full: html, text
- src/lib/tests/input/YRI.low_coverage.2010_07_excerpt.genotypes.vcf.gz - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
- src/lib/tests/input/YRI.low_coverage.2010_07_excerpt.genotypes.vcf.gz.tbi - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
- src/lib/tests/input/YRI.trio.2010_06.novelsequences.sites.vcf.gz - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
- src/lib/tests/input/YRI.trio.2010_06.novelsequences.sites.vcf.gz.tbi - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
- src/lib/tests/makefile - lines changed 37, context: html, text, full: html, text
- src/lib/tests/tabixFetch.c - lines changed 1, context: html, text, full: html, text
- Feature #2821 (VCF parser): adding workaround for annoying non-ASCIIcharacters in the header of a file included in 1000 Genomes' pilot
release, found when adding basic test case.
- Bug #3208 (hg19 HGDP Allele Freq hgc position links are broken):doh, using a *StaticLoad and then immediately doing a sqlFreeResult
is a bad idea. No need to scrounge for memory w/StaticLoad in hgc.
- Track #1684 (SNPs 132 (dbSNP)): oops, overwriting snp125->name whenchimp allele is added (in dbb7cbfd) caused the name+allele string to
be passed to hgc as the item name, which causes an errAbort because
the item can't be found. So now we need a mapItemName that strips
off the allele string if any is added.
- src/hg/hgTracks/variation.c - lines changed 14, context: html, text, full: html, text
- Fixing Ubuntu gcc warnings by using puts instead of printf-without-format.
- src/hg/hgFileSearch/hgFileSearch.c - lines changed 1, context: html, text, full: html, text
- src/hg/hgTracks/searchTracks.c - lines changed 1, context: html, text, full: html, text
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