File Changes for angie

v248_base to v249_preview (2011-03-08 to 2011-03-15) v249

• src/hg/hgFileSearch/hgFileSearch.c
  • lines changed 1, context: html, text, full: html, text
    Fixing Ubuntu gcc warnings by using puts instead of printf-without-format.
• src/hg/hgTrackUi/hgTrackUi.c
  • lines changed 6, 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/hgTracks/bedTrack.c
  • lines changed 28, 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/searchTracks.c
  • lines changed 1, context: html, text, full: html, text
    Fixing Ubuntu gcc warnings by using puts instead of printf-without-format.
• src/hg/hgTracks/variation.c
  • lines changed 14, context: html, text, full: html, text
    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/hgc/hgdpClick.c
  • lines changed 7, context: html, text, full: html, text
    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.
• src/hg/inc/cart.h
  • 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.
• src/hg/lib/cart.c
  • lines changed 49, 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.
• src/hg/lib/trackDbCustom.c
  • lines changed 1, context: html, text, full: html, text
    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/makeDb/doc/hg19.txt
  • lines changed 51, context: html, text, full: html, text
    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/hgTrackDb/hgTrackDb.c
  • lines changed 28, 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/trackDb/README
  • lines changed 3, 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/trackDb/human/hg19/snp132ParTweak.html
  • lines changed 13, 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/snp132.shared.html
  • lines changed 1, 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/utils/refSeqGet/makefile
  • lines changed 1, context: html, text, full: html, text
    Recurse to tests in the clean target.
• src/inc/linefile.h
  • lines changed 2, 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/inc/vcf.h
  • lines changed 181, 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/jkOwnLib/genoFind.c
  • lines changed 1, 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/lib/linefile.c
  • lines changed 9, 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/lib/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/lib/regexHelper.c
  • lines changed 9, context: html, text, full: html, text
    Build a more accurate description in regexMatchSubstrMaybeCase.
• src/lib/tests/expected/tabixFetch1kGNoGenotypes.out
  • lines changed 6, 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/tabixFetch1kGWithGenotypes.out
  • lines changed 7, 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/vcfParse1kGNoGenotypes.out
  • lines changed 7, 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/vcfParse1kGWithGenotypes.out
  • lines changed 8, 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/input/YRI.low_coverage.2010_07_excerpt.genotypes.vcf.gz
  • lines changed 0, 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/input/YRI.low_coverage.2010_07_excerpt.genotypes.vcf.gz.tbi
  • lines changed 0, 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/input/YRI.trio.2010_06.novelsequences.sites.vcf.gz
  • lines changed 0, 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/input/YRI.trio.2010_06.novelsequences.sites.vcf.gz.tbi
  • lines changed 0, 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/makefile
  • lines changed 37, 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/tabixFetch.c
  • lines changed 114, 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...
  • lines changed 1, 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/vcfParseTest.c
  • lines changed 56, 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/vcf.c
  • lines changed 767, 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.]
  • lines changed 8, 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.
• src/oneShot/tabixFetch/makefile
  • lines changed 18, 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/oneShot/tabixFetch/tabixFetch.c
  • lines changed 114, 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/oneShot/vcfParseTest/makefile
  • lines changed 18, 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.]
  • lines changed 18, 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/oneShot/vcfParseTest/vcfParseTest.c
  • lines changed 56, 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.]
  • lines changed 56, 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...