File Changes for angie

v243_base to v244_preview (2010-11-02 to 2010-11-16) v244

• src/hg/hgTracks/simpleTracks.c
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    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.
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    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/lib/customFactory.c
  • lines changed 5, 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/hgFind.c
  • 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).
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    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.
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    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.
• src/hg/makeDb/doc/hg17.txt
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    Track #1702 (DGV update): need to update hg17 too (minimal changes).
• src/hg/makeDb/doc/hg18.txt
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    Track #1702 (DGV update): done in hg18 and hg19.
• src/hg/makeDb/doc/hg19.txt
  • lines changed 61, context: html, text, full: html, text
    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.
  • lines changed 8, context: html, text, full: html, text
    Track #1702 (DGV update): done in hg18 and hg19.
  • lines changed 429, 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/makeDb/trackDb/human/hg18/pgSnp.html
  • lines changed 160, context: html, text, full: html, text
    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.
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    Removed a bit of pubmed link cruft.
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    Track #683: Moving the new pgIrish from pgSnpHgwdev to pgSnp.
• src/hg/makeDb/trackDb/human/hg18/trackDb.ra
  • lines changed 15, context: html, text, full: html, text
    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/hg19/trackDb.ra
  • lines changed 11, 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/makeDb/trackDb/human/trackDb.ra
  • lines changed 270, context: html, text, full: html, text
    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.
  • lines changed 51, context: html, text, full: html, text
    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.
  • lines changed 8, context: html, text, full: html, text
    Oops, lost pgYoruban2 (which will remain hgwdev-only) when merging mypgSnp human/trackDb.ra changes with Belinda's.
  • lines changed 15, context: html, text, full: html, text
    Track #683: Moving the new pgIrish from pgSnpHgwdev to pgSnp.
  • lines changed 17, context: html, text, full: html, text
    Track #1702 (DGV update): add release alpha definition for dataVersion v9 -> v10.
• src/hg/makeDb/trackDb/tagTypes.tab
  • lines changed 1, 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/makeDb/trackDb/trackDb.ra
  • lines changed 12, 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/snp/snpLoad/snpNcbiToUcsc.c
  • lines changed 7, context: html, text, full: html, text
    Tweaks for successfully parsing dbSNP human 132 data.
  • lines changed 7, context: html, text, full: html, text
    Revert "Tweaks for successfully parsing dbSNP human 132 data." This reverts commit 2deaf8fc3e14d917fda89a30aa15809a7dc4d08e.
  • lines changed 7, context: html, text, full: html, text
    Track #1684 (SNPs 132 (dbSNP)): Tweaks for successfully parsinghuman b132 data.