Commits for angie

v259_base to v260_preview (2011-11-07 to 2011-11-15) v260

• Track #5710 (dbSNP 135): minor adjustments to deal with the firstround of dbSNP's FTP files. They will dump a new version, hopefully available next week and hopefully with fewer anomalies.
  • src/hg/snp/snpLoad/snpNcbiToUcsc.c - lines changed 15, context: html, text, full: html, text
• SNP automation: more efficient way to summarize exceptions at end.
  • src/hg/utils/automation/doDbSnp.pl - lines changed 1, context: html, text, full: html, text
• Track #5710 (dbSNP 135): Adding track def's and overrides (exceptthose that would require a new tag...) for snp135 tracks.
  • src/hg/makeDb/trackDb/human/hg19/trackDb.ra - lines changed 43, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/trackDb.ra - lines changed 88, context: html, text, full: html, text
• Track #5710 (dbSNP 135): Adding html descriptions.
  • src/hg/makeDb/trackDb/snp135.html - lines changed 36, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/snp135.shared.html - lines changed 362, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/snp135Common.html - lines changed 28, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/snp135Flagged.html - lines changed 29, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/snp135Mult.html - lines changed 25, context: html, text, full: html, text
• Performance improvement for safencpy when src is a very long string(e.g. chrom sequence): don't do a full strlen; count chars and stop counting if/when we get to specified limit n.
  • src/lib/common.c - lines changed 5, context: html, text, full: html, text
• Track #5710 (dbSNP 135): most of the 2.8M InconsistentAlleles caseswere caused by homozygous non-reference singleton variants submitted by personal genome projects, so I added a new exception, SingleAlleleFreq (2.3M of those in snp135). Now InconsistentAlleles is only for non-singletons (474k in snp135). Also, snp135 has a lot of items with locType="between" but unexpected coords and/or alleles; seems like locType should be something else, and I emailed dbSNP some examples. Meanwhile, those coords need to be adjusted as if their locType weren't "between" in order to avoid other errors that are simply side-effects of the root inconsistency. I removed the error check for refNCBI having the wrong length because it usually overlapped with another error or exception and doesn't really warrant dropping the SNP if there's no other error.
  • src/hg/snp/snpLoad/snpNcbiToUcsc.c - lines changed 34, context: html, text, full: html, text
• Track #5710 (dbSNP 135): built SNP tracks and aux tables & files used by hgc.
  • src/hg/makeDb/doc/hg19.txt - lines changed 380, context: html, text, full: html, text
• Track #5710 (dbSNP 135): added snp135 tables. Removed snp134 tables because only snp135 is going to QA.
  • src/hg/makeDb/schema/all.joiner - lines changed 13, context: html, text, full: html, text