Commits for angie

v277_base to v278_preview (2012-12-18 to 2013-01-08) v278

• Code Review #9844 - Hiram pointed out that localmem.h is not protectedagainst multiple inclusion; fixed. Also cleaned up some redundant
  inclusions of localmem.h in files that already include bbiFile.h.
  
  • src/inc/localmem.h - lines changed 5, context: html, text, full: html, text
  • src/lib/bbiRead.c - lines changed 1, context: html, text, full: html, text
  • src/lib/bbiWrite.c - lines changed 1, context: html, text, full: html, text
  • src/lib/bigBed.c - lines changed 1, context: html, text, full: html, text
  • src/lib/bwgCreate.c - lines changed 1, context: html, text, full: html, text
  • src/lib/bwgQuery.c - lines changed 1, context: html, text, full: html, text
  • src/lib/bwgValsOnChrom.c - lines changed 1, context: html, text, full: html, text
• html tag typo fix (found by hgTablesTest).
  • src/hg/makeDb/trackDb/human/hg19/snp137.shared.html - lines changed 1, context: html, text, full: html, text
• IGTC member link corrections from Steve.
  • src/hg/makeDb/trackDb/mouse/igtc.html - lines changed 6, context: html, text, full: html, text
• Track #7043 (SNPs for mm10): added ignoreDbSnpContigsFile config.ra option (see -help output).
  • src/hg/utils/automation/doDbSnp.pl - lines changed 28, context: html, text, full: html, text
• Track #7043 (SNPs for mm10): build snp137* for mouse.
  • src/hg/makeDb/doc/mm10.txt - lines changed 213, context: html, text, full: html, text
• Track #7043 (SNPs for mm10): bump up MAX_SNP_ID.
  • src/hg/snp/snpLoad/snpNcbiToUcsc.c - lines changed 2, context: html, text, full: html, text
• Track #7043 (SNPs for mm10): Move trackDb & html stuff for Common SNPs,Mult SNPs and All SNPs up from human/hg19 to top level for sharing
  with mouse. Leave Flagged SNPs in human/hg19 because that track is
  human-only, and mention Flagged SNPs only in human description.
  
  • src/hg/makeDb/trackDb/human/hg19/snp137.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/snp137.shared.html - lines changed 462, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/snp137Common.html - lines changed 28, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/snp137Flagged.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/snp137FlaggedMention.html - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/snp137Mult.html - lines changed 25, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/trackDb.ra - lines changed 47, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm10/trackDb.ra - lines changed 10, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/snp137.html - lines changed 31, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/snp137.shared.html - lines changed 460, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/snp137Common.html - lines changed 28, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/snp137Mult.html - lines changed 25, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/trackDb.ra - lines changed 50, context: html, text, full: html, text
• Bug #9860 (Table Browser paste identifiers button not working for 1000 genomes ph1 Accessible Regions):getExamples() was unaware of bigBed, so an illegal mysql query was constructed.
  Fix: added randomBigBedIds(). While in there, enhanced ramdomVcfIds() to ignore
  runs of identical IDs because those are placeholders, and might otherwise crowd
  out a few meaningful IDs (#8886 note 28).
  
  • src/hg/hgTables/bigBed.c - lines changed 41, context: html, text, full: html, text
  • src/hg/hgTables/hgTables.h - lines changed 3, context: html, text, full: html, text
  • src/hg/hgTables/identifiers.c - lines changed 13, context: html, text, full: html, text
  • src/hg/hgTables/vcf.c - lines changed 9, context: html, text, full: html, text