File Changes for angie

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

• src/hg/hgTables/bigBed.c
  • lines changed 41, 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/hgTables.h
  • lines changed 3, 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/identifiers.c
  • lines changed 13, 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/vcf.c
  • lines changed 9, 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/makeDb/doc/mm10.txt
  • lines changed 213, context: html, text, full: html, text
    Track #7043 (SNPs for mm10): build snp137* for mouse.
• src/hg/makeDb/trackDb/human/hg19/snp137.html
  • lines changed 1, 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.shared.html
  • lines changed 1, context: html, text, full: html, text
    html tag typo fix (found by hgTablesTest).
  • lines changed 462, 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/snp137Common.html
  • lines changed 28, 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/snp137Flagged.html
  • lines changed 1, 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/snp137FlaggedMention.html
  • lines changed 4, 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/snp137Mult.html
  • lines changed 25, 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/trackDb.ra
  • lines changed 47, 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/mouse/igtc.html
  • lines changed 6, context: html, text, full: html, text
    IGTC member link corrections from Steve.
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.ra
  • lines changed 10, 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/snp137.html
  • lines changed 31, 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/snp137.shared.html
  • lines changed 460, 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/snp137Common.html
  • lines changed 28, 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/snp137Mult.html
  • lines changed 25, 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/trackDb.ra
  • lines changed 50, 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/snp/snpLoad/snpNcbiToUcsc.c
  • lines changed 2, context: html, text, full: html, text
    Track #7043 (SNPs for mm10): bump up MAX_SNP_ID.
• src/hg/utils/automation/doDbSnp.pl
  • lines changed 28, context: html, text, full: html, text
    Track #7043 (SNPs for mm10): added ignoreDbSnpContigsFile config.ra option (see -help output).
• src/inc/localmem.h
  • lines changed 5, context: html, text, full: html, text
    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/lib/bbiRead.c
  • lines changed 1, context: html, text, full: html, text
    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/lib/bbiWrite.c
  • lines changed 1, context: html, text, full: html, text
    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/lib/bigBed.c
  • lines changed 1, context: html, text, full: html, text
    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/lib/bwgCreate.c
  • lines changed 1, context: html, text, full: html, text
    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/lib/bwgQuery.c
  • lines changed 1, context: html, text, full: html, text
    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/lib/bwgValsOnChrom.c
  • lines changed 1, context: html, text, full: html, text
    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.