hiram: changes by file

review to branch (2009-03-03 to 2009-03-10) v202

• src/hg/makeDb/doc/hg19.txt
  • 1.2 lines changed: 145, context: html, text, full: html, text
    Done with masking, ready to start genbank when that gets out there
  • 1.1 lines changed: 142, context: html, text, full: html, text
    Initial database established
• src/hg/makeDb/genbank/etc/genbank.conf
  • 1.329 lines changed: 24, context: html, text, full: html, text
    Added hg19.
• src/hg/makeDb/trackDb/makefile
  • 1.264 lines changed: 1, context: html, text, full: html, text
    Adding hg19Haps
  • 1.263 lines changed: 1, context: html, text, full: html, text
    Adding hg19
• src/hg/makeDb/trackDb/haplotypes/hg19Haps/description.html
  • 1.2 lines changed: 1, context: html, text, full: html, text
    fixup ssto_hap6 name to ssto_hap7
  • 1.1 lines changed: 33, context: html, text, full: html, text
    Initial set of files describing these haplotypes
• src/hg/makeDb/trackDb/haplotypes/hg19Haps/gap.html
  • 1.1 lines changed: 10, context: html, text, full: html, text
    Initial set of files describing these haplotypes
• src/hg/makeDb/trackDb/haplotypes/hg19Haps/gold.html
  • 1.2 lines changed: 1, context: html, text, full: html, text
    fixup ssto_hap6 name to ssto_hap7
  • 1.1 lines changed: 21, context: html, text, full: html, text
    Initial set of files describing these haplotypes
• src/hg/makeDb/trackDb/haplotypes/hg19Haps/trackDb.ra
  • 1.1 lines changed: 19, context: html, text, full: html, text
    Initial set of files describing these haplotypes
• src/hg/makeDb/trackDb/human/hg19/description.html
  • 1.1 lines changed: 129, context: html, text, full: html, text
    Initial set of files from makeGenomeDb.pl
• src/hg/makeDb/trackDb/human/hg19/gap.html
  • 1.1 lines changed: 63, context: html, text, full: html, text
    Initial set of files from makeGenomeDb.pl
• src/hg/makeDb/trackDb/human/hg19/gold.html
  • 1.1 lines changed: 22, context: html, text, full: html, text
    Initial set of files from makeGenomeDb.pl
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • 1.2 lines changed: 11, context: html, text, full: html, text
    Add haplotypeChain track
  • 1.1 lines changed: 20, context: html, text, full: html, text
    Initial set of files from makeGenomeDb.pl
• src/hg/utils/automation/HgAutomate.pm
  • 1.22 lines changed: 8, context: html, text, full: html, text
    Fixup specification of filesystem locations, and add -noGoldGapSplit option to makeGenomeDb
• src/hg/utils/automation/doHgNearBlastp.pl
  • 1.6 lines changed: 1, context: html, text, full: html, text
    change blastPath
• src/hg/utils/automation/makeDownloads.pl
  • 1.19 lines changed: 20, context: html, text, full: html, text
    Add -ignoreRepeatMasker flag to avoid looking for the *.out files
• src/hg/utils/automation/makeGenomeDb.pl
  • 1.20 lines changed: 17, context: html, text, full: html, text
    add -noGoldGapSplit option
• src/hg/utils/automation/makePushQSql.pl
  • 1.22 lines changed: 3, context: html, text, full: html, text
    Special case the 2micron chrom name on sacCer2
• src/hg/utils/gapToLift/gapToLift.c
  • 1.7 lines changed: 10, context: html, text, full: html, text
    Fixup counting of parts to be more accurate and a uniform %02d output