hiram: changes by commit

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

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