hiram: changes by file

branch to review (2010-04-06 to 2010-04-13) v229

• src/hg/bedItemOverlapCount/bedItemOverlapCount.c
  • 1.21 lines changed: 11, context: html, text, full: html, text
    fixup error in checking argc must be 3 and rework usage message
• src/hg/hgTracks/wigTrack.c
  • 1.103 lines changed: 3, context: html, text, full: html, text
    fix a drawing bug in whiskers plot when graphRange is very near zero
• src/hg/makeDb/doc/ailMel1.txt
  • 1.9 lines changed: 4, context: html, text, full: html, text
    rerun genbank for panda
  • 1.8 lines changed: 1, context: html, text, full: html, text
    add time from gap finding
  • 1.7 lines changed: 45, context: html, text, full: html, text
    done with all.joiner featureBits downloads and in the pushQ
• src/hg/makeDb/doc/hg19.txt
  • 1.98 lines changed: 69, context: html, text, full: html, text
    working on H-Inv 7.0 and new Ensembl name mapping table
  • 1.96 lines changed: 28, context: html, text, full: html, text
    vegaGene update to 37 for mouse to 38 for human
• src/hg/makeDb/doc/makeEnsembl.txt
  • 1.16 lines changed: 244, context: html, text, full: html, text
    finished with v57 ensGene update
• src/hg/makeDb/doc/mm9.txt
  • 1.133 lines changed: 28, context: html, text, full: html, text
    vegaGene update to 37 for mouse to 38 for human
• src/hg/makeDb/doc/susScr2.txt
  • 1.5 lines changed: 14, context: html, text, full: html, text
    finished with v57 ensGene update
• src/hg/makeDb/genbank/etc/align.dbs
  • 1.117 lines changed: 1, context: html, text, full: html, text
    reenable panda ailMel1
  • 1.115 lines changed: 1, context: html, text, full: html, text
    restart ailMel1 panda to fix up xeno Ref Seqs
• src/hg/makeDb/genbank/etc/hgwbeta.dbs
  • 1.107 lines changed: 1, context: html, text, full: html, text
    restart ailMel1 panda to fix up xeno Ref Seqs
• src/hg/makeDb/genbank/etc/hgwdev.dbs
  • 1.121 lines changed: 1, context: html, text, full: html, text
    reenable panda ailMel1
  • 1.119 lines changed: 1, context: html, text, full: html, text
    restart ailMel1 panda to fix up xeno Ref Seqs
• src/hg/makeDb/genbank/src/lib/gbGenome.c
  • 1.78 lines changed: 3, context: html, text, full: html, text
    limit panda to just panda
• src/hg/makeDb/schema/all.joiner
  • 1.786 lines changed: 3, context: html, text, full: html, text
    add HINV-7.0 tables to ignore list for hg19
  • 1.785 lines changed: 19, context: html, text, full: html, text
    fixup hg19 references so it is clean on beta
  • 1.781 lines changed: 1, context: html, text, full: html, text
    SusScr2 leaked into chainDest twice
  • 1.778 lines changed: 2, context: html, text, full: html, text
    adding calJac3
• src/hg/makeDb/trackDb/trackDb.chainNet.ra
  • 1.89 lines changed: 51, context: html, text, full: html, text
    adding susScr2
• src/hg/makeDb/trackDb/human/hg19/hinv70Composite.html
  • 1.2 lines changed: 19, context: html, text, full: html, text
    fixup URL links to HINV db resources
  • 1.1 lines changed: 63, context: html, text, full: html, text
    Adding HInv-7.0 gene prediction update
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • 1.110 lines changed: 1, context: html, text, full: html, text
    fixup URL links to HINV db resources
  • 1.109 lines changed: 11, context: html, text, full: html, text
    experimental gc5Base track as bigWig
  • 1.108 lines changed: 31, context: html, text, full: html, text
    Adding HInv-7.0 gene prediction update
• src/hg/makeDb/trackDb/pig/susScr2/trackDb.ra
  • 1.5 lines changed: 11, context: html, text, full: html, text
    adding broken bigWig illustration
• src/hg/utils/automation/doBlastzChainNet.pl
  • 1.33 lines changed: 2, context: html, text, full: html, text
    default big hub is swarm and workhorse is hgwdev
• src/hg/utils/automation/makeDownloads.pl
  • 1.25 lines changed: 7, context: html, text, full: html, text
    indicate sequence is masked in chromosomes/README and bigZips/README
• src/product/README.trackDb
  • 1.7 lines changed: 1, context: html, text, full: html, text
    missing the root designation on the hgTrackDb command