markd: changes by file

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

• src/hg/hgTables/gffOut.c
  • 1.21 lines changed: 3, context: html, text, full: html, text
    Switch GTF output to being true GTF
• src/hg/hgTables/hgTables.c
  • 1.190 lines changed: 3, context: html, text, full: html, text
    Switch GTF output to being true GTF
• src/hg/hgTables/hgTables.h
  • 1.140 lines changed: 2, context: html, text, full: html, text
    Switch GTF output to being true GTF
• src/hg/hgTracks/simpleTracks.c
  • 1.131 lines changed: 4, context: html, text, full: html, text
    Better handling of rounding when capping width of label area to 1/2 of width of size of image
• src/hg/makeDb/doc/encodeHg18.txt
  • 1.33 lines changed: 12, context: html, text, full: html, text
    reload encodeGencodeGeneKnownMar07
• src/hg/makeDb/doc/panTro1.txt
  • 1.9 lines changed: 15, context: html, text, full: html, text
    redo chimp genbank to not special case huamn
• src/hg/makeDb/doc/panTro2.txt
  • 1.19 lines changed: 12, context: html, text, full: html, text
    redo chimp genbank to not special case huamn
• src/hg/makeDb/genbank/common.mk
  • 1.27 lines changed: 4, context: html, text, full: html, text
    fixed library dependency problems
• src/hg/makeDb/genbank/makefile
  • 1.17 lines changed: 1, context: html, text, full: html, text
    fixed library dependency problems
• src/hg/makeDb/genbank/etc/align.dbs
  • 1.116 lines changed: 2, context: html, text, full: html, text
    disable chimp
• src/hg/makeDb/genbank/etc/genbank.conf
  • 1.369 lines changed: 1, context: html, text, full: html, text
    disable native panda refgene, since there are none
  • 1.368 lines changed: 7, context: html, text, full: html, text
    remove hacks to align human as native on chimp
• src/hg/makeDb/genbank/etc/hgwbeta.dbs
  • 1.108 lines changed: 2, context: html, text, full: html, text
    disable chimp
• src/hg/makeDb/genbank/etc/hgwdev.dbs
  • 1.120 lines changed: 2, context: html, text, full: html, text
    disable chimp
• src/hg/makeDb/genbank/etc/rr.dbs
  • 1.89 lines changed: 2, context: html, text, full: html, text
    disable chimp
• src/hg/makeDb/genbank/src/align/gbAlignCommon.c
  • 1.6 lines changed: 9, context: html, text, full: html, text
    remove hacks to align human as native on chimp
• src/hg/makeDb/genbank/src/align/gbAlignRun
  • 1.11 lines changed: 1, context: html, text, full: html, text
    don't include /cluster/bin in PATH when not running on build server to avoid annoy our kind admins by fill up the log with autofs errors
• src/hg/makeDb/genbank/src/align/gbAlignStep
  • 1.25 lines changed: 1, context: html, text, full: html, text
    don't include /cluster/bin in PATH when not running on build server to avoid annoy our kind admins by fill up the log with autofs errors
• src/hg/makeDb/genbank/src/align/gbBlat
  • 1.70 lines changed: 7, context: html, text, full: html, text
    remove hacks to align human as native on chimp
• src/hg/makeDb/genbank/src/copy/gbMakeDownload
  • 1.22 lines changed: 1, context: html, text, full: html, text
    need /cluster/bin/ for making downloads
• src/hg/makeDb/genbank/src/download/gbDownloadStep
  • 1.16 lines changed: 1, context: html, text, full: html, text
    don't include /cluster/bin in PATH when not running on build server to avoid annoy our kind admins by fill up the log with autofs errors
• src/hg/makeDb/genbank/src/lib/gbCommon.pm
  • 1.49 lines changed: 19, context: html, text, full: html, text
    don't include /cluster/bin in PATH when not running on build server to avoid annoy our kind admins by fill up the log with autofs errors
• src/hg/makeDb/genbank/src/lib/gbGenome.c
  • 1.79 lines changed: 6, context: html, text, full: html, text
    remove hacks to align human as native on chimp
• src/hg/makeDb/genbank/src/process/gbProcessStep
  • 1.14 lines changed: 1, context: html, text, full: html, text
    don't include /cluster/bin in PATH when not running on build server to avoid annoy our kind admins by fill up the log with autofs errors
• src/hg/makeDb/trackDb/chimp/panTro1/trackDb.ra
  • 1.42 lines changed: 2, context: html, text, full: html, text
    remove hack to treat human cDNAs and RefSeqs as native chimp
• src/hg/makeDb/trackDb/chimp/panTro1/xenoRefGene.html
  • 1.6 lines changed: 55, context: html, text, full: html, text
    remove hack to treat human cDNAs and RefSeqs as native chimp
• src/hg/makeDb/trackDb/chimp/panTro1/xenoRefGeneNoHs.html
  • 1.1 lines changed: 55, context: html, text, full: html, text
    remove hack to treat human cDNAs and RefSeqs as native chimp
• src/hg/makeDb/trackDb/chimp/panTro2/est.html
  • 1.4 lines changed: 108, context: html, text, full: html, text
    remove hack to treat human cDNAs and RefSeqs as native chimp
• src/hg/makeDb/trackDb/chimp/panTro2/estWithHs.html
  • 1.1 lines changed: 108, context: html, text, full: html, text
    remove hack to treat human cDNAs and RefSeqs as native chimp
• src/hg/makeDb/trackDb/chimp/panTro2/intronEst.html
  • 1.6 lines changed: 117, context: html, text, full: html, text
    remove hack to treat human cDNAs and RefSeqs as native chimp
• src/hg/makeDb/trackDb/chimp/panTro2/intronEstWithHs.html
  • 1.1 lines changed: 117, context: html, text, full: html, text
    remove hack to treat human cDNAs and RefSeqs as native chimp
• src/hg/makeDb/trackDb/chimp/panTro2/mrna.html
  • 1.4 lines changed: 73, context: html, text, full: html, text
    remove hack to treat human cDNAs and RefSeqs as native chimp
• src/hg/makeDb/trackDb/chimp/panTro2/mrnaWithHs.html
  • 1.1 lines changed: 73, context: html, text, full: html, text
    remove hack to treat human cDNAs and RefSeqs as native chimp
• src/hg/makeDb/trackDb/chimp/panTro2/refGene.html
  • 1.5 lines changed: 64, context: html, text, full: html, text
    remove hack to treat human cDNAs and RefSeqs as native chimp
• src/hg/makeDb/trackDb/chimp/panTro2/refGeneWithHs.html
  • 1.1 lines changed: 64, context: html, text, full: html, text
    remove hack to treat human cDNAs and RefSeqs as native chimp
• src/hg/makeDb/trackDb/chimp/panTro2/trackDb.ra
  • 1.56 lines changed: 12, context: html, text, full: html, text
    remove hack to treat human cDNAs and RefSeqs as native chimp
• src/hg/makeDb/trackDb/chimp/panTro2/xenoMrna.html
  • 1.5 lines changed: 80, context: html, text, full: html, text
    remove hack to treat human cDNAs and RefSeqs as native chimp
• src/hg/makeDb/trackDb/chimp/panTro2/xenoMrnaNoHs.html
  • 1.1 lines changed: 80, context: html, text, full: html, text
    remove hack to treat human cDNAs and RefSeqs as native chimp
• src/hg/makeDb/trackDb/chimp/panTro2/xenoRefGene.html
  • 1.7 lines changed: 55, context: html, text, full: html, text
    remove hack to treat human cDNAs and RefSeqs as native chimp
• src/hg/makeDb/trackDb/chimp/panTro2/xenoRefGeneNoHs.html
  • 1.1 lines changed: 55, context: html, text, full: html, text
    remove hack to treat human cDNAs and RefSeqs as native chimp