kuhn: changes by file

branch to review (2010-01-19 to 2010-01-26) v224

• src/hg/makeDb/trackDb/trackDb.chainNet.ra
  • 1.49 lines changed: 4, context: html, text, full: html, text
    moved all galGal3 chains and nets to composite and dropped individual tracks
  • 1.47 lines changed: 4, context: html, text, full: html, text
    moved all galGal22 chains and nets to composite and dropped individual tracks
  • 1.46 lines changed: 6, context: html, text, full: html, text
    moved all rheMac2 chains and nets to composite and dropped individual tracks
  • 1.45 lines changed: 3, context: html, text, full: html, text
    moved all panTro2 chains and nets to composite and dropped individual tracks
  • 1.44 lines changed: 6, context: html, text, full: html, text
    moved all panTro1 chains and nets to composite and dropped individual tracks. only hg17 and mm7 on RR
  • 1.43 lines changed: 3, context: html, text, full: html, text
    moved all ponAbe2 chains and nets to composite and dropped individual tracks
  • 1.39 lines changed: 3, context: html, text, full: html, text
    moved all calJac1 chains and nets to composite and dropped individual tracks
• src/hg/makeDb/trackDb/trackDb.ra
  • 1.594 lines changed: 26, context: html, text, full: html, text
    moved all galGal3 chains and nets to composite and dropped individual tracks
  • 1.592 lines changed: 27, context: html, text, full: html, text
    moved all galGal22 chains and nets to composite and dropped individual tracks
  • 1.591 lines changed: 26, context: html, text, full: html, text
    moved all rheMac2 chains and nets to composite and dropped individual tracks
  • 1.590 lines changed: 26, context: html, text, full: html, text
    moved all panTro2 chains and nets to composite and dropped individual tracks
  • 1.589 lines changed: 25, context: html, text, full: html, text
    moved all panTro1 chains and nets to composite and dropped individual tracks. only hg17 and mm7 on RR
  • 1.587 lines changed: 26, context: html, text, full: html, text
    moved all ponAbe2 chains and nets to composite and dropped individual tracks
  • 1.586 lines changed: 22, context: html, text, full: html, text
    dropped track blocks for chain and netPonAbe1, as no assembly has these tracks
  • 1.584 lines changed: 26, context: html, text, full: html, text
    moved all calJac1 chains and nets to composite and dropped individual tracks
• src/hg/makeDb/trackDb/chicken/galGal2/trackDb.ra
  • 1.75 lines changed: 28, context: html, text, full: html, text
    moved all panTro2 chains and nets to composite and dropped individual tracks
• src/hg/makeDb/trackDb/chimp/trackDb.ra
  • 1.29 lines changed: 26, context: html, text, full: html, text
    moved all rheMac2 chains and nets to composite and dropped individual tracks
  • 1.28 lines changed: 3, context: html, text, full: html, text
    moved all calJac1 chains and nets to composite and dropped individual tracks
• src/hg/makeDb/trackDb/chimp/panTro2/trackDb.ra
  • 1.49 lines changed: 3, context: html, text, full: html, text
    moved all galGal22 chains and nets to composite and dropped individual tracks
  • 1.48 lines changed: 4, context: html, text, full: html, text
    moved all rheMac2 chains and nets to composite and dropped individual tracks
  • 1.47 lines changed: 0, context: html, text, full: html, text
    moved all calJac1 chains and nets to composite and dropped individual tracks
• src/hg/makeDb/trackDb/dog/trackDb.ra
  • 1.37 lines changed: 8, context: html, text, full: html, text
    moved all rheMac2 chains and nets to composite and dropped individual tracks
  • 1.36 lines changed: 6, context: html, text, full: html, text
    moved all panTro2 chains and nets to composite and dropped individual tracks
  • 1.34 lines changed: 7, context: html, text, full: html, text
    moved all calJac1 chains and nets to composite and dropped individual tracks
• src/hg/makeDb/trackDb/dog/canFam2/trackDb.ra
  • 1.46 lines changed: 7, context: html, text, full: html, text
    moved all panTro2 chains and nets to composite and dropped individual tracks
  • 1.45 lines changed: 6, context: html, text, full: html, text
    moved all calJac1 chains and nets to composite and dropped individual tracks
• src/hg/makeDb/trackDb/fugu/trackDb.ra
  • 1.71 lines changed: 26, context: html, text, full: html, text
    moved all galGal3 chains and nets to composite and dropped individual tracks
• src/hg/makeDb/trackDb/horse/trackDb.ra
  • 1.23 lines changed: 6, context: html, text, full: html, text
    moved all galGal3 chains and nets to composite and dropped individual tracks
• src/hg/makeDb/trackDb/human/trackDb.ra
  • 1.497 lines changed: 4, context: html, text, full: html, text
    moved all calJac1 chains and nets to composite and dropped individual tracks
• src/hg/makeDb/trackDb/human/hg16/trackDb.ra
  • 1.583 lines changed: 18, context: html, text, full: html, text
    moved all galGal22 chains and nets to composite and dropped individual tracks
• src/hg/makeDb/trackDb/human/hg17/trackDb.chainNet.ra
  • 1.11 lines changed: 1, context: html, text, full: html, text
    moved all panTro1 chains and nets to composite and dropped individual tracks. only hg17 and mm7 on RR
• src/hg/makeDb/trackDb/human/hg17/trackDb.ra
  • 1.439 lines changed: 16, context: html, text, full: html, text
    moved all galGal22 chains and nets to composite and dropped individual tracks
  • 1.438 lines changed: 24, context: html, text, full: html, text
    moved all rheMac2 chains and nets to composite and dropped individual tracks
  • 1.437 lines changed: 6, context: html, text, full: html, text
    moved all panTro1 chains and nets to composite and dropped individual tracks. only hg17 and mm7 on RR
• src/hg/makeDb/trackDb/human/hg18/trackDb.ra
  • 1.456 lines changed: 28, context: html, text, full: html, text
    moved all rheMac2 chains and nets to composite and dropped individual tracks
  • 1.455 lines changed: 28, context: html, text, full: html, text
    moved all panTro2 chains and nets to composite and dropped individual tracks
  • 1.454 lines changed: 12, context: html, text, full: html, text
    moved all panTro1 chains and nets to composite and dropped individual tracks. only hg17 and mm7 on RR
• src/hg/makeDb/trackDb/lizard/trackDb.ra
  • 1.9 lines changed: 6, context: html, text, full: html, text
    moved all galGal3 chains and nets to composite and dropped individual tracks
• src/hg/makeDb/trackDb/marmoset/trackDb.ra
  • 1.11 lines changed: 6, context: html, text, full: html, text
    moved all rheMac2 chains and nets to composite and dropped individual tracks
  • 1.10 lines changed: 4, context: html, text, full: html, text
    moved all panTro2 chains and nets to composite and dropped individual tracks
  • 1.9 lines changed: 5, context: html, text, full: html, text
    moved all ponAbe2 chains and nets to composite and dropped individual tracks
• src/hg/makeDb/trackDb/mouse/trackDb.chainNet.ra
  • 1.28 lines changed: 1, context: html, text, full: html, text
    moved all panTro1 chains and nets to composite and dropped individual tracks. only hg17 and mm7 on RR
• src/hg/makeDb/trackDb/mouse/trackDb.ra
  • 1.189 lines changed: 7, context: html, text, full: html, text
    moved all rheMac2 chains and nets to composite and dropped individual tracks
  • 1.188 lines changed: 28, context: html, text, full: html, text
    moved all panTro2 chains and nets to composite and dropped individual tracks
  • 1.187 lines changed: 8, context: html, text, full: html, text
    moved all panTro1 chains and nets to composite and dropped individual tracks. only hg17 and mm7 on RR
  • 1.186 lines changed: 13, context: html, text, full: html, text
    moved all ponAbe2 chains and nets to composite and dropped individual tracks
  • 1.184 lines changed: 7, context: html, text, full: html, text
    moved all calJac1 chains and nets to composite and dropped individual tracks
• src/hg/makeDb/trackDb/mouse/mm7/knownGene.html
  • 1.10 lines changed: 1, context: html, text, full: html, text
    moved all panTro2 chains and nets to composite and dropped individual tracks
• src/hg/makeDb/trackDb/mouse/mm7/trackDb.chainNet.ra
  • 1.9 lines changed: 1, context: html, text, full: html, text
    moved all panTro1 chains and nets to composite and dropped individual tracks. only hg17 and mm7 on RR
• src/hg/makeDb/trackDb/mouse/mm8/knownGene.html
  • 1.7 lines changed: 1, context: html, text, full: html, text
    moved all panTro2 chains and nets to composite and dropped individual tracks
• src/hg/makeDb/trackDb/opossum/trackDb.ra
  • 1.43 lines changed: 17, context: html, text, full: html, text
    moved all galGal22 chains and nets to composite and dropped individual tracks
  • 1.42 lines changed: 28, context: html, text, full: html, text
    moved all panTro2 chains and nets to composite and dropped individual tracks
  • 1.41 lines changed: 7, context: html, text, full: html, text
    moved all calJac1 chains and nets to composite and dropped individual tracks
• src/hg/makeDb/trackDb/opossum/monDom4/trackDb.chainNet.ra
  • 1.9 lines changed: 1, context: html, text, full: html, text
    moved all galGal22 chains and nets to composite and dropped individual tracks
• src/hg/makeDb/trackDb/opossum/monDom5/trackDb.chainNet.ra
  • 1.5 lines changed: 8, context: html, text, full: html, text
    moved all galGal3 chains and nets to composite and dropped individual tracks
• src/hg/makeDb/trackDb/opossum/monDom5/trackDb.ra
  • 1.29 lines changed: 17, context: html, text, full: html, text
    moved all galGal3 chains and nets to composite and dropped individual tracks
  • 1.28 lines changed: 10, context: html, text, full: html, text
    moved all rheMac2 chains and nets to composite and dropped individual tracks
  • 1.27 lines changed: 10, context: html, text, full: html, text
    moved all panTro2 chains and nets to composite and dropped individual tracks
  • 1.26 lines changed: 10, context: html, text, full: html, text
    moved all ponAbe2 chains and nets to composite and dropped individual tracks
• src/hg/makeDb/trackDb/orangutan/trackDb.ra
  • 1.10 lines changed: 6, context: html, text, full: html, text
    moved all panTro2 chains and nets to composite and dropped individual tracks
  • 1.9 lines changed: 3, context: html, text, full: html, text
    moved all calJac1 chains and nets to composite and dropped individual tracks
• src/hg/makeDb/trackDb/platypus/trackDb.ra
  • 1.13 lines changed: 3, context: html, text, full: html, text
    moved all calJac1 chains and nets to composite and dropped individual tracks
• src/hg/makeDb/trackDb/platypus/ornAna1/trackDb.ra
  • 1.19 lines changed: 9, context: html, text, full: html, text
    moved all ponAbe2 chains and nets to composite and dropped individual tracks
  • 1.18 lines changed: 8, context: html, text, full: html, text
    moved all calJac1 chains and nets to composite and dropped individual tracks
• src/hg/makeDb/trackDb/rat/trackDb.ra
  • 1.69 lines changed: 14, context: html, text, full: html, text
    moved all galGal3 chains and nets to composite and dropped individual tracks
  • 1.68 lines changed: 14, context: html, text, full: html, text
    moved all rheMac2 chains and nets to composite and dropped individual tracks
• src/hg/makeDb/trackDb/rat/rn4/trackDb.ra
  • 1.49 lines changed: 28, context: html, text, full: html, text
    moved all panTro2 chains and nets to composite and dropped individual tracks
• src/hg/makeDb/trackDb/rhesus/trackDb.ra
  • 1.20 lines changed: 9, context: html, text, full: html, text
    moved all ponAbe2 chains and nets to composite and dropped individual tracks
  • 1.19 lines changed: 7, context: html, text, full: html, text
    moved all calJac1 chains and nets to composite and dropped individual tracks
• src/hg/makeDb/trackDb/rhesus/rheMac2/trackDb.ra
  • 1.52 lines changed: 28, context: html, text, full: html, text
    moved all panTro2 chains and nets to composite and dropped individual tracks
• src/hg/makeDb/trackDb/stickleback/trackDb.ra
  • 1.25 lines changed: 27, context: html, text, full: html, text
    moved all galGal3 chains and nets to composite and dropped individual tracks
• src/hg/makeDb/trackDb/xenTro/xenTro1/trackDb.ra
  • 1.42 lines changed: 17, context: html, text, full: html, text
    moved all galGal22 chains and nets to composite and dropped individual tracks
• src/hg/makeDb/trackDb/zebraFinch/trackDb.ra
  • 1.9 lines changed: 22, context: html, text, full: html, text
    moved all galGal3 chains and nets to composite and dropped individual tracks
• src/hg/makeDb/trackDb/zebrafish/danRer4/trackDb.ra
  • 1.41 lines changed: 28, context: html, text, full: html, text
    moved all panTro2 chains and nets to composite and dropped individual tracks
• src/utils/qa/checkMachineName.csh
  • 1.6 lines changed: 1, context: html, text, full: html, text
    fixed getAssemblies.csh to work with RR machines and several other programs that it depends on. it broke when we went to a single mysql machine and genbank dumps only grab from hgnfs1
• src/utils/qa/countPerChrom.csh
  • 1.15 lines changed: 39, context: html, text, full: html, text
    added support for second set of data in histogram
  • 1.14 lines changed: 46, context: html, text, full: html, text
    made graph.csh to draw a bar graph from a two-column file and added option for countPerChrom.csh to use it
• src/utils/qa/getAssemblies.csh
  • 1.23 lines changed: 38, context: html, text, full: html, text
    fixed getAssemblies.csh to work with RR machines and several other programs that it depends on. it broke when we went to a single mysql machine and genbank dumps only grab from hgnfs1
• src/utils/qa/getRRdatabases.csh
  • 1.12 lines changed: 11, context: html, text, full: html, text
    fixed getAssemblies.csh to work with RR machines and several other programs that it depends on. it broke when we went to a single mysql machine and genbank dumps only grab from hgnfs1
• src/utils/qa/getRRtables.csh
  • 1.6 lines changed: 10, context: html, text, full: html, text
    fixed getAssemblies.csh to work with RR machines and several other programs that it depends on. it broke when we went to a single mysql machine and genbank dumps only grab from hgnfs1
• src/utils/qa/graph.csh
  • 1.3 lines changed: 17, context: html, text, full: html, text
    added formatting for variable first column width
  • 1.2 lines changed: 5, context: html, text, full: html, text
    forgot to implement configurable bar length after adding option in usage statement
  • 1.1 lines changed: 22, context: html, text, full: html, text
    made graph.csh to draw a bar graph from a two-column file and added option for countPerChrom.csh to use it
• src/utils/qa/makefile
  • 1.117 lines changed: 1, context: html, text, full: html, text
    made graph.csh to draw a bar graph from a two-column file and added option for countPerChrom.csh to use it
• src/utils/qa/syncAday.csh
  • 1.10 lines changed: 4, context: html, text, full: html, text
    removed checking for multiple RR machines since we've gone to single mysql database