hiram: changes by commit

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

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