markd: changes by commit

branch to review (2009-12-14 to 2010-01-04) v222

• added problem case example
  • src/hg/makeDb/genbank/doc/to-do.txt 1.119 - lines changed: 2, context: html, text, full: html, text
• remove fixed length restrion on size of item names. reduce per-item memory usage by removing unusaed array
  • src/hg/hgTracks/bamTrack.c 1.21 - lines changed: 2, context: html, text, full: html, text
  • src/hg/hgTracks/bedTrack.c 1.21 - lines changed: 1, context: html, text, full: html, text
  • src/hg/hgTracks/cgapSageTrack.c 1.14 - lines changed: 5, context: html, text, full: html, text
  • src/hg/hgTracks/chainTrack.c 1.38 - lines changed: 5, context: html, text, full: html, text
  • src/hg/hgTracks/encode.c 1.23 - lines changed: 1, context: html, text, full: html, text
  • src/hg/hgTracks/hgTracks.c 1.1616 - lines changed: 2, context: html, text, full: html, text
  • src/hg/hgTracks/hgTracks.h 1.194 - lines changed: 2, context: html, text, full: html, text
  • src/hg/hgTracks/loweLabTracks.c 1.31 - lines changed: 2, context: html, text, full: html, text
  • src/hg/hgTracks/pslTrack.c 1.33 - lines changed: 4, context: html, text, full: html, text
  • src/hg/hgTracks/retroGene.c 1.18 - lines changed: 1, context: html, text, full: html, text
  • src/hg/hgTracks/sampleTracks.c 1.9 - lines changed: 1, context: html, text, full: html, text
  • src/hg/hgTracks/simpleTracks.c 1.117 - lines changed: 7, context: html, text, full: html, text
  • src/hg/hgTracks/switchGear.c 1.6 - lines changed: 1, context: html, text, full: html, text
• changes to support diff of what happend on a branch
  • src/utils/qa/weeklybld/cvs-reports-d 1.13 - lines changed: 39, context: html, text, full: html, text
• added transmap build doc
  • src/hg/makeDb/doc/danRer6.txt 1.14 - lines changed: 8, context: html, text, full: html, text
• integrated change from stanford to no print out a error message when trf actually succeeded
  • src/hg/trfBig/trfBig.c 1.19 - lines changed: 14, context: html, text, full: html, text
• correctly check return status of system; removed confusing function that is no longer used
  • src/inc/common.h 1.165 - lines changed: 3, context: html, text, full: html, text
  • src/lib/common.c 1.142 - lines changed: 22, context: html, text, full: html, text
• forgot check for fork failure
  • src/hg/trfBig/trfBig.c 1.20 - lines changed: 6, context: html, text, full: html, text
• modified extFile updating to match new server configuration
  • src/hg/makeDb/genbank/src/extFileUpdate/extFileTool 1.9 - lines changed: 2, context: html, text, full: html, text
  • src/hg/makeDb/genbank/src/extFileUpdate/extFileTool 1.8 - lines changed: 41, context: html, text, full: html, text
  • src/hg/makeDb/genbank/src/extFileUpdate/extFileUpdate.c 1.13 - lines changed: 42, context: html, text, full: html, text
• fix path for hgnfs1 (fixed premature commit)
  • src/hg/makeDb/genbank/src/extFileUpdate/extFileTool 1.10 - lines changed: 1, context: html, text, full: html, text
• changed panda params
  • src/hg/makeDb/genbank/etc/genbank.conf 1.355 - lines changed: 3, context: html, text, full: html, text
• added panda
  • src/hg/makeDb/genbank/etc/align.dbs 1.104 - lines changed: 1, context: html, text, full: html, text
  • src/hg/makeDb/genbank/etc/hgwdev.dbs 1.109 - lines changed: 5, context: html, text, full: html, text
• put database update lists in alphabetical order to make comparisons easy
  • src/hg/makeDb/genbank/etc/align.dbs 1.105 - lines changed: 11, context: html, text, full: html, text
  • src/hg/makeDb/genbank/etc/hgwbeta.dbs 1.102 - lines changed: 2, context: html, text, full: html, text
  • src/hg/makeDb/genbank/etc/hgwdev.dbs 1.110 - lines changed: 16, context: html, text, full: html, text
  • src/hg/makeDb/genbank/etc/rr.dbs 1.84 - lines changed: 10, context: html, text, full: html, text
• added credit
  • src/hg/makeDb/trackDb/chicken/galGal3/caCondor454.html 1.3 - lines changed: 1, context: html, text, full: html, text
• don't update danRer1
  • src/hg/makeDb/genbank/etc/hgwdev.dbs 1.111 - lines changed: 1, context: html, text, full: html, text
• don't align for genomes no longer being updated
  • src/hg/makeDb/genbank/etc/align.dbs 1.106 - lines changed: 6, context: html, text, full: html, text
• sort to make finding differences easy
  • src/hg/makeDb/genbank/etc/hgwbeta.dbs 1.103 - lines changed: 2, context: html, text, full: html, text
• don't align dropped database
  • src/hg/makeDb/genbank/etc/align.dbs 1.107 - lines changed: 1, context: html, text, full: html, text
  • src/hg/makeDb/genbank/etc/rr.dbs 1.85 - lines changed: 1, context: html, text, full: html, text
• change content-type for DAS results to text/xml
  • src/hg/das/das.c 1.46 - lines changed: 1, context: html, text, full: html, text