hiram: changes by commit

review to branch (2009-09-22 to 2009-09-29) v216

• Fixup compile error due to incorrect type from sizeof() in a printf format
  • src/utils/bedToBigBed/bedToBigBed.c 1.10 - lines changed: 1, context: html, text, full: html, text
• Tried to get the sanger genes up, not complete
  • src/hg/makeDb/doc/ce8.txt 1.3 - lines changed: 72, context: html, text, full: html, text
• Reset default position
  • src/hg/makeDb/doc/ce7.txt 1.4 - lines changed: 6, context: html, text, full: html, text
• Finish tetNig2 chain/net
  • src/hg/makeDb/doc/gasAcu1.txt 1.39 - lines changed: 94, context: html, text, full: html, text
• Working on the 46way conservation, oryCun2 lastz chain net cavPor3 synNet and reload cavPor3 extra large chain tables
  • src/hg/makeDb/doc/hg19.txt 1.39 - lines changed: 464, context: html, text, full: html, text
• Finish off repeat tracks, lastz run with hg19
  • src/hg/makeDb/doc/oryCun2.txt 1.3 - lines changed: 83, context: html, text, full: html, text
• add automatic generation of upstream files to genbank configuration
  • src/hg/makeDb/doc/ornAna1.txt 1.28 - lines changed: 5, context: html, text, full: html, text
• add automatic generation of upstream files to genbank conf, and danRer6 swap lastz running and tetNig2 lastz done
  • src/hg/makeDb/doc/oryLat2.txt 1.15 - lines changed: 136, context: html, text, full: html, text
• Finish lastz oryLat2 <-> danRer6
  • src/hg/makeDb/doc/danRer6.txt 1.9 - lines changed: 20, context: html, text, full: html, text
  • src/hg/makeDb/doc/oryLat2.txt 1.16 - lines changed: 3, context: html, text, full: html, text
• Properly release lable the ornAna1 chain and net composite and separate tracks
  • src/hg/makeDb/trackDb/trackDb.ra 1.535 - lines changed: 4, context: html, text, full: html, text
• Eliminate the call to chainDbNormScoreAvailable() and instead use the trackDb variable
  • src/hg/lib/hui.c 1.239 - lines changed: 23, context: html, text, full: html, text
• Eliminate use of chainDbNormScoreAvailable() function and use the trackDb variable instead
  • src/hg/hgTrackUi/hgTrackUi.c 1.501 - lines changed: 8, context: html, text, full: html, text
  • src/hg/hgc/hgc.c 1.1574 - lines changed: 7, context: html, text, full: html, text
• Settle on a single function to determine chainNormScoreDb()
  • src/hg/hgTrackUi/hgTrackUi.c 1.502 - lines changed: 5, context: html, text, full: html, text
  • src/hg/hgTracks/chainTrack.c 1.37 - lines changed: 5, context: html, text, full: html, text
  • src/hg/hgc/hgc.c 1.1575 - lines changed: 5, context: html, text, full: html, text
  • src/hg/inc/chainDb.h 1.7 - lines changed: 5, context: html, text, full: html, text
  • src/hg/inc/hui.h 1.139 - lines changed: 3, context: html, text, full: html, text
  • src/hg/lib/chainDb.c 1.13 - lines changed: 23, context: html, text, full: html, text
  • src/hg/lib/hui.c 1.240 - lines changed: 16, context: html, text, full: html, text
• Using hTableOrSplitExists() instead of just hTableExists() to get composite tracks to properly work with split tables
  • src/hg/lib/trackDbCustom.c 1.71 - lines changed: 1, context: html, text, full: html, text
• Adding Baboon papHam1
  • src/hg/makeDb/genbank/etc/genbank.conf 1.350 - lines changed: 18, context: html, text, full: html, text
• Adding Baboon Papio hamadryas hamadryas
  • src/hg/makeDb/genbank/src/lib/gbGenome.c 1.72 - lines changed: 2, context: html, text, full: html, text
• Adding Wallaby Macropus eugenii
  • src/hg/makeDb/genbank/src/lib/gbGenome.c 1.73 - lines changed: 2, context: html, text, full: html, text
• Adding rabbit and wallaby oryCun2 and macEug1
  • src/hg/makeDb/genbank/etc/genbank.conf 1.351 - lines changed: 38, context: html, text, full: html, text
• Added macEug1 - Macropus eugenii - Wallaby and Papio Hamadryas - Baboon
  • src/hg/makeDb/genbank/etc/align.dbs 1.102 - lines changed: 2, context: html, text, full: html, text
  • src/hg/makeDb/genbank/etc/hgwdev.dbs 1.107 - lines changed: 2, context: html, text, full: html, text
• Initial files from makeGenomeDb.pl
  • src/hg/makeDb/trackDb/wallaby/macEug1/description.html 1.1 - lines changed: 129, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/wallaby/macEug1/gap.html 1.1 - lines changed: 63, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/wallaby/macEug1/gold.html 1.1 - lines changed: 22, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/wallaby/macEug1/trackDb.ra 1.1 - lines changed: 40, context: html, text, full: html, text
• Added oryCun2 - Oryctolagus cuniculus - Rabbit
  • src/hg/makeDb/genbank/etc/align.dbs 1.103 - lines changed: 1, context: html, text, full: html, text
  • src/hg/makeDb/genbank/etc/hgwdev.dbs 1.108 - lines changed: 1, context: html, text, full: html, text