hiram: changes by file

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

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