hiram: changes by file

branch to review (2010-02-02 to 2010-02-10) v225

• src/hg/hgGateway/hgGateway.c
  • 1.113 lines changed: 3, context: html, text, full: html, text
    have default clade mammal if none found
• src/hg/lib/customFactory.c
  • 1.116 lines changed: 2, context: html, text, full: html, text
    limit custom tracks short label to 128 characters to avoid buffer overflow elsewhere
• src/hg/lib/simpleRepeat.sql
  • 1.9 lines changed: 1, context: html, text, full: html, text
    the extra ; in the comment causes it to be invalid SQL ?
• src/hg/lib/wikiTrack.c
  • 1.27 lines changed: 19, context: html, text, full: html, text
    do not error out just because the wiki WEB site has disappeared
• src/hg/makeDb/doc/calJac3.txt
  • 1.1 lines changed: 62, context: html, text, full: html, text
    Downloading new Marmoset assembly
• src/hg/makeDb/doc/mm9.txt
  • 1.122 lines changed: 18, context: html, text, full: html, text
    re-run the Panda chain net
• src/hg/makeDb/doc/monDom5.txt
  • 1.18 lines changed: 9, context: html, text, full: html, text
    re-run the Panda chain net
• src/hg/makeDb/genbank/etc/align.dbs
  • 1.110 lines changed: 1, context: html, text, full: html, text
    turning ailMel1 back on after reload
• src/hg/makeDb/genbank/etc/genbank.conf
  • 1.363 lines changed: 17, context: html, text, full: html, text
    adding marmoset calJac3
• src/hg/makeDb/genbank/etc/hgwdev.dbs
  • 1.114 lines changed: 1, context: html, text, full: html, text
    turning ailMel1 back on after reload
• src/hg/makeDb/trackDb/makefile
  • 1.283 lines changed: 1, context: html, text, full: html, text
    adding calJac3 to the build
• src/hg/makeDb/trackDb/marmoset/calJac3/description.html
  • 1.1 lines changed: 129, context: html, text, full: html, text
    initial files from makeGenomeDb.pl
• src/hg/makeDb/trackDb/marmoset/calJac3/gap.html
  • 1.1 lines changed: 63, context: html, text, full: html, text
    initial files from makeGenomeDb.pl
• src/hg/makeDb/trackDb/marmoset/calJac3/gold.html
  • 1.1 lines changed: 22, context: html, text, full: html, text
    initial files from makeGenomeDb.pl
• src/hg/makeDb/trackDb/marmoset/calJac3/trackDb.ra
  • 1.1 lines changed: 40, context: html, text, full: html, text
    initial files from makeGenomeDb.pl
• src/hg/utils/automation/doRecipBest.pl
  • 1.12 lines changed: 9, context: html, text, full: html, text
    allow use of lastz or blastz directory
• src/hg/utils/automation/makeGenomeDb.pl
  • 1.27 lines changed: 5, context: html, text, full: html, text
    handle chrom names for chromInfo that are longer than 16 chars
  • 1.26 lines changed: 11, context: html, text, full: html, text
    fixup usage of AGP files with comments and FASTA with Genbank ID lines
• src/hg/utils/pslUniq/pslUniq.c
  • 1.4 lines changed: 8, context: html, text, full: html, text
    Clean up pslUniq and place it into the build