angie: changes by file

branch to review (2010-05-25 to 2010-06-01) v233

• src/hg/hgGetAnn/tests/makefile
  • 1.4 lines changed: 1, context: html, text, full: html, text
    Use blatFugu instead of mrna; code now uses all_mrna but that has no bin column in hg15.
• src/hg/hgTracks/bamTrack.c
  • 1.32 lines changed: 59, context: html, text, full: html, text
    When building without USE_BAM=1, install a dummy track handler for bam that prints a message in place of track items, so we don't pop up an annoying 'No track handler' warnbox.
• src/hg/hgTracks/hgTracks.c
  • 1.1649 lines changed: 3, context: html, text, full: html, text
    When building without USE_BAM=1, install a dummy track handler for bam that prints a message in place of track items, so we don't pop up an annoying 'No track handler' warnbox.
• src/hg/hgTracks/hgTracks.h
  • 1.212 lines changed: 2, context: html, text, full: html, text
    When building without USE_BAM=1, install a dummy track handler for bam that prints a message in place of track items, so we don't pop up an annoying 'No track handler' warnbox.
• src/hg/hgTracks/simpleTracks.c
  • 1.143 lines changed: 2, context: html, text, full: html, text
    When building without USE_BAM=1, install a dummy track handler for bam that prints a message in place of track items, so we don't pop up an annoying 'No track handler' warnbox.
• src/hg/lib/snp125Ui.c
  • 1.33 lines changed: 3, context: html, text, full: html, text
    Added new func code cds-indel, moved coding-synonymy-unknown from synonymous category (oops) to non-synon category. Thanks Mary!
• src/hg/lib/snpSeq.as
  • 1.4 lines changed: 1, context: html, text, full: html, text
    Corrected table description (thanks Mary!).
• src/hg/makeDb/doc/hg19.txt
  • 1.115 lines changed: 130, context: html, text, full: html, text
    Made snp131-masked genome sequences.
  • 1.114 lines changed: 73, context: html, text, full: html, text
    Rebuilt snp131 and snp131CodingDbSnp with corrected function codes from dbSNP.
• src/hg/makeDb/schema/all.joiner
  • 1.806 lines changed: 19, context: html, text, full: html, text
    Added snp131 & exceptions.
  • 1.805 lines changed: 19, context: html, text, full: html, text
    Adding some missing entries found by Antonio.
• src/hg/makeDb/trackDb/snp131.html
  • 1.2 lines changed: 5, context: html, text, full: html, text
    Added new functional annotattion codes cds-indel, coding-synonymy-unknown; added 1000Genomes as validation type. Thanks Mary!
• src/hg/makeDb/trackDb/trackDb.ra
  • 1.634 lines changed: 31, context: html, text, full: html, text
    Adding back all_mrna and all_est with release public for backwards compatibility with CGIs currently on RR.
• src/test/buildTableDescriptions.pl
  • 1.46 lines changed: 2, context: html, text, full: html, text
    Warn, don't die, when there are duplicate .as files, so tableDescriptions tables are still updated.