angie: changes by commit

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

• Warn, don't die, when there are duplicate .as files, so tableDescriptions tables are still updated.
  • src/test/buildTableDescriptions.pl 1.46 - lines changed: 2, context: html, text, full: html, text
• Adding some missing entries found by Antonio.
  • src/hg/makeDb/schema/all.joiner 1.805 - lines changed: 19, 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/hgGetAnn/tests/makefile 1.4 - lines changed: 1, context: html, text, full: html, text
• Rebuilt snp131 and snp131CodingDbSnp with corrected function codes from dbSNP.
  • src/hg/makeDb/doc/hg19.txt 1.114 - lines changed: 73, context: html, text, full: html, text
• Added snp131 & exceptions.
  • src/hg/makeDb/schema/all.joiner 1.806 - lines changed: 19, 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/hg/makeDb/trackDb/trackDb.ra 1.634 - lines changed: 31, 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/bamTrack.c 1.32 - lines changed: 59, context: html, text, full: html, text
  • src/hg/hgTracks/hgTracks.c 1.1649 - lines changed: 3, context: html, text, full: html, text
  • src/hg/hgTracks/hgTracks.h 1.212 - lines changed: 2, context: html, text, full: html, text
  • src/hg/hgTracks/simpleTracks.c 1.143 - lines changed: 2, context: html, text, full: html, text
• Made snp131-masked genome sequences.
  • src/hg/makeDb/doc/hg19.txt 1.115 - lines changed: 130, 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/snp131.html 1.2 - lines changed: 5, 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/snp125Ui.c 1.33 - lines changed: 3, context: html, text, full: html, text
• Corrected table description (thanks Mary!).
  • src/hg/lib/snpSeq.as 1.4 - lines changed: 1, context: html, text, full: html, text