markd: changes by commit

review to branch (2010-04-27 to 2010-05-04) v230

• fixed breakage noticed by JK during code review
  • src/hg/hgTracks/simpleTracks.c 1.137 - lines changed: 1, context: html, text, full: html, text
• removed human-as-chimp xeno refgene hack
  • src/hg/makeDb/trackDb/chimp/panTro1/xenoRefGene.html 1.6 - lines changed: 55, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/chimp/panTro2/xenoRefGene.html 1.7 - lines changed: 55, context: html, text, full: html, text
• removed html related to chimp/human hack
  • src/hg/makeDb/trackDb/chimp/panTro2/est.html 1.4 - lines changed: 108, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/chimp/panTro2/intronEst.html 1.6 - lines changed: 117, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/chimp/panTro2/mrna.html 1.4 - lines changed: 73, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/chimp/panTro2/refGene.html 1.5 - lines changed: 64, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/chimp/panTro2/xenoMrna.html 1.5 - lines changed: 80, context: html, text, full: html, text
• Fixed incorrect calculation of CDS refactor
  • src/hg/genePredToFakePsl/genePredToFakePsl.c 1.4 - lines changed: 79, context: html, text, full: html, text
• bad tandem dup example
  • src/hg/makeDb/genbank/doc/to-do.txt 1.122 - lines changed: 2, context: html, text, full: html, text
• added gbStatus schema doc
  • src/hg/lib/gbStatus.as 1.1 - lines changed: 19, context: html, text, full: html, text
• update schema doc
  • src/hg/lib/gbCdnaInfo.as 1.4 - lines changed: 2, context: html, text, full: html, text
• fixed incorrect documentation
  • src/inc/errCatch.h 1.3 - lines changed: 1, context: html, text, full: html, text
• fixed invalid autoSql that prevented descriptions from being displayed
  • src/hg/lib/extFile.as 1.2 - lines changed: 1, context: html, text, full: html, text
  • src/hg/lib/gbSeq.as 1.2 - lines changed: 25, context: html, text, full: html, text
  • src/hg/lib/genbankTables.as 1.7 - lines changed: 4, context: html, text, full: html, text
  • src/hg/lib/history.as 1.2 - lines changed: 1, context: html, text, full: html, text
  • src/hg/lib/metaInfo.as 1.2 - lines changed: 1, context: html, text, full: html, text
  • src/hg/lib/namedSessionDb.as 1.3 - lines changed: 2, context: html, text, full: html, text
  • src/hg/lib/seq.as 1.2 - lines changed: 2, context: html, text, full: html, text
  • src/hg/lib/swInterPro.as 1.4 - lines changed: 1, context: html, text, full: html, text
  • src/hg/lib/targetDb.as 1.3 - lines changed: 1, context: html, text, full: html, text
  • src/hg/lib/trackVersion.as 1.2 - lines changed: 1, context: html, text, full: html, text
  • src/hg/lib/transRegCodeMotif.as 1.2 - lines changed: 1, context: html, text, full: html, text
• enabled indel display controls for BAM tracks
  • src/hg/lib/hui.c 1.281 - lines changed: 1, context: html, text, full: html, text
• include link back to browser in tables of PSL. also fix corner case on PAR were link to wrong chrom
  • src/hg/hgc/hgc.c 1.1618 - lines changed: 26, context: html, text, full: html, text
• fixed manic editing overwrite of file
  • src/hg/lib/gbSeq.as 1.3 - lines changed: 25, context: html, text, full: html, text
• use bigint for file offsets
  • src/hg/lib/seq.as 1.3 - lines changed: 2, context: html, text, full: html, text