braney: changes by commit

review to branch (2010-03-16 to 2010-03-23) v227

• add a test to catch a problem with where regions were clipped by one base at the beginning
  • src/hg/ratStuff/mafSplit/test/makefile 1.1 - lines changed: 5, context: html, text, full: html, text
  • src/hg/ratStuff/mafSplit/test/test1.bed 1.1 - lines changed: 1, context: html, text, full: html, text
  • src/hg/ratStuff/mafSplit/test/test1.correct.0.maf 1.1 - lines changed: 13, context: html, text, full: html, text
  • src/hg/ratStuff/mafSplit/test/test1.correct.1.maf 1.1 - lines changed: 13, context: html, text, full: html, text
  • src/hg/ratStuff/mafSplit/test/test1.maf 1.1 - lines changed: 13, context: html, text, full: html, text
• fix from adk. MafSplit was clipping off the first base of every split
  • src/hg/ratStuff/mafSplit/mafSplit.c 1.6 - lines changed: 1, context: html, text, full: html, text
• add test. Prolly need to change the target to something other than test?
  • src/hg/ratStuff/mafSplit/makefile 1.4 - lines changed: 3, context: html, text, full: html, text
• remove slReverse to fix problem with menus in hgTables being in the opposite order. Used to be that pruneEmpties ended up flipping the list
  • src/hg/lib/hdb.c 1.421 - lines changed: 5, context: html, text, full: html, text
• fixing my earlier fix. The "right" solution is to make sure that we keep the list in the right order when we return the list.
  • src/hg/lib/hdb.c 1.422 - lines changed: 7, context: html, text, full: html, text
• add a check in BAM validation to require that chroms be specified and that they are the correct chroms with the right sizes
  • src/hg/encode/validateFiles/validateFiles.c 1.35 - lines changed: 66, context: html, text, full: html, text
• some view changes
  • src/hg/makeDb/trackDb/human/hg18/wgEncodeCaltechRnaSeq.alpha.ra 1.3 - lines changed: 76, context: html, text, full: html, text
• add support for validating bigWig
  • src/hg/encode/validateFiles/validateFiles.c 1.36 - lines changed: 53, context: html, text, full: html, text
• third times the charm. hTrackDb now returns list sorted by priority
  • src/hg/lib/hdb.c 1.423 - lines changed: 4, context: html, text, full: html, text
• added support for bigWig validation
  • src/hg/encode/encodeValidate/doEncodeValidate.pl 1.215 - lines changed: 19, context: html, text, full: html, text
• first round of doc
  • src/hg/makeDb/trackDb/human/hg19/encHaibMethylRrbs.html 1.1 - lines changed: 69, context: html, text, full: html, text
• first round of HAIB Methyl Rrbs track
  • src/hg/makeDb/trackDb/human/hg19/trackDb.enc.ra 1.6 - lines changed: 40, context: html, text, full: html, text