braney: changes by file

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

• src/hg/encode/encodeValidate/doEncodeValidate.pl
  • 1.215 lines changed: 19, context: html, text, full: html, text
    added support for bigWig validation
• src/hg/encode/validateFiles/validateFiles.c
  • 1.36 lines changed: 53, context: html, text, full: html, text
    add support for validating bigWig
  • 1.35 lines changed: 66, 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/lib/hdb.c
  • 1.423 lines changed: 4, context: html, text, full: html, text
    third times the charm. hTrackDb now returns list sorted by priority
  • 1.422 lines changed: 7, 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.
  • 1.421 lines changed: 5, 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/makeDb/trackDb/human/hg18/wgEncodeCaltechRnaSeq.alpha.ra
  • 1.3 lines changed: 76, context: html, text, full: html, text
    some view changes
• src/hg/makeDb/trackDb/human/hg19/encHaibMethylRrbs.html
  • 1.1 lines changed: 69, context: html, text, full: html, text
    first round of doc
• src/hg/makeDb/trackDb/human/hg19/trackDb.enc.ra
  • 1.6 lines changed: 40, context: html, text, full: html, text
    first round of HAIB Methyl Rrbs track
• src/hg/ratStuff/mafSplit/mafSplit.c
  • 1.6 lines changed: 1, context: html, text, full: html, text
    fix from adk. MafSplit was clipping off the first base of every split
• src/hg/ratStuff/mafSplit/makefile
  • 1.4 lines changed: 3, context: html, text, full: html, text
    add test. Prolly need to change the target to something other than test?
• src/hg/ratStuff/mafSplit/test/makefile
  • 1.1 lines changed: 5, context: html, text, full: html, text
    add a test to catch a problem with where regions were clipped by one base at the beginning
• src/hg/ratStuff/mafSplit/test/test1.bed
  • 1.1 lines changed: 1, context: html, text, full: html, text
    add a test to catch a problem with where regions were clipped by one base at the beginning
• src/hg/ratStuff/mafSplit/test/test1.correct.0.maf
  • 1.1 lines changed: 13, context: html, text, full: html, text
    add a test to catch a problem with where regions were clipped by one base at the beginning
• src/hg/ratStuff/mafSplit/test/test1.correct.1.maf
  • 1.1 lines changed: 13, context: html, text, full: html, text
    add a test to catch a problem with where regions were clipped by one base at the beginning
• src/hg/ratStuff/mafSplit/test/test1.maf
  • 1.1 lines changed: 13, context: html, text, full: html, text
    add a test to catch a problem with where regions were clipped by one base at the beginning