braney: changes by file

branch to review (2009-12-01 to 2009-12-09) v221

• src/hg/encode/DAFs/HAIBRnaSeq.daf
  • 1.1 lines changed: 33, context: html, text, full: html, text
    first pass at DAF for Myers RNA-seq
• src/hg/encode/encodeValidate/doEncodeValidate.pl
  • 1.206 lines changed: 36, context: html, text, full: html, text
    add support for SAM and BAM files (call validateFiles)
  • 1.204 lines changed: 1, context: html, text, full: html, text
    add restrictionEnzyme to list of non-validated variables
• src/hg/encode/encodeValidate/config/cv.ra
  • 1.146 lines changed: 1, context: html, text, full: html, text
    add some words to the definition of total
• src/hg/encode/validateFiles/validateFiles.c
  • 1.31 lines changed: 20, context: html, text, full: html, text
    add stubs for SAM and BAM format checking
  • 1.30 lines changed: 2, context: html, text, full: html, text
    when checking fasta sequence names, stop checking at space to allow extra stuff that folks often put after the sequence name
• src/hg/makeDb/trackDb/loadTracks
  • 1.18 lines changed: 1, context: html, text, full: html, text
    add root option to tdbQuery
• src/hg/makeDb/trackDb/human/wgEncodeGencode.html
  • 1.6 lines changed: 10, context: html, text, full: html, text
    add release notes for release 3c
• src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra
  • 1.714 lines changed: 28, context: html, text, full: html, text
    add two letter codes to the CalTech RNA-seq short labels
  • 1.713 lines changed: 4, context: html, text, full: html, text
    put cell types in alphabetical order for RNA-seq tracks
  • 1.712 lines changed: 3, context: html, text, full: html, text
    change view terms *RawSig* to *_Raw_Signal
  • 1.711 lines changed: 105, context: html, text, full: html, text
    RNA-Seq to RNA-seq
  • 1.710 lines changed: 2, context: html, text, full: html, text
    take out unused views from settingsByView and defaults
  • 1.706 lines changed: 1, context: html, text, full: html, text
    change viewLimitsMax to viewLimits
  • 1.705 lines changed: 48, context: html, text, full: html, text
    fix some short labels
  • 1.704 lines changed: 82, context: html, text, full: html, text
    add some new cell and compartment types to the RNA-pet set
  • 1.702 lines changed: 9, context: html, text, full: html, text
    drop entry for wgEncodeGencode2WayV3 which is for hgwdev-gencode only
  • 1.698 lines changed: 24, context: html, text, full: html, text
    show mismatches in GIS Rna-seq alignments
  • 1.697 lines changed: 45, context: html, text, full: html, text
    show different bases in CSHL short RNA-seq track
  • 1.696 lines changed: 49, context: html, text, full: html, text
    don't do LOG transform on RNA-seq or RNA-pet tracks
• src/hg/makeDb/trackDb/human/hg18/wgEncodeGisRnaSeq.html
  • 1.4 lines changed: 2, context: html, text, full: html, text
    change in to on
• src/hg/utils/automation/Encode.pm
  • 1.52 lines changed: 2, context: html, text, full: html, text
    move pairedTagAlign to bigBedTypes