braney: changes by commit

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

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