braney: changes by file

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

• src/hg/encode/encodeValidate/doEncodeValidate.pl
  • 1.223 lines changed: 14, context: html, text, full: html, text
    add support for bigWig's to put min and max in trackDb file
• src/hg/encode/encodeValidate/config/labs.ra
  • 1.13 lines changed: 3, context: html, text, full: html, text
    add Tullius
• src/hg/encode/validateFiles/validateFiles.c
  • 1.40 lines changed: 57, context: html, text, full: html, text
    first pass at BAM sequence validation. Only supports alignments with no indels or trimming.
• src/hg/hgTracks/bedGraph.c
  • 1.22 lines changed: 5, context: html, text, full: html, text
    first pass at multiWiggle. This shouldn't change existing behavior. Add extTable to your bigWig trackDb to get two tables into one bigWig wiggle track.
• src/hg/hgTracks/bigWigTrack.c
  • 1.10 lines changed: 47, context: html, text, full: html, text
    first pass at multiWiggle. This shouldn't change existing behavior. Add extTable to your bigWig trackDb to get two tables into one bigWig wiggle track.
• src/hg/hgTracks/wigCommon.h
  • 1.10 lines changed: 7, context: html, text, full: html, text
    first pass at multiWiggle. This shouldn't change existing behavior. Add extTable to your bigWig trackDb to get two tables into one bigWig wiggle track.
• src/hg/hgTracks/wigTrack.c
  • 1.106 lines changed: 62, context: html, text, full: html, text
    first pass at multiWiggle. This shouldn't change existing behavior. Add extTable to your bigWig trackDb to get two tables into one bigWig wiggle track.
• src/hg/hgc/hgc.c
  • 1.1617 lines changed: 27, context: html, text, full: html, text
    add links out of gencode track to yale pseudogenes
• src/hg/inc/yaleGencodeAssoc.h
  • 1.1 lines changed: 63, context: html, text, full: html, text
    yale pseudogene association with gencode ids
• src/hg/lib/makefile
  • 1.408 lines changed: 2, context: html, text, full: html, text
    add yaleGencodeAssoc
• src/hg/lib/yaleGencodeAssoc.as
  • 1.1 lines changed: 8, context: html, text, full: html, text
    files to describe and load table that maps gencode id's to yale pseudogene id's
• src/hg/lib/yaleGencodeAssoc.c
  • 1.1 lines changed: 132, context: html, text, full: html, text
    files to describe and load table that maps gencode id's to yale pseudogene id's
• src/hg/lib/yaleGencodeAssoc.sql
  • 1.1 lines changed: 13, context: html, text, full: html, text
    files to describe and load table that maps gencode id's to yale pseudogene id's
• src/hg/makeDb/doc/oryCun2.txt
  • 1.10 lines changed: 27, context: html, text, full: html, text
    Human Proteins
  • 1.9 lines changed: 161, context: html, text, full: html, text
    starting human proteins
• src/hg/makeDb/schema/all.joiner
  • 1.790 lines changed: 2, context: html, text, full: html, text
    add oryCun2 to Human Protein tracks
• src/hg/makeDb/trackDb/tagTypes.tab
  • 1.13 lines changed: 1, context: html, text, full: html, text
    add extTable
• src/hg/makeDb/trackDb/human/hg18/trackDb.ra
  • 1.478 lines changed: 10, context: html, text, full: html, text
    add brTestPlus for test of multiWig
• src/hg/makeDb/trackDb/human/hg19/trackDb.enc.ra
  • 1.11 lines changed: 5, context: html, text, full: html, text
    some label changes for RRBS. Some data for link out for Yale pseudo in gencode
• src/hg/oneShot/timeGifPng/makefile
  • 1.1 lines changed: 18, context: html, text, full: html, text
    a little test program to test gif and png timing
• src/hg/oneShot/timeGifPng/timeGifPng.c
  • 1.1 lines changed: 203, context: html, text, full: html, text
    a little test program to test gif and png timing
• src/utils/bigWigInfo/bigWigInfo.c
  • 1.8 lines changed: 10, context: html, text, full: html, text
    add minMax option for the ENCODE validator to use