File Changes for braney

v235_preview to v235_base (2010-06-29 to 2010-07-06) v235

• src/ameme/ameme.c
  • lines changed 9, context: html, text, full: html, text
    switch to using PNG
• src/ameme/makefile
  • lines changed 7, context: html, text, full: html, text
    switch to using PNG
• src/hg/encode/validateFiles/validateFiles.c
  • lines changed 10, context: html, text, full: html, text
    fix totally brain dead bug that my code buddy should have caught (take that anonymous buddy!). Also add option for testing
• src/hg/hgTracks/cds.c
  • lines changed 7, context: html, text, full: html, text
    make 32-bit PNG the default, use painter's algorithm for mRNA track
• src/hg/makeDb/doc/encodeDccHg19/gencodeV4.txt
  • lines changed 8, context: html, text, full: html, text
    download new gtf files from FelixK. Need to re-load and change release notes
• src/hg/makeDb/trackDb/human/hg18/trackDb.ra
  • lines changed 20, context: html, text, full: html, text
    UCSF Brain Methyl: take out Brain from individual tracks long and short labels, change RNAseq to RNA-seq
  • lines changed 3, context: html, text, full: html, text
    change some stuff that Mary wanted
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/makefile
  • lines changed 1, context: html, text, full: html, text
    add GIS RNA-seq data
  • lines changed 1, context: html, text, full: html, text
    add wgEncodeHaibMethylSeq.ra
  • lines changed 1, context: html, text, full: html, text
    add some riken tracks
  • lines changed 4, context: html, text, full: html, text
    add some ra files to the makefile
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlShortRnaSeq.ra
  • lines changed 595, context: html, text, full: html, text
    metadata for CSHL Small RNA-seq
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGisRnaSeq.ra
  • lines changed 229, context: html, text, full: html, text
    add GIS RNA-seq data
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibMethylSeq.ra
  • lines changed 829, context: html, text, full: html, text
    add Haib MethylSeq to hg19
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeRikenCage.ra
  • lines changed 970, context: html, text, full: html, text
    add some riken tracks
• src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra
  • lines changed 1, context: html, text, full: html, text
    add GIS RNA-seq data
  • lines changed 1, context: html, text, full: html, text
    add Haib MethylSeq to hg19
  • lines changed 1, context: html, text, full: html, text
    first pass at CSHL short RNA
• src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncodeCaltechRnaSeq.ra
  • lines changed 1, context: html, text, full: html, text
    add noInherit on
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlShortRnaSeq.ra
  • lines changed 393, context: html, text, full: html, text
    first pass at CSHL short RNA
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGisRnaSeq.ra
  • lines changed 173, context: html, text, full: html, text
    add GIS RNA-seq data
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethylSeq.ra
  • lines changed 123, context: html, text, full: html, text
    forgot to commit this
  • lines changed 16, context: html, text, full: html, text
    add Haib MethylSeq to hg19
• src/hg/makeDb/trackDb/human/hg19/wgEncodeRikenCage.ra
  • lines changed 1, context: html, text, full: html, text
    add to RNA-seq supertrack
  • lines changed 494, context: html, text, full: html, text
    add some riken tracks
• src/hg/phyloGif/phyloGif.c
  • lines changed 12, context: html, text, full: html, text
    set up HTML to have the right file type
  • lines changed 7, context: html, text, full: html, text
    fix phyloGif to write out PNG, and make sure no one can write out GIF if USE_PNG is set
• src/inc/common.mk
  • lines changed 5, context: html, text, full: html, text
    make 32-bit PNG the default, use painter's algorithm for mRNA track
• src/lib/gifLabel.c
  • lines changed 7, context: html, text, full: html, text
    use png instead of gif if USE_PNG is set
• src/lib/gifwrite.c
  • lines changed 2, context: html, text, full: html, text
    fix phyloGif to write out PNG, and make sure no one can write out GIF if USE_PNG is set
• src/lib/pngwrite.c
  • lines changed 2, context: html, text, full: html, text
    don't fiddle with palette transparency if we're 32-bit
• src/tracks/tracks.c
  • lines changed 5, context: html, text, full: html, text
    use PNG if USE_PNG
• src/weblet/counter/counter.c
  • lines changed 5, context: html, text, full: html, text
    more GIF to PNG changes
• src/weblet/counter/makefile
  • lines changed 1, context: html, text, full: html, text
    more GIF to PNG changes