File Changes for braney

v237_preview to v237_base (2010-07-27 to 2010-08-03) v237

• src/hg/encode/encodeLoad/doEncodeLoad.pl
  • lines changed 242, context: html, text, full: html, text
    first pass at modifying load scripts
• src/hg/encode/encodeLoad/doEncodeUnload.pl
  • lines changed 3, context: html, text, full: html, text
    first pass at modifying load scripts
• src/hg/encode/encodeValidate/config/labs.ra
  • lines changed 16, context: html, text, full: html, text
    take out tim and brian
• src/hg/encode/encodeValidate/doEncodeValidate.pl
  • lines changed 1, context: html, text, full: html, text
    some changes to support CSHL short transfrags
• src/hg/encode/validateFiles/validateFiles.c
  • lines changed 35, context: html, text, full: html, text
    add optional quality checks
  • lines changed 1, context: html, text, full: html, text
    add a verbose statement telling user what chrom is being looked at
• src/hg/inc/versionInfo.h
  • lines changed 1, context: html, text, full: html, text
    "New version number v237"
• src/hg/lib/encode/cshlShortTransfrag.as
  • lines changed 30, context: html, text, full: html, text
    cshl small rna clusters
• src/hg/lib/encode/shortFrags.as
  • lines changed 1, context: html, text, full: html, text
    changed title to match file name
  • lines changed 30, context: html, text, full: html, text
    some changes to support CSHL short transfrags
• src/hg/lib/encode/shortFrags.sql
  • lines changed 37, context: html, text, full: html, text
    some changes to support CSHL short transfrags
• src/hg/makeDb/doc/encodeDccHg19/gencodeV4.txt
  • lines changed 3, context: html, text, full: html, text
    add 2waypseudocons
  • lines changed 45, context: html, text, full: html, text
    reload with v4fix and load Yale pseudo gene table
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeCaltechRnaSeq.ra
  • lines changed 493, context: html, text, full: html, text
    add some d's onto the 1x75 sets
• src/hg/makeDb/trackDb/human/hg18/trackDb.ra
  • lines changed 20, context: html, text, full: html, text
    set Brain Methyl to show mismatches, discover all the alignments are off by one
  • lines changed 0, context: html, text, full: html, text
    take out some spaces in Brain Methyl short labels (per Mary)
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlShortRnaSeq.ra
  • lines changed 221, context: html, text, full: html, text
    add transfrags
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGisDnaPet.ra
  • lines changed 31, context: html, text, full: html, text
    add origAssembly, and get submission and restriction end dates from hg18
• src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra
  • lines changed 7, context: html, text, full: html, text
    add 2waypseudocons to gencode track
  • lines changed 2, context: html, text, full: html, text
    add yale pseudoGene track for gencode v4
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlShortRnaSeq.html
  • lines changed 106, context: html, text, full: html, text
    copy over from hg18
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlShortRnaSeq.ra
  • lines changed 121, context: html, text, full: html, text
    add transfrags
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencode.html
  • lines changed 25, context: html, text, full: html, text
    changes from Felix
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGisDnaPet.ra
  • lines changed 72, context: html, text, full: html, text
    set BAM options to show mismatches etc
  • lines changed 18, context: html, text, full: html, text
    fix labels and defaults
• src/hg/utils/automation/Encode.pm
  • lines changed 1, context: html, text, full: html, text
    some changes to support CSHL short transfrags
• src/hg/utils/makefile
  • lines changed 2, context: html, text, full: html, text
    add gffToPsl
• src/inc/memgfx.h
  • lines changed 3, context: html, text, full: html, text
    add transparency for 32-bit PNG. Tim needs it for drag scroll
• src/lib/memgfx.c
  • lines changed 13, context: html, text, full: html, text
    add transparency for 32-bit PNG. Tim needs it for drag scroll
• src/lib/vPng.c
  • lines changed 3, context: html, text, full: html, text
    add transparency for 32-bit PNG. Tim needs it for drag scroll
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 3, context: html, text, full: html, text
    v237 final build