Commits for braney

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

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