File Changes for hiram

v239_preview to v239_base (2010-08-24 to 2010-08-31) v239

• src/hg/hgCustom/hgCustom.c
  • lines changed 15, context: html, text, full: html, text
    add measureTiming CGI option to measure custom track loading time
  • lines changed 2, context: html, text, full: html, text
    a couple of routines can be static
• src/hg/hgTracks/simpleTracks.c
  • lines changed 3, context: html, text, full: html, text
    do not check for base coloring if itemRgb is on
• src/hg/hgTracks/wigTrack.c
  • lines changed 14, context: html, text, full: html, text
    fix extra useless reading of data blocks when not really necessary
• src/hg/makeDb/doc/hg19.txt
  • lines changed 176, context: html, text, full: html, text
    beginning of altSequence track and Vega gene update v39 done
• src/hg/makeDb/doc/hg19Patch2.txt
  • lines changed 209, context: html, text, full: html, text
    initial contents for hg19 Patch2
  • lines changed 154, context: html, text, full: html, text
    adding ctgPos, ctgPos2, altSequence, and running genbank
• src/hg/makeDb/genbank/etc/align.dbs
  • lines changed 1, context: html, text, full: html, text
    Added hg19Patch2 - Human - GRCh37.p2
• src/hg/makeDb/genbank/etc/genbank.conf
  • lines changed 23, context: html, text, full: html, text
    adding hg19Patch2
  • lines changed 1, context: html, text, full: html, text
    need lift file for hg19Patch2
• src/hg/makeDb/genbank/etc/hgwdev.dbs
  • lines changed 1, context: html, text, full: html, text
    Added hg19Patch2 - Human - GRCh37.p2
• src/hg/makeDb/trackDb/human/altSequence.html
  • lines changed 16, context: html, text, full: html, text
    adding altSequence to hg19Patch2;
• src/hg/makeDb/trackDb/human/hg19/altSequence.html
  • lines changed 16, context: html, text, full: html, text
    moving up one level
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    bed 9 . will turn on score filters and add scoreFilterByRange
  • lines changed 1, context: html, text, full: html, text
    adding altSequence to hg19Patch2;
  • lines changed 9, context: html, text, full: html, text
    naming patch2 alignments as chainHg19 and chainHg19Patch2
  • lines changed 1, context: html, text, full: html, text
    table chainHg19Patch2 becomes testChainHg19Patch2
• src/hg/makeDb/trackDb/human/hg19/vegaGeneComposite.html
  • lines changed 1, context: html, text, full: html, text
    update comment to include Non-Coding on the description
• src/hg/makeDb/trackDb/human/hg19Patch2/description.html
  • lines changed 129, context: html, text, full: html, text
    initial files for hg19Patch2
  • lines changed 216, context: html, text, full: html, text
    update documents to hg19 status and adding ctgPos2 track to trackDb.ra
• src/hg/makeDb/trackDb/human/hg19Patch2/gap.html
  • lines changed 64, context: html, text, full: html, text
    initial files for hg19Patch2
  • lines changed 68, context: html, text, full: html, text
    update documents to hg19 status and adding ctgPos2 track to trackDb.ra
• src/hg/makeDb/trackDb/human/hg19Patch2/gold.html
  • lines changed 23, context: html, text, full: html, text
    initial files for hg19Patch2
  • lines changed 38, context: html, text, full: html, text
    update documents to hg19 status and adding ctgPos2 track to trackDb.ra
• src/hg/makeDb/trackDb/human/hg19Patch2/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    initial files for hg19Patch2
  • lines changed 7, context: html, text, full: html, text
    update documents to hg19 status and adding ctgPos2 track to trackDb.ra
  • lines changed 12, context: html, text, full: html, text
    adding altSequence to hg19Patch2;
  • lines changed 12, context: html, text, full: html, text
    naming patch2 alignments as chainHg19 and chainHg19Patch2
  • lines changed 1, context: html, text, full: html, text
    chainHg19 to be replaced now called testChainHg19
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 13, context: html, text, full: html, text
    no need for a naked chainHg19 table definition here
• src/hg/makeDb/trackDb/makefile
  • lines changed 1, context: html, text, full: html, text
    adding hg19Patch2 to the build
• src/hg/makeDb/trackDb/trackDb.chainNet.ra
  • lines changed 51, context: html, text, full: html, text
    adding chainNetHg19Patch2 definition
• src/hg/utils/automation/HgAutomate.pm
  • lines changed 1, context: html, text, full: html, text
    using /scratch/data instead of /hive/data/genomes
• src/hg/utils/automation/doEnsGeneUpdate.pl
  • lines changed 5, context: html, text, full: html, text
    update human vegaGene peptide file name for version 39 human vega release
• src/hg/utils/automation/doSameSpeciesLiftOver.pl
  • lines changed 1, context: html, text, full: html, text
    do not use expr, use awk instead
  • lines changed 2, context: html, text, full: html, text
    do not use expr, use awk instead
  • lines changed 4, context: html, text, full: html, text
    using /scratch/data instead of /hive/data/genomes
  • lines changed 9, context: html, text, full: html, text
    must force /scratch/data for sequences ?