Commits for hiram

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

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