mikep: changes by file

branch to review (2009-03-10 to 2009-03-17) v202

• src/hg/bedItemOverlapCount/bedItemOverlapCount.c
  • 1.9 lines changed: 1, context: html, text, full: html, text
    plug the memory leak, > 100bytes per input line, fatal for ENCODE
• src/hg/encode/makefile
  • 1.11 lines changed: 1, context: html, text, full: html, text
    add validateFiles to makefile directory list
• src/hg/encode/encodeLoad/doEncodeLoad.pl
  • 1.59 lines changed: 10, context: html, text, full: html, text
    added an option to not do downloads (and implicitly not do table load) so that I could regenerate pushq and whatever else gets done, because I loaded 16 GB of data and got a mysql error on the trackDb step immediaetly after the load was complete.
• src/hg/encode/encodeValidate/doEncodeValidate.pl
  • 1.167 lines changed: 69, context: html, text, full: html, text
    adding downloadOnly property to Views in DAF, adding validateFiles support in broadPeak, fastq, tagAlign so can validate CSHL data in reasonable time
  • 1.166 lines changed: 21, context: html, text, full: html, text
    mods to keep massive sorts under control; sort files independently with mem limit, then do merge sort of all
• src/hg/encode/encodeValidate/config/fields.ra
  • 1.14 lines changed: 10, context: html, text, full: html, text
    noAutoCreate setting at top-level of daf to control generation of autoRawSignal files, and downloadOnly setting in DAF views to control whether files are loaded or not
• src/hg/encode/validateFiles/makefile
  • 1.1 lines changed: 14, context: html, text, full: html, text
    first version of a validator for encode, currently supports tagAlign and pairedTagAlign, much faster than Perl adn does extra checking on start<end, chrom, chromSize, etc
• src/hg/encode/validateFiles/validateFiles.c
  • 1.11 lines changed: 3, context: html, text, full: html, text
    mods to usage message
  • 1.10 lines changed: 36, context: html, text, full: html, text
    added bedGraph as bedType variant and modified usage text
  • 1.9 lines changed: 49, context: html, text, full: html, text
    adding narrow and gapped peaks
  • 1.8 lines changed: 62, context: html, text, full: html, text
    support for broadPeak
  • 1.7 lines changed: 138, context: html, text, full: html, text
    improved usage message, continue after error in # columns, add csqual, put colorSpace as option
  • 1.6 lines changed: 11, context: html, text, full: html, text
    provide colorspace as option to include chars 0-3 in DNA
  • 1.5 lines changed: 53, context: html, text, full: html, text
    making everythign use linefile so .gz/.bzip2 files handled automatically
  • 1.4 lines changed: 128, context: html, text, full: html, text
    fix so comment lines only appear at top of fastq, and added csfasta format
  • 1.3 lines changed: 117, context: html, text, full: html, text
    support for fastq
  • 1.2 lines changed: 1, context: html, text, full: html, text
    add -type= to main usage line
  • 1.1 lines changed: 328, context: html, text, full: html, text
    first version of a validator for encode, currently supports tagAlign and pairedTagAlign, much faster than Perl adn does extra checking on start<end, chrom, chromSize, etc
• src/hg/makeDb/trackDb/human/hg18/trackDb.ra
  • 1.384 lines changed: 1, context: html, text, full: html, text
    fixing tpyo
• src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra
  • 1.213 lines changed: 376, context: html, text, full: html, text
    removing GIS RNA PET Project while I reload it
  • 1.209 lines changed: 17, context: html, text, full: html, text
    fixing problem with CSHL where this track should be short rna not shortDeplRrna
  • 1.207 lines changed: 275, context: html, text, full: html, text
    tracks finally loaded
  • 1.201 lines changed: 185, context: html, text, full: html, text
    last of the affy freeze
• src/hg/makeDb/trackDb/human/hg18/wgEncodeCshlRnaSeq.html
  • 1.4 lines changed: 31, context: html, text, full: html, text
    adding standard blurbs to CSHL
• src/hg/makeDb/trackDb/human/hg18/wgEncodeGisPet.html
  • 1.5 lines changed: 51, context: html, text, full: html, text
    adding standard blurbs
• src/hg/utils/automation/SafePipe.pm
  • 1.4 lines changed: 2, context: html, text, full: html, text
    these error files get too large for /tmp so put them in /data/tmp where the rest of the tmp files go
• src/lib/common.c
  • 1.128 lines changed: 1, context: html, text, full: html, text
    making it easier to find .ra bugs
• src/utils/qa/weeklybld/buildCvsReports.csh
  • 1.18 lines changed: 2, context: html, text, full: html, text
    adding a link to the history
• src/utils/qa/weeklybld/buildEnv.csh
  • 1.51 lines changed: 2, context: html, text, full: html, text
    v203 preview