mikep: changes by commit

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

• last of the affy freeze
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra 1.201 - lines changed: 185, 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/hg/utils/automation/SafePipe.pm 1.4 - lines changed: 2, context: html, text, full: html, text
• adding a link to the history
  • src/utils/qa/weeklybld/buildCvsReports.csh 1.18 - lines changed: 2, 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/makefile 1.1 - lines changed: 14, context: html, text, full: html, text
  • src/hg/encode/validateFiles/validateFiles.c 1.1 - lines changed: 328, context: html, text, full: html, text
• add -type= to main usage line
  • src/hg/encode/validateFiles/validateFiles.c 1.2 - lines changed: 1, context: html, text, full: html, text
• support for fastq
  • src/hg/encode/validateFiles/validateFiles.c 1.3 - lines changed: 117, context: html, text, full: html, text
• plug the memory leak, > 100bytes per input line, fatal for ENCODE
  • src/hg/bedItemOverlapCount/bedItemOverlapCount.c 1.9 - lines changed: 1, context: html, text, full: html, text
• fix so comment lines only appear at top of fastq, and added csfasta format
  • src/hg/encode/validateFiles/validateFiles.c 1.4 - lines changed: 128, context: html, text, full: html, text
• making everythign use linefile so .gz/.bzip2 files handled automatically
  • src/hg/encode/validateFiles/validateFiles.c 1.5 - lines changed: 53, context: html, text, full: html, text
• provide colorspace as option to include chars 0-3 in DNA
  • src/hg/encode/validateFiles/validateFiles.c 1.6 - lines changed: 11, context: html, text, full: html, text
• improved usage message, continue after error in # columns, add csqual, put colorSpace as option
  • src/hg/encode/validateFiles/validateFiles.c 1.7 - lines changed: 138, context: html, text, full: html, text
• support for broadPeak
  • src/hg/encode/validateFiles/validateFiles.c 1.8 - lines changed: 62, context: html, text, full: html, text
• adding narrow and gapped peaks
  • src/hg/encode/validateFiles/validateFiles.c 1.9 - lines changed: 49, context: html, text, full: html, text
• added bedGraph as bedType variant and modified usage text
  • src/hg/encode/validateFiles/validateFiles.c 1.10 - lines changed: 36, context: html, text, full: html, text
• mods to usage message
  • src/hg/encode/validateFiles/validateFiles.c 1.11 - lines changed: 3, 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/doEncodeValidate.pl 1.166 - lines changed: 21, 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
  • src/hg/encode/encodeValidate/doEncodeValidate.pl 1.167 - lines changed: 69, 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/encodeValidate/config/fields.ra 1.14 - lines changed: 10, context: html, text, full: html, text
• add validateFiles to makefile directory list
  • src/hg/encode/makefile 1.11 - lines changed: 1, context: html, text, full: html, text
• adding standard blurbs to CSHL
  • src/hg/makeDb/trackDb/human/hg18/wgEncodeCshlRnaSeq.html 1.4 - lines changed: 31, context: html, text, full: html, text
• tracks finally loaded
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra 1.207 - lines changed: 275, 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/encodeLoad/doEncodeLoad.pl 1.59 - lines changed: 10, context: html, text, full: html, text
• fixing problem with CSHL where this track should be short rna not shortDeplRrna
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra 1.209 - lines changed: 17, context: html, text, full: html, text
• removing GIS RNA PET Project while I reload it
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra 1.213 - lines changed: 376, context: html, text, full: html, text
• making it easier to find .ra bugs
  • src/lib/common.c 1.128 - lines changed: 1, context: html, text, full: html, text
• fixing tpyo
  • src/hg/makeDb/trackDb/human/hg18/trackDb.ra 1.384 - lines changed: 1, context: html, text, full: html, text
• adding standard blurbs
  • src/hg/makeDb/trackDb/human/hg18/wgEncodeGisPet.html 1.5 - lines changed: 51, context: html, text, full: html, text
• v203 preview
  • src/utils/qa/weeklybld/buildEnv.csh 1.51 - lines changed: 2, context: html, text, full: html, text