mikep: changes by commit

branch to review (2009-02-09 to 2009-02-17) v200

• draft including discordant tag alignments
  • src/hg/encode/DAFs/GisDnaPet.daf 1.3 - lines changed: 38, context: html, text, full: html, text
• dont hang on input
  • src/utils/qa/weeklybld/doNewBranch32.csh 1.6 - lines changed: 1, context: html, text, full: html, text
  • src/utils/qa/weeklybld/doZip.csh 1.7 - lines changed: 3, context: html, text, full: html, text
• get stdin from dev/null
  • src/utils/qa/weeklybld/doRobots.csh 1.12 - lines changed: 3, context: html, text, full: html, text
• new tag map algorithms for Wold
  • src/hg/encode/encodeValidate/config/cv.ra 1.69 - lines changed: 10, context: html, text, full: html, text
• added null validators for rpkm, fasta, bowtie, psl formats
  • src/hg/encode/encodeValidate/doEncodeValidate.pl 1.142 - lines changed: 48, context: html, text, full: html, text
• validation rules for new Wold download types
  • src/hg/encode/encodeValidate/doEncodeValidate.pl 1.143 - lines changed: 85, context: html, text, full: html, text
• RawData3 and RawData4 types are for Wold lab
  • src/hg/encode/encodeValidate/doEncodeValidate.pl 1.144 - lines changed: 3, context: html, text, full: html, text
• allowing gene name to comprise any char but <tab>
  • src/hg/encode/encodeValidate/doEncodeValidate.pl 1.145 - lines changed: 3, context: html, text, full: html, text
• allow pipes in the name in bowtie
  • src/hg/encode/encodeValidate/doEncodeValidate.pl 1.146 - lines changed: 6, context: html, text, full: html, text
• no algorithm applicable for some data like download only sequences
  • src/hg/encode/encodeValidate/config/cv.ra 1.70 - lines changed: 4, context: html, text, full: html, text
• allow dots in there
  • src/hg/encode/encodeValidate/doEncodeValidate.pl 1.147 - lines changed: 1, context: html, text, full: html, text
• allow commas
  • src/hg/encode/encodeValidate/doEncodeValidate.pl 1.148 - lines changed: 3, context: html, text, full: html, text
• assuming last column is optional as missing from some data
  • src/hg/encode/encodeValidate/doEncodeValidate.pl 1.149 - lines changed: 2, context: html, text, full: html, text
• fixes to first 21 ccolumns of psl format (commas at end of last 3)
  • src/hg/encode/encodeValidate/doEncodeValidate.pl 1.150 - lines changed: 6, context: html, text, full: html, text
• forgot a <tab>
  • src/hg/encode/encodeValidate/doEncodeValidate.pl 1.152 - lines changed: 7, context: html, text, full: html, text
  • src/hg/encode/encodeValidate/doEncodeValidate.pl 1.151 - lines changed: 1, context: html, text, full: html, text
• fixed mismatched duplicates of downloadOnly logic by moving to a function
  • src/hg/encode/encodeValidate/doEncodeValidate.pl 1.153 - lines changed: 17, context: html, text, full: html, text
• first version of helicos rna seq daf
  • src/hg/encode/DAFs/HelicosRnaSeq.daf 1.1 - lines changed: 48, context: html, text, full: html, text
• shortening for table name limit of 64 chars for Wold
  • src/hg/encode/encodeValidate/config/cv.ra 1.71 - lines changed: 2, context: html, text, full: html, text
• allow 12-column beds for Wold
  • src/hg/encode/encodeLoad/doEncodeLoad.pl 1.56 - lines changed: 1, context: html, text, full: html, text
• test for table name too long
  • src/hg/encode/encodeValidate/doEncodeValidate.pl 1.154 - lines changed: 2, context: html, text, full: html, text
• shortening names for sake of 64 char table name limit in mysql
  • src/hg/encode/encodeValidate/config/cv.ra 1.72 - lines changed: 4, context: html, text, full: html, text
• version of D?F that was successfully loaded
  • src/hg/encode/DAFs/WoldRnaSeq.daf 1.2 - lines changed: 30, context: html, text, full: html, text
  • src/hg/encode/DAFs/WoldRnaSeq.ex.ddf 1.3 - lines changed: 33, context: html, text, full: html, text
• First version of Wold tracks
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra 1.153 - lines changed: 484, context: html, text, full: html, text
• v201 preview
  • src/utils/qa/weeklybld/buildEnv.csh 1.47 - lines changed: 2, context: html, text, full: html, text