mikep: changes by commit

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

• fixing to copy the kent src over to each new release because cvs-reports-d does a cvs update, not cvs checkout
  • src/utils/qa/weeklybld/buildCvsReports.csh 1.17 - lines changed: 18, context: html, text, full: html, text
• forgot A targets
  • src/hg/makeDb/trackDb/human/hg18/wgEncodeAffyRnaChip.html 1.4 - lines changed: 5, context: html, text, full: html, text
• added contact email
  • src/hg/makeDb/trackDb/human/hg18/wgEncodeAffyRnaChip.html 1.5 - lines changed: 1, context: html, text, full: html, text
• friendlier labels
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra 1.177 - lines changed: 3, context: html, text, full: html, text
• final adjustments to text
  • src/hg/makeDb/trackDb/human/hg18/wgEncodeAffyRnaChip.html 1.6 - lines changed: 27, context: html, text, full: html, text
• adding links to pubmed and tidying up generally
  • src/hg/makeDb/trackDb/human/hg18/wgEncodeSunyalbanyRnaGeneChip.html 1.4 - lines changed: 102, context: html, text, full: html, text
• tidy up
  • src/hg/makeDb/trackDb/human/hg18/wgEncodeSunyalbanyRnaGeneChip.html 1.5 - lines changed: 2, context: html, text, full: html, text
• put the url around the term id
  • src/hg/encode/hgEncodeVocab/hgEncodeVocab.c 1.19 - lines changed: 10, context: html, text, full: html, text
• tidying up description page
  • src/hg/makeDb/trackDb/human/hg18/wgEncodeSunyalbanyRnaGeneChip.html 1.6 - lines changed: 134, context: html, text, full: html, text
• explain why a single view
  • src/hg/makeDb/trackDb/human/hg18/wgEncodeSunyalbanyRnaGeneChip.html 1.7 - lines changed: 2, context: html, text, full: html, text
• validator for frag size for GIS gDNA PET
  • src/hg/encode/encodeValidate/doEncodeValidate.pl 1.158 - lines changed: 6, context: html, text, full: html, text
• adding data release policy, cell culture specs, and changing bold to italics
  • src/hg/makeDb/trackDb/human/hg18/wgEncodeAffyRnaChip.html 1.7 - lines changed: 21, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg18/wgEncodeSunyalbanyRnaGeneChip.html 1.8 - lines changed: 16, context: html, text, full: html, text
• adding boilerplate
  • src/hg/makeDb/trackDb/human/hg18/wgEncodeCaltechRnaSeq.html 1.2 - lines changed: 11, context: html, text, full: html, text
• standardising text
  • src/hg/makeDb/trackDb/human/hg18/wgEncodeUwDnaseSeq.html 1.4 - lines changed: 56, context: html, text, full: html, text
• add contact
  • src/hg/makeDb/trackDb/human/hg18/wgEncodeUwDnaseSeq.html 1.5 - lines changed: 4, context: html, text, full: html, text
• adding TARGET to HREF
  • src/hg/makeDb/trackDb/human/hg18/wgEncodeUwDnaseSeq.html 1.6 - lines changed: 5, context: html, text, full: html, text
• 3 different flavors of rpkm; just check the cols are there
  • src/hg/encode/encodeValidate/doEncodeValidate.pl 1.159 - lines changed: 20, context: html, text, full: html, text
• Reformatting Caltech tracks and description
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra 1.190 - lines changed: 188, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg18/wgEncodeCaltechRnaSeq.html 1.3 - lines changed: 29, context: html, text, full: html, text
• removed some gnarly chars for javascript
  • src/hg/encode/encodeValidate/config/cv.ra 1.80 - lines changed: 2, context: html, text, full: html, text
• new variable readType for Caltech
  • src/hg/encode/encodeValidate/config/cv.ra 1.81 - lines changed: 9, context: html, text, full: html, text
• fixed typo
  • src/hg/encode/encodeValidate/config/cv.ra 1.82 - lines changed: 1, context: html, text, full: html, text
• adding links to publication (not in PubMed yet tho) and new cv.ra entry for reads
  • src/hg/makeDb/trackDb/human/hg18/wgEncodeCaltechRnaSeq.html 1.4 - lines changed: 7, context: html, text, full: html, text
• fixing up cell types by removing (+) chars
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra 1.191 - lines changed: 8, context: html, text, full: html, text
• get rid of @_ deprecated warning
  • src/hg/encode/encodeValidate/doEncodeValidate.pl 1.160 - lines changed: 2, context: html, text, full: html, text
• readType validator for Wold/Caltech
  • src/hg/encode/encodeValidate/doEncodeValidate.pl 1.161 - lines changed: 6, context: html, text, full: html, text
• shorter codes
  • src/hg/encode/encodeValidate/config/cv.ra 1.84 - lines changed: 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra 1.192 - lines changed: 1, context: html, text, full: html, text
• updated DAF to handle more raw data files
  • src/hg/encode/DAFs/WoldRnaSeq.daf 1.3 - lines changed: 38, context: html, text, full: html, text
• adding rawdata files for Wold pipeline input data
  • src/hg/encode/DAFs/WoldRnaSeq.daf 1.4 - lines changed: 12, context: html, text, full: html, text
• cant put pipeline data in daf as it doesnt have variables associated
  • src/hg/encode/DAFs/WoldRnaSeq.daf 1.5 - lines changed: 12, context: html, text, full: html, text
• wrapping at 80 chars
  • src/hg/makeDb/trackDb/human/hg18/wgEncodeAffyRnaChip.html 1.8 - lines changed: 63, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg18/wgEncodeCaltechRnaSeq.html 1.5 - lines changed: 88, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg18/wgEncodeCshlRnaSeq.html 1.3 - lines changed: 23, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg18/wgEncodeGisDnaPet.html 1.2 - lines changed: 23, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg18/wgEncodeGisPet.html 1.4 - lines changed: 24, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg18/wgEncodeSunyalbanyRnaGeneChip.html 1.9 - lines changed: 20, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg18/wgEncodeUwDnaseSeq.html 1.7 - lines changed: 20, context: html, text, full: html, text
• added text for download file method
  • src/hg/makeDb/trackDb/human/hg18/wgEncodeCaltechRnaSeq.html 1.6 - lines changed: 22, context: html, text, full: html, text
• shortend name for table name
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra 1.193 - lines changed: 24, context: html, text, full: html, text
• added link to downloads
  • src/hg/makeDb/trackDb/human/hg18/wgEncodeCaltechRnaSeq.html 1.7 - lines changed: 3, context: html, text, full: html, text
• adding second set of data, new cv.ra type
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra 1.194 - lines changed: 375, context: html, text, full: html, text
• fixing view names
  • src/hg/makeDb/trackDb/human/hg18/wgEncodeCaltechRnaSeq.html 1.8 - lines changed: 4, context: html, text, full: html, text
• maybe there are more rawdatas in future...
  • src/hg/encode/encodeValidate/doEncodeValidate.pl 1.162 - lines changed: 3, context: html, text, full: html, text
• diff header coming from GIS
  • src/hg/encode/encodeValidate/doEncodeValidate.pl 1.163 - lines changed: 6, context: html, text, full: html, text
• added original Caltech data
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra 1.198 - lines changed: 398, context: html, text, full: html, text
• dont add name indexes onto this highthroughput data
  • src/hg/encode/encodeLoad/doEncodeLoad.pl 1.57 - lines changed: 3, context: html, text, full: html, text
• check if a file is a tar
  • src/hg/utils/automation/Encode.pm 1.35 - lines changed: 7, context: html, text, full: html, text
• open tars
  • src/hg/encode/encodeValidate/doEncodeValidate.pl 1.164 - lines changed: 4, context: html, text, full: html, text
• CS fasta can have G sequences evidnetly
  • src/hg/encode/encodeValidate/doEncodeValidate.pl 1.165 - lines changed: 1, context: html, text, full: html, text
• Transfrags not required at this stage
  • src/hg/encode/DAFs/HelicosRnaSeq.daf 1.3 - lines changed: 1, context: html, text, full: html, text
• first draft of RIKEN doco
  • src/hg/makeDb/trackDb/human/hg18/wgEncodeRikenCage.html 1.1 - lines changed: 134, context: html, text, full: html, text
• fixing tpyo
  • src/hg/makeDb/trackDb/human/hg18/wgEncodeAffyRnaChip.html 1.9 - lines changed: 1, context: html, text, full: html, text
• last tracks for RIKEN
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra 1.199 - lines changed: 183, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg18/wgEncodeRikenCage.html 1.2 - lines changed: 68, context: html, text, full: html, text
• adding standard text like Yale
  • src/hg/makeDb/trackDb/human/hg18/wgEncodeRikenCage.html 1.3 - lines changed: 10, context: html, text, full: html, text
• removing CSHL stuff while it is reprocessed
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra 1.200 - lines changed: 89, context: html, text, full: html, text
• v202 final build
  • src/utils/qa/weeklybld/buildEnv.csh 1.50 - lines changed: 3, context: html, text, full: html, text
• "New version number v202"
  • src/hg/inc/versionInfo.h 1.142 - lines changed: 1, context: html, text, full: html, text