mikep: changes by file

review to branch (2009-03-17 to 2009-03-31) v203

• src/hg/encode/encodeValidate/doEncodeValidate.pl
  • 1.170 lines changed: 7, context: html, text, full: html, text
    adding chrom/size checking against hg18
• src/hg/encode/validateFiles/validateFiles.c
  • 1.13 lines changed: 73, context: html, text, full: html, text
    adding better error reporting on signed/unsigned ints and allow dots in sequence in tagAlign/pairedTagAlign
  • 1.12 lines changed: 12, context: html, text, full: html, text
    make library function to read all chromInfo, and add chromDb option to validateFiles to get chromInfo from DB
• src/hg/featureBits/featureBits.c
  • 1.54 lines changed: 2, context: html, text, full: html, text
    made this a library function, but need to make sure it is semantically identical and tested before removing from featureBits
• src/hg/inc/chromInfo.h
  • 1.4 lines changed: 5, context: html, text, full: html, text
    make library function to read all chromInfo, and add chromDb option to validateFiles to get chromInfo from DB
• src/hg/inc/versionInfo.h
  • 1.143 lines changed: 1, context: html, text, full: html, text
    "New version number v203"
• src/hg/lib/baseMaskCommon.c
  • 1.8 lines changed: 45, context: html, text, full: html, text
    make library function to read all chromInfo, and add chromDb option to validateFiles to get chromInfo from DB
• src/hg/lib/chromInfo.c
  • 1.7 lines changed: 47, context: html, text, full: html, text
    make library function to read all chromInfo, and add chromDb option to validateFiles to get chromInfo from DB
• src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra
  • 1.217 lines changed: 19, context: html, text, full: html, text
    removing a broken track while it is regnerated
  • 1.216 lines changed: 19, context: html, text, full: html, text
    removing a broken track while it is regnerated
  • 1.215 lines changed: 208, context: html, text, full: html, text
    fixing conflicts
• src/hg/mouseStuff/mafToClustalw/mafToClustalw.c
  • 1.1 lines changed: 61, context: html, text, full: html, text
    convert maf to clustalw-like format
• src/hg/mouseStuff/mafToClustalw/makefile
  • 1.1 lines changed: 14, context: html, text, full: html, text
    convert maf to clustalw-like format
• src/hg/mouseStuff/mafToFa/mafToFa.c
  • 1.2 lines changed: 13, context: html, text, full: html, text
    option to strip dots and dashes
  • 1.1 lines changed: 77, context: html, text, full: html, text
    utility to convert maf to fasta
• src/hg/mouseStuff/mafToFa/makefile
  • 1.1 lines changed: 14, context: html, text, full: html, text
    utility to convert maf to fasta
• src/utils/qa/weeklybld/buildEnv.csh
  • 1.52 lines changed: 3, context: html, text, full: html, text
    v203 final build
• src/utils/qa/weeklybld/doNewReview.csh
  • 1.14 lines changed: 1, context: html, text, full: html, text
    adding link to reports