File Changes for cline

v252_preview to v252_preview2 (2011-05-17 to 2011-05-31) v252

• src/hg/encode/encodeMkChangeNotes/encodeMkChangeNotes
  • lines changed 1, context: html, text, full: html, text
    Added peptideMapping to the list of expected types
• src/hg/inc/cdsEvidence.h
  • lines changed 2, context: html, text, full: html, text
    I previously modified txCdsToGene so that it would issue a warning and not errAbort when it came across a CDS with a premature stop codon. That change was at the urging of Markd, who pointed out that the CDS transcripts in question had not been provisionally accepted or rejected yet, and that it's now accepted that we don't understand NMD as well as we'd thought. But when I changed the premature stop codon condition from an errAbort to warning condition, I'd neglected to do the second part: addressing what sort of thick start and end to have in the output bed. I decided that if a PTC is detected when trying to generate a protein sequence (which yields no protein sequence), then the thickStart and thickEnd should be the same
• src/hg/lib/cdsEvidence.c
  • lines changed 3, context: html, text, full: html, text
    I previously modified txCdsToGene so that it would issue a warning and not errAbort when it came across a CDS with a premature stop codon. That change was at the urging of Markd, who pointed out that the CDS transcripts in question had not been provisionally accepted or rejected yet, and that it's now accepted that we don't understand NMD as well as we'd thought. But when I changed the premature stop codon condition from an errAbort to warning condition, I'd neglected to do the second part: addressing what sort of thick start and end to have in the output bed. I decided that if a PTC is detected when trying to generate a protein sequence (which yields no protein sequence), then the thickStart and thickEnd should be the same
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeUncBsuProt.release1.notes
  • lines changed 48, context: html, text, full: html, text
    Adding the release notes for the UNC/BSU Prot track, which was just added to the pushQ
• src/hg/makeDb/doc/ucscGenes/hg19.ucscGenes13.csh
  • lines changed 39, context: html, text, full: html, text
    Replaced a mkdir command for creating a temporary directory with mkdir -p, so that the code won't blow up if it has to be rerun before it reaches the point where that temporary directory is removed
  • lines changed 9, context: html, text, full: html, text
    Added a -p switch to some mkdir commands for making temporary directories, so that the script doesn't fail if it has to be restarted after the temp directories are created but before they're removed
  • lines changed 11, context: html, text, full: html, text
    Changed the (previously incorrect) order of some arguments for a testing script.
• src/hg/makeDb/trackDb/cv/alpha/cv.ra
  • lines changed 18, context: html, text, full: html, text
    Commented out the SK-N-SH_RA 'cell type', since this term is now obsolete. SK-N-SH_RA didn't represent a separate cell type so much as a separate treatment performed on SK-N-SH cells. Instances of SK-N-SH_RA have been replaced with SK-N-SH in trackDb and metaDb, and SK-N-SH_RA is now commented out and should be deleted soon
  • lines changed 134, context: html, text, full: html, text
    Numerous small changes to address validation errors. Collectively, these have reduced the number of validation errors from 597 to 220
  • lines changed 5, context: html, text, full: html, text
    Fixed a couple more easy validation errors
  • lines changed 1, context: html, text, full: html, text
    changed an orderUrl tag from ordrUrl. All human cell types are now validating - yay
  • lines changed 18, context: html, text, full: html, text
    Reinstated SK-N-SH_RA, which had been removed prematurely
• src/hg/txCds/txCdsRepick/txCdsRepick.c
  • lines changed 1, context: html, text, full: html, text
    Added the missing third argument to to cdsEvidenceSetBedThick
• src/hg/txCds/txCdsToGene/txCdsToGene.c
  • lines changed 8, context: html, text, full: html, text
    I previously modified txCdsToGene so that it would issue a warning and not errAbort when it came across a CDS with a premature stop codon. That change was at the urging of Markd, who pointed out that the CDS transcripts in question had not been provisionally accepted or rejected yet, and that it's now accepted that we don't understand NMD as well as we'd thought. But when I changed the premature stop codon condition from an errAbort to warning condition, I'd neglected to do the second part: addressing what sort of thick start and end to have in the output bed. I decided that if a PTC is detected when trying to generate a protein sequence (which yields no protein sequence), then the thickStart and thickEnd should be the same