File Changes for braney

v271_preview to v271_preview2 (2012-07-24 to 2012-07-31) v271

• src/hg/encode/validateFiles/validateFiles.c
  • lines changed 1, context: html, text, full: html, text
    fix bug where buffer is known to be too small, but its growth may still not be enough
• src/hg/hgGene/hgGeneData/Mouse/mm10/otherOrgs.ra
  • lines changed 9, context: html, text, full: html, text
    use rn5 refGene for mm10 UCSC genes... maybe we should be using rn4 RGD gene?
• src/hg/makeDb/doc/ucscGenes/mm10.ucscGenes13.csh
  • lines changed 124, context: html, text, full: html, text
    ongoing work on mm10 UCSC genes. Fixed KEGG tables, rn5 blastp tables, and technique to lift genes from old assembly. Also added some comments to document the size of some of the tables for future reference.
• src/hg/makefile
  • lines changed 1, context: html, text, full: html, text
    add pslToBed to directories to test
• src/hg/pslToBed/makefile
  • lines changed 5, context: html, text, full: html, text
    add some tests, make the code easier to understand, and fix a problem with no CDS being indicated by thickStart == chromStart && thickEnd == chromEnd, instead of thickStart==thickEnd==0 as should have been the case. Thanks Tim for the code review!!!
• src/hg/pslToBed/pslToBed.c
  • lines changed 46, context: html, text, full: html, text
    add some tests, make the code easier to understand, and fix a problem with no CDS being indicated by thickStart == chromStart && thickEnd == chromEnd, instead of thickStart==thickEnd==0 as should have been the case. Thanks Tim for the code review!!!
  • lines changed 17, context: html, text, full: html, text
    oops... wasn't dealing with CDS start and stop correctly on '-' strand
  • lines changed 6, context: html, text, full: html, text
    round #3. Now genePredToBed matches what comes out of genePredToFakePsl followed by pslToBed if you make thickStart and thickEnd equal 0 when they equal each other. Now cdsEnd points to the base after the last base in CDS, even if that base is not in one of the exons.
• src/hg/pslToBed/tests/expected/doTest1.bed
  • lines changed 285, context: html, text, full: html, text
    add some tests, make the code easier to understand, and fix a problem with no CDS being indicated by thickStart == chromStart && thickEnd == chromEnd, instead of thickStart==thickEnd==0 as should have been the case. Thanks Tim for the code review!!!
• src/hg/pslToBed/tests/expected/doTest2.bed
  • lines changed 55307, context: html, text, full: html, text
    add some tests, make the code easier to understand, and fix a problem with no CDS being indicated by thickStart == chromStart && thickEnd == chromEnd, instead of thickStart==thickEnd==0 as should have been the case. Thanks Tim for the code review!!!
  • lines changed 20685, context: html, text, full: html, text
    oops... wasn't dealing with CDS start and stop correctly on '-' strand
  • lines changed 236, context: html, text, full: html, text
    round #3. Now genePredToBed matches what comes out of genePredToFakePsl followed by pslToBed if you make thickStart and thickEnd equal 0 when they equal each other. Now cdsEnd points to the base after the last base in CDS, even if that base is not in one of the exons.
• src/hg/pslToBed/tests/input/mm10.chrom.sizes
  • lines changed 66, context: html, text, full: html, text
    add some tests, make the code easier to understand, and fix a problem with no CDS being indicated by thickStart == chromStart && thickEnd == chromEnd, instead of thickStart==thickEnd==0 as should have been the case. Thanks Tim for the code review!!!
• src/hg/pslToBed/tests/input/test1.psl
  • lines changed 285, context: html, text, full: html, text
    add some tests, make the code easier to understand, and fix a problem with no CDS being indicated by thickStart == chromStart && thickEnd == chromEnd, instead of thickStart==thickEnd==0 as should have been the case. Thanks Tim for the code review!!!
• src/hg/pslToBed/tests/input/test2.cds
  • lines changed 43689, context: html, text, full: html, text
    add some tests, make the code easier to understand, and fix a problem with no CDS being indicated by thickStart == chromStart && thickEnd == chromEnd, instead of thickStart==thickEnd==0 as should have been the case. Thanks Tim for the code review!!!
• src/hg/pslToBed/tests/input/test2.psl
  • lines changed 55307, context: html, text, full: html, text
    add some tests, make the code easier to understand, and fix a problem with no CDS being indicated by thickStart == chromStart && thickEnd == chromEnd, instead of thickStart==thickEnd==0 as should have been the case. Thanks Tim for the code review!!!
• src/hg/pslToBed/tests/makefile
  • lines changed 31, context: html, text, full: html, text
    add some tests, make the code easier to understand, and fix a problem with no CDS being indicated by thickStart == chromStart && thickEnd == chromEnd, instead of thickStart==thickEnd==0 as should have been the case. Thanks Tim for the code review!!!