Commits for braney

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

• fix bug where buffer is known to be too small, but its growth may still not be enough
  • src/hg/encode/validateFiles/validateFiles.c - lines changed 1, 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/makefile - lines changed 5, context: html, text, full: html, text
  • src/hg/pslToBed/pslToBed.c - lines changed 46, context: html, text, full: html, text
  • src/hg/pslToBed/tests/expected/doTest1.bed - lines changed 285, context: html, text, full: html, text
  • src/hg/pslToBed/tests/expected/doTest2.bed - lines changed 55307, context: html, text, full: html, text
  • src/hg/pslToBed/tests/input/mm10.chrom.sizes - lines changed 66, context: html, text, full: html, text
  • src/hg/pslToBed/tests/input/test1.psl - lines changed 285, context: html, text, full: html, text
  • src/hg/pslToBed/tests/input/test2.cds - lines changed 43689, context: html, text, full: html, text
  • src/hg/pslToBed/tests/input/test2.psl - lines changed 55307, context: html, text, full: html, text
  • src/hg/pslToBed/tests/makefile - lines changed 31, context: html, text, full: html, text
• add pslToBed to directories to test
  • src/hg/makefile - lines changed 1, context: html, text, full: html, text
• oops... wasn't dealing with CDS start and stop correctly on '-' strand
  • src/hg/pslToBed/pslToBed.c - lines changed 17, context: html, text, full: html, text
  • src/hg/pslToBed/tests/expected/doTest2.bed - lines changed 20685, 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/pslToBed.c - lines changed 6, context: html, text, full: html, text
  • src/hg/pslToBed/tests/expected/doTest2.bed - lines changed 236, context: html, text, full: html, text
• use rn5 refGene for mm10 UCSC genes... maybe we should be using rn4 RGD gene?
  • src/hg/hgGene/hgGeneData/Mouse/mm10/otherOrgs.ra - lines changed 9, 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/makeDb/doc/ucscGenes/mm10.ucscGenes13.csh - lines changed 124, context: html, text, full: html, text