markd: changes by file

review to branch (2010-03-16 to 2010-03-23) v227

• src/hg/makeDb/genbank/etc/ignore.idx
  • 1.102 lines changed: 265, context: html, text, full: html, text
    fixed incorrect syntax in last change
  • 1.101 lines changed: 1554, context: html, text, full: html, text
    added ignore entries, removed old ones
• src/hg/mouseStuff/chainToAxt/chainToAxt.c
  • 1.7 lines changed: 53, context: html, text, full: html, text
    support using twobit as well as nib
• src/hg/mouseStuff/chainToAxt/expected/chrM.axt
  • 1.2 lines changed: 12, context: html, text, full: html, text
    fixed broken tests results
• src/hg/utils/gff3ToGenePred/gff3ToGenePred.c
  • 1.4 lines changed: 4, context: html, text, full: html, text
    fixed various issues with error reporting
  • 1.3 lines changed: 28, context: html, text, full: html, text
    fixed crash on nodes with no ID or Parent attrs
  • 1.2 lines changed: 58, context: html, text, full: html, text
    report multiple conversions errors before failing
• src/hg/utils/gff3ToGenePred/tests/README
  • 1.1 lines changed: 17, context: html, text, full: html, text
    fixed crash on nodes with no ID or Parent attrs
• src/hg/utils/gff3ToGenePred/tests/makefile
  • 1.4 lines changed: 13, context: html, text, full: html, text
    fixed various issues with error reporting
  • 1.3 lines changed: 5, context: html, text, full: html, text
    fixed crash on nodes with no ID or Parent attrs
  • 1.2 lines changed: 5, context: html, text, full: html, text
    report multiple conversions errors before failing
• src/hg/utils/gff3ToGenePred/tests/expected/errCases1Test.out
  • 1.1 lines changed: 11, context: html, text, full: html, text
    fixed various issues with error reporting
• src/hg/utils/gff3ToGenePred/tests/expected/multCdsOutOfExonTest.out
  • 1.2 lines changed: 2, context: html, text, full: html, text
    fixed various issues with error reporting
  • 1.1 lines changed: 3, context: html, text, full: html, text
    report multiple conversions errors before failing
• src/hg/utils/gff3ToGenePred/tests/expected/noIdTest.gp
  • 1.1 lines changed: 1, context: html, text, full: html, text
    fixed crash on nodes with no ID or Parent attrs
• src/hg/utils/gff3ToGenePred/tests/input/errCases1.gff3
  • 1.1 lines changed: 17, context: html, text, full: html, text
    fixed various issues with error reporting
• src/hg/utils/gff3ToGenePred/tests/input/multCdsOutOfExon.gff3
  • 1.1 lines changed: 11, context: html, text, full: html, text
    report multiple conversions errors before failing
• src/hg/utils/gff3ToGenePred/tests/input/noId.gff3
  • 1.1 lines changed: 12, context: html, text, full: html, text
    fixed crash on nodes with no ID or Parent attrs
• src/inc/nibTwo.h
  • 1.3 lines changed: 3, context: html, text, full: html, text
    added function to get sequence size
• src/lib/gff3.c
  • 1.4 lines changed: 30, context: html, text, full: html, text
    spec unclear where phase is allowed, so don't reject for non-CDS feeatures
• src/lib/nibTwo.c
  • 1.6 lines changed: 9, context: html, text, full: html, text
    added function to get sequence size
• src/lib/pipeline.c
  • 1.23 lines changed: 120, context: html, text, full: html, text
    wait on process group rather than individual process to prevent deadlocks in certain cases