markd: changes by commit

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

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