markd: changes by commit

review to branch (2009-04-21 to 2009-04-28) v205

• added initial implementation of gff3 parser. Still has some rough edges and problems due to ambiguities in the GFF3 specification
  • src/inc/gff3.h 1.1 - lines changed: 211, context: html, text, full: html, text
  • src/lib/gff3.c 1.1 - lines changed: 914, context: html, text, full: html, text
  • src/lib/makefile 1.151 - lines changed: 1, context: html, text, full: html, text
  • src/lib/tests/gff3Tester.c 1.1 - lines changed: 31, context: html, text, full: html, text
  • src/lib/tests/input/errorCasesTest.gff3 1.1 - lines changed: 28, context: html, text, full: html, text
  • src/lib/tests/input/sacCerTest.gff3 1.1 - lines changed: 43, context: html, text, full: html, text
  • src/lib/tests/input/specialCasesTest.gff3 1.1 - lines changed: 9, context: html, text, full: html, text
  • src/lib/tests/makefile 1.35 - lines changed: 21, context: html, text, full: html, text
• • src/hg/makeDb/genbank/etc/ignore.idx 1.93 - lines changed: 1, context: html, text, full: html, text
• fixed bogus errors reported for NR refseqs
  • src/hg/makeDb/genbank/src/gbSanity/chkGbIndex.c 1.5 - lines changed: 3, context: html, text, full: html, text
  • src/hg/makeDb/genbank/src/gbSanity/chkMetaDataTbls.c 1.13 - lines changed: 10, context: html, text, full: html, text
  • src/hg/makeDb/genbank/src/gbSanity/chkSeqTbl.c 1.3 - lines changed: 4, context: html, text, full: html, text
• fix bug with lastDir2, made code more robust
  • src/parasol/gensub2/fancy.gsub 1.1 - lines changed: 3, context: html, text, full: html, text
  • src/parasol/gensub2/fancy1.lst 1.1 - lines changed: 4, context: html, text, full: html, text
  • src/parasol/gensub2/fancy2.lst 1.1 - lines changed: 4, context: html, text, full: html, text
  • src/parasol/gensub2/gensub2.c 1.13 - lines changed: 11, context: html, text, full: html, text
• positionalTblCheck wasn't being and had code rot
  • src/hg/utils/makefile 1.13 - lines changed: 2, context: html, text, full: html, text
  • src/hg/utils/positionalTblCheck/positionalTblCheck.c 1.2 - lines changed: 4, context: html, text, full: html, text
• fixed typo in description
  • src/hg/makeDb/trackDb/zebraFinch/taeGut1/trackDb.ra 1.3 - lines changed: 1, context: html, text, full: html, text