File Changes for markd

v243_base to v244_preview (2010-11-02 to 2010-11-16) v244

• src/hg/hgTables/hgTables.c
  • lines changed 2, context: html, text, full: html, text
    removed print of sql stats to stderr, which was there for debugging socket leak in hgTables
• src/hg/makeDb/doc/felCat4.txt
  • lines changed 24, context: html, text, full: html, text
    added felCat4 N-SCAN
• src/hg/makeDb/doc/rheMac2.txt
  • lines changed 8, context: html, text, full: html, text
    fixed result of cascading yank and put error (renamed track to drop extra n)
• src/hg/makeDb/genbank/doc/to-do.txt
  • lines changed 3, context: html, text, full: html, text
    added problem case RefSeq NR to doc
• src/hg/makeDb/schema/all.joiner
  • lines changed 1, context: html, text, full: html, text
    added ccdsNotes
• src/hg/makeDb/trackDb/cat/felCat4/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    added felCat4 N-SCAN
• src/hg/makeDb/trackDb/rhesus/refSeqAnno.html
  • lines changed 32, context: html, text, full: html, text
    fixed result of cascading yank and put error (renamed track to drop extra n)
• src/hg/makeDb/trackDb/rhesus/refSeqAnnon.html
  • lines changed 32, context: html, text, full: html, text
    fixed result of cascading yank and put error (renamed track to drop extra n)
• src/hg/makeDb/trackDb/rhesus/rheMac2/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    fixed result of cascading yank and put error (renamed track to drop extra n)
• src/hg/makeDb/trackDb/rhesus/trackDb.ra
  • lines changed 4, context: html, text, full: html, text
    fixed result of cascading yank and put error (renamed track to drop extra n)
• src/hg/makeDb/trackDb/tagTypes.tab
  • lines changed 1, context: html, text, full: html, text
    fixed result of cascading yank and put error (renamed track to drop extra n)
• src/hg/utils/gff3ToGenePred/tests/expected/discontinuousTest.gp
  • lines changed 3, context: html, text, full: html, text
    added support for GFF3 discontinuous features
• src/hg/utils/gff3ToGenePred/tests/expected/errCases1Test.out
  • lines changed 5, context: html, text, full: html, text
    added support for GFF3 discontinuous features
• src/hg/utils/gff3ToGenePred/tests/input/discontinuous.gff3
  • lines changed 31, context: html, text, full: html, text
    added support for GFF3 discontinuous features
• src/hg/utils/gff3ToGenePred/tests/makefile
  • lines changed 5, context: html, text, full: html, text
    added support for GFF3 discontinuous features
• src/hg/utils/gff3ToPsl/gff3ToPsl.c
  • lines changed 64, context: html, text, full: html, text
    librarized the cigar to psl code
  • lines changed 1, context: html, text, full: html, text
    renamed cigar converter to make it clear that this is the GFF3 cigar format, not the ENSEMBL cigar
• src/inc/gff3.h
  • lines changed 9, context: html, text, full: html, text
    added support for GFF3 discontinuous features
• src/inc/psl.h
  • lines changed 5, context: html, text, full: html, text
    librarized the cigar to psl code
  • lines changed 2, context: html, text, full: html, text
    renamed cigar converter to make it clear that this is the GFF3 cigar format, not the ENSEMBL cigar
• src/lib/gff3.c
  • lines changed 127, context: html, text, full: html, text
    added support for GFF3 discontinuous features
• src/lib/psl.c
  • lines changed 75, context: html, text, full: html, text
    librarized the cigar to psl code
  • lines changed 2, context: html, text, full: html, text
    renamed cigar converter to make it clear that this is the GFF3 cigar format, not the ENSEMBL cigar
• src/lib/tests/expected/gff3DiscontiousTest.out
  • lines changed 31, context: html, text, full: html, text
    added support for GFF3 discontinuous features
• src/lib/tests/expected/gff3ErrorCasesTest.err
  • lines changed 4, context: html, text, full: html, text
    added support for GFF3 discontinuous features
  • lines changed 1, context: html, text, full: html, text
    fixed error case caused by fixing typo in error message
• src/lib/tests/expected/gff3SacCerTest.out
  • lines changed 36, context: html, text, full: html, text
    added support for GFF3 discontinuous features
• src/lib/tests/input/discontinuous.gff3
  • lines changed 31, context: html, text, full: html, text
    added support for GFF3 discontinuous features
• src/lib/tests/makefile
  • lines changed 7, context: html, text, full: html, text
    added support for GFF3 discontinuous features