markd: changes by file

review to branch (2010-04-13 to 2010-04-19) v229

• src/hg/blastToPsl/blastXmlToPsl.c
  • 1.2 lines changed: 9, context: html, text, full: html, text
    add options to convert TBLASTN to codon nucleotide/nucleotide coordinates, fixed bug with tStart/tEnd extending beyond actual range
• src/hg/blastToPsl/pslBuild.c
  • 1.2 lines changed: 43, context: html, text, full: html, text
    add options to convert TBLASTN to codon nucleotide/nucleotide coordinates, fixed bug with tStart/tEnd extending beyond actual range
• src/hg/blastToPsl/pslBuild.h
  • 1.2 lines changed: 8, context: html, text, full: html, text
    add options to convert TBLASTN to codon nucleotide/nucleotide coordinates, fixed bug with tStart/tEnd extending beyond actual range
• src/hg/blastToPsl/scoreSort.c
  • 1.7 lines changed: 132, context: html, text, full: html, text
    add options to convert TBLASTN to codon nucleotide/nucleotide coordinates, fixed bug with tStart/tEnd extending beyond actual range
• src/hg/blastToPsl/tests/makefile
  • 1.25 lines changed: 52, context: html, text, full: html, text
    add options to convert TBLASTN to codon nucleotide/nucleotide coordinates, fixed bug with tStart/tEnd extending beyond actual range
• src/hg/blastToPsl/tests/expected/prot1NucCoordTest.psl
  • 1.1 lines changed: 72, context: html, text, full: html, text
    add options to convert TBLASTN to codon nucleotide/nucleotide coordinates, fixed bug with tStart/tEnd extending beyond actual range
• src/hg/hgTables/gffOut.c
  • 1.22 lines changed: 2, context: html, text, full: html, text
    forgot to use parameter that was added to get either GTF or GTF (per Hiram)
• src/hg/makeDb/doc/susScr2.txt
  • 1.8 lines changed: 26, context: html, text, full: html, text
    add N-SCAN to susScr2
• src/hg/makeDb/genbank/etc/align.dbs
  • 1.118 lines changed: 2, context: html, text, full: html, text
    reenabled chimp alignments
• src/hg/makeDb/genbank/etc/hgwdev.dbs
  • 1.122 lines changed: 2, context: html, text, full: html, text
    reenabled chimp alignments
• src/hg/makeDb/trackDb/nscanGene.html
  • 1.5 lines changed: 7, context: html, text, full: html, text
    add N-SCAN to susScr2
• src/hg/makeDb/trackDb/trackDb.ra
  • 1.625 lines changed: 1, context: html, text, full: html, text
    add N-SCAN to susScr2
• src/hg/makeDb/trackDb/pig/susScr2/trackDb.ra
  • 1.6 lines changed: 5, context: html, text, full: html, text
    add N-SCAN to susScr2
• src/lib/psl.c
  • 1.83 lines changed: 2, context: html, text, full: html, text
    fixed bug were target name index was not created if bin was not created
  • 1.82 lines changed: 145, context: html, text, full: html, text
    have pslCheck catch overall ranges that don't match block ranges