markd: changes by file

branch to review (2010-02-02 to 2010-02-10) v225

• src/hg/blastToPsl/blast0To8.c
  • 1.3 lines changed: 287, context: html, text, full: html, text
    removed dead programs not being compiled
• src/hg/blastToPsl/blastToPsl.c
  • 1.24 lines changed: 304, context: html, text, full: html, text
    added blastXmlToPsl
• src/hg/blastToPsl/blastXmlToPsl.c
  • 1.1 lines changed: 203, context: html, text, full: html, text
    added blastXmlToPsl
• src/hg/blastToPsl/makefile
  • 1.29 lines changed: 9, context: html, text, full: html, text
    try number tree to get link rules to behave
  • 1.28 lines changed: 4, context: html, text, full: html, text
    even more dependency issues
  • 1.27 lines changed: 2, context: html, text, full: html, text
    fixed dependency problem
  • 1.26 lines changed: 5, context: html, text, full: html, text
    attempt to get autobuild working again by forcing a relink
  • 1.25 lines changed: 1, context: html, text, full: html, text
    fixed make issue
  • 1.24 lines changed: 4, context: html, text, full: html, text
    moved pslUniq out of complelely unrelated directory
  • 1.23 lines changed: 60, context: html, text, full: html, text
    added blastXmlToPsl
• src/hg/blastToPsl/ncbiBlast.c
  • 1.1 lines changed: 4640, context: html, text, full: html, text
    added blastXmlToPsl
• src/hg/blastToPsl/ncbiBlast.h
  • 1.1 lines changed: 1484, context: html, text, full: html, text
    added blastXmlToPsl
• src/hg/blastToPsl/pslBuild.c
  • 1.1 lines changed: 284, context: html, text, full: html, text
    added blastXmlToPsl
• src/hg/blastToPsl/pslBuild.h
  • 1.1 lines changed: 32, context: html, text, full: html, text
    added blastXmlToPsl
• src/hg/blastToPsl/pslChain.c
  • 1.8 lines changed: 1092, context: html, text, full: html, text
    removed dead programs not being compiled
• src/hg/blastToPsl/pslUniq.c
  • 1.5 lines changed: 56, context: html, text, full: html, text
    moved pslUniq out of complelely unrelated directory
• src/hg/blastToPsl/tests/makefile
  • 1.24 lines changed: 1, context: html, text, full: html, text
    fixed make issue
  • 1.23 lines changed: 41, context: html, text, full: html, text
    added blastXmlToPsl
  • 1.22 lines changed: 13, context: html, text, full: html, text
    added (disabled) test case for blast+
• src/hg/blastToPsl/tests/expected/identityBugTest.psl
  • 1.4 lines changed: 2, context: html, text, full: html, text
    added blastXmlToPsl
• src/hg/blastToPsl/tests/expected/mrna1Test.bscores
  • 1.1 lines changed: 13, context: html, text, full: html, text
    added blastXmlToPsl
• src/hg/blastToPsl/tests/expected/mrna1Test.psl
  • 1.1 lines changed: 12, context: html, text, full: html, text
    added blastXmlToPsl
• src/hg/blastToPsl/tests/expected/prot1Test.bscores
  • 1.1 lines changed: 39, context: html, text, full: html, text
    added blastXmlToPsl
• src/hg/blastToPsl/tests/expected/prot1Test.psl
  • 1.1 lines changed: 72, context: html, text, full: html, text
    added blastXmlToPsl
• src/hg/blastToPsl/tests/expected/prot2Test.bscores
  • 1.1 lines changed: 4, context: html, text, full: html, text
    added blastXmlToPsl
• src/hg/blastToPsl/tests/expected/prot2Test.psl
  • 1.1 lines changed: 3, context: html, text, full: html, text
    added blastXmlToPsl
• src/hg/blastToPsl/tests/expected/protDnaTest.psl
  • 1.5 lines changed: 52, context: html, text, full: html, text
    added blastXmlToPsl
• src/hg/blastToPsl/tests/expected/protMrnaEval1Test.psl
  • 1.4 lines changed: 27, context: html, text, full: html, text
    added blastXmlToPsl
• src/hg/blastToPsl/tests/expected/protMrnaEval2Test.psl
  • 1.4 lines changed: 3, context: html, text, full: html, text
    added blastXmlToPsl
• src/hg/blastToPsl/tests/expected/protMrnaTest.psl
  • 1.5 lines changed: 59, context: html, text, full: html, text
    added blastXmlToPsl
• src/hg/blastToPsl/tests/expected/tblastnTest.psl
  • 1.2 lines changed: 2, context: html, text, full: html, text
    added blastXmlToPsl
• src/hg/blastToPsl/tests/input/blastn+.blast
  • 1.1 lines changed: 206, context: html, text, full: html, text
    added (disabled) test case for blast+
• src/hg/blastToPsl/tests/input/mrna1.blastn.xml
  • 1.1 lines changed: 335, context: html, text, full: html, text
    added blastXmlToPsl
• src/hg/blastToPsl/tests/input/prot1.tblastn.xml
  • 1.1 lines changed: 1446, context: html, text, full: html, text
    added blastXmlToPsl
• src/hg/blastToPsl/tests/input/prot2.psiblast.xml
  • 1.1 lines changed: 229, context: html, text, full: html, text
    added blastXmlToPsl
• src/hg/gbToFaRa/gbToFaRa.c
  • 1.25 lines changed: 14, context: html, text, full: html, text
    added option to include version in output fasta
• src/hg/makeDb/doc/equCab2.txt
  • 1.29 lines changed: 5, context: html, text, full: html, text
    enabled xeno refgene
• src/hg/makeDb/genbank/etc/genbank.conf
  • 1.360 lines changed: 1, context: html, text, full: html, text
    enable xeno refseq on equCab2
• src/hg/utils/makefile
  • 1.20 lines changed: 2, context: html, text, full: html, text
    moved pslUniq out of complelely unrelated directory
• src/hg/utils/pslUniq/makefile
  • 1.1 lines changed: 17, context: html, text, full: html, text
    moved pslUniq out of complelely unrelated directory