markd: changes by commit

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

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