markd: changes by commit

review to branch (2009-04-07 to 2009-04-14) v204

• added tests for hgwbeta using hgsqlbeta
  • src/hg/makeDb/genbank/src/align/gbAlignStep 1.23 - lines changed: 1, context: html, text, full: html, text
  • src/hg/makeDb/genbank/src/lib/gbCommon.pm 1.39 - lines changed: 5, context: html, text, full: html, text
• added support for PSI BLAST madness
  • src/hg/blastToPsl/blastToPsl.c 1.23 - lines changed: 7, context: html, text, full: html, text
  • src/hg/blastToPsl/tests/expected/blastpPsiTest.bscores 1.1 - lines changed: 4, context: html, text, full: html, text
  • src/hg/blastToPsl/tests/expected/blastpPsiTest.psl 1.1 - lines changed: 3, context: html, text, full: html, text
  • src/hg/blastToPsl/tests/input/blastpPsi.blast 1.1 - lines changed: 244, context: html, text, full: html, text
  • src/hg/blastToPsl/tests/makefile 1.17 - lines changed: 9, context: html, text, full: html, text
  • src/inc/blastParse.h 1.6 - lines changed: 2, context: html, text, full: html, text
  • src/lib/blastParse.c 1.22 - lines changed: 40, context: html, text, full: html, text
• fixed bug parsing PSI BLAST output with no hits
  • src/hg/blastToPsl/tests/expected/psiNoHitsTest.bscores 1.1 - lines changed: 1, context: html, text, full: html, text
  • src/hg/blastToPsl/tests/expected/psiNoHitsTest.psl 1.1 - lines changed: 0, context: html, text, full: html, text
  • src/hg/blastToPsl/tests/input/psiNoHits.blast 1.1 - lines changed: 61, context: html, text, full: html, text
  • src/hg/blastToPsl/tests/makefile 1.18 - lines changed: 8, context: html, text, full: html, text
  • src/lib/blastParse.c 1.23 - lines changed: 38, context: html, text, full: html, text
• skip bogus blocks in PSI BLAST output
  • src/hg/blastToPsl/tests/expected/psiBadFormatTest.bscores 1.1 - lines changed: 10, context: html, text, full: html, text
  • src/hg/blastToPsl/tests/expected/psiBadFormatTest.err 1.1 - lines changed: 5, context: html, text, full: html, text
  • src/hg/blastToPsl/tests/expected/psiBadFormatTest.psl 1.1 - lines changed: 9, context: html, text, full: html, text
  • src/hg/blastToPsl/tests/input/psiBadFormat.blast 1.1 - lines changed: 220, context: html, text, full: html, text
  • src/hg/blastToPsl/tests/makefile 1.19 - lines changed: 10, context: html, text, full: html, text
  • src/lib/blastParse.c 1.24 - lines changed: 133, context: html, text, full: html, text
• don't pslCheck empty file, writes warning to stderr
  • src/hg/blastToPsl/tests/makefile 1.20 - lines changed: 1, context: html, text, full: html, text
• added to-do item
  • src/hg/makeDb/genbank/doc/to-do.txt 1.111 - lines changed: 3, context: html, text, full: html, text
• added function to determine if a mysql server appears to be remote; ignore SQL_TAB_FILE_ON_SERVER if server is remote
  • src/hg/inc/jksql.h 1.82 - lines changed: 7, context: html, text, full: html, text
  • src/hg/lib/jksql.c 1.129 - lines changed: 10, context: html, text, full: html, text