markd: changes by file

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

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