markd: changes by commit

review to branch (2009-06-30 to 2009-07-07) v210

• fixed library list so SSL can be included
  • src/parasol/paraHub/makefile 1.20 - lines changed: 1, context: html, text, full: html, text
• clairfed documentation
  • src/hg/pslCDnaFilter/overlapFilter.c 1.7 - lines changed: 2, context: html, text, full: html, text
  • src/hg/pslCDnaFilter/overlapFilter.h 1.4 - lines changed: 2, context: html, text, full: html, text
  • src/hg/pslCDnaFilter/usage.txt 1.9 - lines changed: 2, context: html, text, full: html, text
• adjust enum/set values to be valid C indentifiers
  • src/hg/autoSql/autoSql.c 1.38 - lines changed: 10, context: html, text, full: html, text
  • src/hg/autoSql/makefile 1.16 - lines changed: 6, context: html, text, full: html, text
• deleted no longer needed function
  • src/hg/inc/hCommon.h 1.25 - lines changed: 4, context: html, text, full: html, text
• added some .h files for genbank tables
  • src/hg/inc/gbSeq.h 1.1 - lines changed: 81, context: html, text, full: html, text
  • src/hg/inc/refSeqStatus.h 1.2 - lines changed: 42, context: html, text, full: html, text
  • src/hg/lib/gbSeq.as 1.1 - lines changed: 14, context: html, text, full: html, text
  • src/hg/lib/gbSeq.c 1.1 - lines changed: 168, context: html, text, full: html, text
  • src/hg/lib/gbSeq.sql 1.1 - lines changed: 19, context: html, text, full: html, text
  • src/hg/lib/makefile 1.391 - lines changed: 1, context: html, text, full: html, text
  • src/hg/lib/refSeqStatus.as 1.3 - lines changed: 1, context: html, text, full: html, text
  • src/hg/lib/refSeqStatus.c 1.4 - lines changed: 39, context: html, text, full: html, text
  • src/hg/lib/refSeqStatus.sql 1.2 - lines changed: 2, context: html, text, full: html, text
• added program to quickly validate refseq tables
  • src/hg/makeDb/genbank/src/inc/gbDefs.h 1.9 - lines changed: 1, context: html, text, full: html, text
  • src/hg/makeDb/genbank/src/makefile 1.10 - lines changed: 1, context: html, text, full: html, text
• added option to drop weird overlapps independent of other filtering
  • src/hg/pslCDnaFilter/algo.txt 1.2 - lines changed: 3, context: html, text, full: html, text
  • src/hg/pslCDnaFilter/cDnaAligns.c 1.19 - lines changed: 10, context: html, text, full: html, text
  • src/hg/pslCDnaFilter/cDnaAligns.h 1.13 - lines changed: 1, context: html, text, full: html, text
  • src/hg/pslCDnaFilter/cDnaStats.c 1.2 - lines changed: 40, context: html, text, full: html, text
  • src/hg/pslCDnaFilter/cDnaStats.h 1.2 - lines changed: 15, context: html, text, full: html, text
  • src/hg/pslCDnaFilter/overlapFilter.c 1.8 - lines changed: 91, context: html, text, full: html, text
  • src/hg/pslCDnaFilter/overlapFilter.h 1.5 - lines changed: 8, context: html, text, full: html, text
  • src/hg/pslCDnaFilter/pslCDnaFilter.c 1.21 - lines changed: 63, context: html, text, full: html, text
  • src/hg/pslCDnaFilter/tests/expected/globalBestTest/filt.out 1.3 - lines changed: 2, context: html, text, full: html, text
  • src/hg/pslCDnaFilter/tests/expected/hapGlobalTest/filt.out 1.2 - lines changed: 2, context: html, text, full: html, text
  • src/hg/pslCDnaFilter/tests/expected/hapLocalTest/filt.out 1.2 - lines changed: 2, context: html, text, full: html, text
  • src/hg/pslCDnaFilter/tests/expected/hapLocalXenoTest/filt.out 1.2 - lines changed: 2, context: html, text, full: html, text
  • src/hg/pslCDnaFilter/tests/expected/localBestTest/filt.out 1.3 - lines changed: 2, context: html, text, full: html, text
  • src/hg/pslCDnaFilter/tests/expected/minAlnSizeTest/filt.out 1.4 - lines changed: 2, context: html, text, full: html, text
  • src/hg/pslCDnaFilter/tests/expected/nonRepMismatchTest/filt.out 1.2 - lines changed: 2, context: html, text, full: html, text
  • src/hg/pslCDnaFilter/tests/expected/nonRepSizeTest/filt.out 1.4 - lines changed: 2, context: html, text, full: html, text
  • src/hg/pslCDnaFilter/tests/expected/noopTest/filt.out 1.6 - lines changed: 2, context: html, text, full: html, text
  • src/hg/pslCDnaFilter/tests/expected/noopTest/weird.psl 1.2 - lines changed: 9, context: html, text, full: html, text
  • src/hg/pslCDnaFilter/tests/expected/overlapTest/filt.out 1.9 - lines changed: 4, context: html, text, full: html, text
  • src/hg/pslCDnaFilter/tests/expected/overlapTest/weird.psl 1.5 - lines changed: 2, context: html, text, full: html, text
  • src/hg/pslCDnaFilter/tests/expected/repMatchTest/filt.out 1.7 - lines changed: 2, context: html, text, full: html, text
  • src/hg/pslCDnaFilter/tests/makefile 1.13 - lines changed: 9, context: html, text, full: html, text
  • src/hg/pslCDnaFilter/usage.txt 1.10 - lines changed: 9, context: html, text, full: html, text
• fixed typo in help
  • src/hg/pslCDnaFilter/algo.txt 1.3 - lines changed: 1, context: html, text, full: html, text
  • src/hg/pslCDnaFilter/usage.txt 1.11 - lines changed: 2, context: html, text, full: html, text
• don't adjust core limit
  • src/hg/makeDb/genbank/etc/dbload 1.29 - lines changed: 3, context: html, text, full: html, text
• removed gbSeq, as it is in it's own file
  • src/hg/lib/genbankTables.as 1.6 - lines changed: 14, context: html, text, full: html, text