markd: changes by commit

branch to review (2010-02-16 to 2010-02-23) v226

• allow defaulting to TMPDIR directory
  • src/hg/inc/hgRelate.h 1.17 - lines changed: 10, context: html, text, full: html, text
  • src/hg/lib/hgRelate.c 1.26 - lines changed: 21, context: html, text, full: html, text
• added hgPar to load PSL table describing PARs
  • src/hg/makeDb/hgPar/hgPar.c 1.1 - lines changed: 105, context: html, text, full: html, text
  • src/hg/makeDb/hgPar/makefile 1.1 - lines changed: 23, context: html, text, full: html, text
  • src/hg/makeDb/hgPar/parSpec.as 1.1 - lines changed: 11, context: html, text, full: html, text
  • src/hg/makeDb/hgPar/parSpec.c 1.1 - lines changed: 138, context: html, text, full: html, text
  • src/hg/makeDb/hgPar/parSpec.h 1.1 - lines changed: 63, context: html, text, full: html, text
  • src/hg/makeDb/hgPar/tests/input/test.parspec 1.1 - lines changed: 2, context: html, text, full: html, text
  • src/hg/makeDb/hgPar/tests/makefile 1.1 - lines changed: 13, context: html, text, full: html, text
  • src/hg/makeDb/makefile 1.43 - lines changed: 2, context: html, text, full: html, text
• added details page for PAR tracks
  • src/hg/hgc/hgc.c 1.1597 - lines changed: 5, context: html, text, full: html, text
  • src/hg/hgc/makefile 1.65 - lines changed: 1, context: html, text, full: html, text
  • src/hg/hgc/parClick.c 1.1 - lines changed: 150, context: html, text, full: html, text
  • src/hg/hgc/parClick.h 1.1 - lines changed: 8, context: html, text, full: html, text
• added some examples to look at
  • src/hg/makeDb/genbank/doc/to-do.txt 1.121 - lines changed: 2, context: html, text, full: html, text
• used BED format for PAR
  • src/hg/makeDb/hgPar/hgPar.c 1.2 - lines changed: 104, context: html, text, full: html, text
  • src/hg/makeDb/hgPar/tests/expected/par.bed 1.1 - lines changed: 4, context: html, text, full: html, text
  • src/hg/makeDb/hgPar/tests/input/test.parspec 1.2 - lines changed: 2, context: html, text, full: html, text
  • src/hg/makeDb/hgPar/tests/makefile 1.2 - lines changed: 3, context: html, text, full: html, text
• Added option to not give bonus score for apparent introns. Fix test naming inconsitency
  • src/hg/pslCDnaFilter/cDnaAligns.c 1.20 - lines changed: 24, context: html, text, full: html, text
  • src/hg/pslCDnaFilter/cDnaAligns.h 1.14 - lines changed: 5, context: html, text, full: html, text
  • src/hg/pslCDnaFilter/pslCDnaFilter.c 1.22 - lines changed: 7, context: html, text, full: html, text
  • src/hg/pslCDnaFilter/tests/expected/ignoreIntronsTest/drop.psl 1.1 - lines changed: 1, context: html, text, full: html, text
  • src/hg/pslCDnaFilter/tests/expected/ignoreIntronsTest/filt.out 1.1 - lines changed: 4, context: html, text, full: html, text
  • src/hg/pslCDnaFilter/tests/expected/ignoreIntronsTest/keep.psl 1.1 - lines changed: 1, context: html, text, full: html, text
  • src/hg/pslCDnaFilter/tests/expected/ignoreIntronsTest/weird.psl 1.1 - lines changed: 0, context: html, text, full: html, text
  • src/hg/pslCDnaFilter/tests/expected/noIgnoreIntronsTest/drop.psl 1.1 - lines changed: 1, context: html, text, full: html, text
  • src/hg/pslCDnaFilter/tests/expected/noIgnoreIntronsTest/filt.out 1.1 - lines changed: 4, context: html, text, full: html, text
  • src/hg/pslCDnaFilter/tests/expected/noIgnoreIntronsTest/keep.psl 1.1 - lines changed: 1, context: html, text, full: html, text
  • src/hg/pslCDnaFilter/tests/expected/noIgnoreIntronsTest/weird.psl 1.1 - lines changed: 0, context: html, text, full: html, text
  • src/hg/pslCDnaFilter/tests/expected/weirdOverlappedFilterTest/drop.psl 1.1 - lines changed: 6, context: html, text, full: html, text
  • src/hg/pslCDnaFilter/tests/expected/weirdOverlappedFilterTest/filt.out 1.1 - lines changed: 6, context: html, text, full: html, text
  • src/hg/pslCDnaFilter/tests/expected/weirdOverlappedFilterTest/keep.psl 1.1 - lines changed: 11, context: html, text, full: html, text
  • src/hg/pslCDnaFilter/tests/expected/weirdOverlappedFilterTest/weird.psl 1.1 - lines changed: 9, context: html, text, full: html, text
  • src/hg/pslCDnaFilter/tests/input/ignoreIntrons.psl 1.1 - lines changed: 3, context: html, text, full: html, text
  • src/hg/pslCDnaFilter/tests/makefile 1.14 - lines changed: 11, context: html, text, full: html, text
  • src/hg/pslCDnaFilter/usage.txt 1.12 - lines changed: 4, context: html, text, full: html, text
• fixed bug when clicking on one par when both are displayed
  • src/hg/hgc/parClick.c 1.2 - lines changed: 6, context: html, text, full: html, text
• added PAR tracks
  • src/hg/makeDb/doc/hg18.txt 1.398 - lines changed: 6, context: html, text, full: html, text
  • src/hg/makeDb/doc/hg19.txt 1.83 - lines changed: 8, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/par.html 1.1 - lines changed: 13, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/trackDb.ra 1.619 - lines changed: 16, context: html, text, full: html, text
• removed stray space
  • src/hg/makeDb/hgPar/tests/input/test.parspec 1.3 - lines changed: 0, context: html, text, full: html, text
• check that all config files starting with dot are only readable by the owner
  • src/hg/lib/hgConfig.c 1.23 - lines changed: 12, context: html, text, full: html, text