markd: changes by commit

branch to review (2009-07-07 to 2009-07-15) v210

• use contstant for max file path
  • src/parasol/parasol/parasol.c 1.46 - lines changed: 2, context: html, text, full: html, text
• fixed install rule to preserve permissions
  • src/hg/autoSql/makefile 1.17 - lines changed: 2, context: html, text, full: html, text
• moved stackDump stuff to hCommon; added function for user errAbort
  • src/hg/inc/hCommon.h 1.26 - lines changed: 25, context: html, text, full: html, text
  • src/hg/inc/hui.h 1.134 - lines changed: 0, context: html, text, full: html, text
  • src/hg/inc/web.h 1.45 - lines changed: 13, context: html, text, full: html, text
  • src/hg/lib/cart.c 1.111 - lines changed: 3, context: html, text, full: html, text
  • src/hg/lib/hCommon.c 1.39 - lines changed: 65, context: html, text, full: html, text
  • src/hg/lib/hgFind.c 1.221 - lines changed: 25, context: html, text, full: html, text
  • src/hg/lib/web.c 1.169 - lines changed: 48, context: html, text, full: html, text
• use hUserAbort to prevent unneed stack track
  • src/hg/hgGene/hgGene.c 1.116 - lines changed: 2, context: html, text, full: html, text
  • src/hg/hgTracks/hgTracks.c 1.1581 - lines changed: 1, context: html, text, full: html, text
  • src/hg/protein/pbGlobal/pbGlobal.c 1.45 - lines changed: 1, context: html, text, full: html, text
  • src/hg/protein/pbTracks/pbTracks.c 1.57 - lines changed: 1, context: html, text, full: html, text
• build mafToPsl as part of std make
  • src/hg/mouseStuff/makefile 1.21 - lines changed: 1, context: html, text, full: html, text
• fixed comment
  • src/utils/qa/weeklybld/cvs-reports-d 1.12 - lines changed: 1, context: html, text, full: html, text
• flush stdout before forking
  • src/lib/osunix.c 1.43 - lines changed: 1, context: html, text, full: html, text
• allow transMap tracks to work with composite tracks
  • src/hg/hgTracks/transMapTracks.c 1.8 - lines changed: 1, context: html, text, full: html, text
• convert transMap to composite tracks
  • src/hg/makeDb/trackDb/trackDb.ra 1.518 - lines changed: 12, context: html, text, full: html, text
• composite track was premature, switch back to super tracks until controls figured out
  • src/hg/makeDb/trackDb/trackDb.ra 1.519 - lines changed: 12, context: html, text, full: html, text
• updated description
  • src/hg/makeDb/trackDb/transMap.html 1.13 - lines changed: 1, context: html, text, full: html, text
• fixed segv when file doesn't exists and no database was supplied
  • src/hg/pslCheck/pslCheck.c 1.13 - lines changed: 19, context: html, text, full: html, text
• added option to output mapping chain that was used
  • src/hg/pslMap/pslMap.c 1.17 - lines changed: 13, context: html, text, full: html, text
  • src/hg/pslMap/tests/expected/mrnaMapOverChain.mapping.psl 1.1 - lines changed: 1, context: html, text, full: html, text
  • src/hg/pslMap/tests/expected/mrnaMapOverSwap.mapping.psl 1.1 - lines changed: 1, context: html, text, full: html, text
  • src/hg/pslMap/tests/input/mm6ToHg17.psl 1.2 - lines changed: 1, context: html, text, full: html, text
  • src/hg/pslMap/tests/makefile 1.11 - lines changed: 6, context: html, text, full: html, text
  • src/hg/pslMap/usage.txt 1.4 - lines changed: 4, context: html, text, full: html, text
• added option to preserve reference coordinates
  • src/hg/ratStuff/mafFrags/mafFrags.c 1.11 - lines changed: 9, context: html, text, full: html, text
• generate useful error message when there is a huge chromosome name, most likely caused by an invalid table name
  • src/hg/lib/hdb.c 1.406 - lines changed: 5, context: html, text, full: html, text
• fixed some missing closes noticed while search for a bug
  • src/hg/hgLiftOver/hgLiftOver.c 1.62 - lines changed: 5, context: html, text, full: html, text
• don't dump stack on bot trap
  • src/hg/lib/botDelay.c 1.15 - lines changed: 3, context: html, text, full: html, text
• don't close files that function didn't open, which lead to double-free crash
  • src/hg/lib/liftOver.c 1.44 - lines changed: 2, context: html, text, full: html, text
• removed unneeded stackdump
  • src/hg/hgTracks/hgTracks.c 1.1584 - lines changed: 1, context: html, text, full: html, text