markd: changes by file

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

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