File Changes for hiram

v287_preview to v287_preview2 (2013-07-16 to 2013-07-23) v287

• src/hg/hgTracks/hgTracks.h
  • lines changed 4, context: html, text, full: html, text
    checking in Robert's code refs #9741
• src/hg/hgTracks/joinedRmskTrack.c
  • lines changed 1162, context: html, text, full: html, text
    checking in Robert's code refs #9741
• src/hg/hgTracks/makefile
  • lines changed 1, context: html, text, full: html, text
    checking in Robert's code refs #9741
• src/hg/hgTracks/simpleTracks.c
  • lines changed 2, context: html, text, full: html, text
    checking in Robert's code refs #9741
• src/hg/inc/rmskAlign.h
  • lines changed 77, context: html, text, full: html, text
    checking in Robert's code refs #9741
• src/hg/inc/rmskJoined.h
  • lines changed 70, context: html, text, full: html, text
    checking in Robert's code refs #9741
• src/hg/inc/rmskOut2.h
  • lines changed 105, context: html, text, full: html, text
    checking in Robert's code refs #9741
• src/hg/lib/makefile
  • lines changed 1, context: html, text, full: html, text
    checking in Robert's code refs #9741
• src/hg/lib/rmskAlign.as
  • lines changed 21, context: html, text, full: html, text
    checking in Robert's code refs #9741
• src/hg/lib/rmskAlign.c
  • lines changed 209, context: html, text, full: html, text
    checking in Robert's code refs #9741
• src/hg/lib/rmskAlign.sql
  • lines changed 27, context: html, text, full: html, text
    checking in Robert's code refs #9741
• src/hg/lib/rmskJoined.as
  • lines changed 18, context: html, text, full: html, text
    checking in Robert's code refs #9741
• src/hg/lib/rmskJoined.c
  • lines changed 218, context: html, text, full: html, text
    checking in Robert's code refs #9741
• src/hg/lib/rmskJoined.sql
  • lines changed 24, context: html, text, full: html, text
    checking in Robert's code refs #9741
• src/hg/lib/rmskOut2.as
  • lines changed 20, context: html, text, full: html, text
    checking in Robert's code refs #9741
• src/hg/lib/rmskOut2.c
  • lines changed 442, context: html, text, full: html, text
    checking in Robert's code refs #9741
• src/hg/lib/rmskOut2.sql
  • lines changed 26, context: html, text, full: html, text
    checking in Robert's code refs #9741
• src/hg/makeDb/doc/gadMor1.txt
  • lines changed 41, context: html, text, full: html, text
    adding ucscToEnsembl table refs #11114
• src/hg/makeDb/doc/hg19.txt
  • lines changed 44, context: html, text, full: html, text
    finishing up lastz for panPan1 latCha1 jacJac1 capHir1 panHod1 hetGla2 refs #10272
  • lines changed 21, context: html, text, full: html, text
    finished lastz for jacJac1 panHod1 capHir1 hetGla2 refs #10272
• src/hg/makeDb/doc/mm10.txt
  • lines changed 7, context: html, text, full: html, text
    lastz for vicPac2 completed refs #10833
• src/hg/makeDb/doc/ochPri2.txt
  • lines changed 21, context: html, text, full: html, text
    liftOver to ochPri3 refs #9347
• src/hg/makeDb/doc/ochPri3.txt
  • lines changed 13, context: html, text, full: html, text
    finish off cpgIslands and genscan refs #9347
• src/hg/makeDb/doc/oviAri3.txt
  • lines changed 8, context: html, text, full: html, text
    finished pushQ entry refs #9409 pushQ 007056
• src/hg/makeDb/doc/panPan1.txt
  • lines changed 75, context: html, text, full: html, text
    completed genscan and cytoBandIdeo discovered broken contig JH650633 refs #8231
• src/hg/makeDb/doc/taeGut2.txt
  • lines changed 122, context: html, text, full: html, text
    ready for final steps to pushQ entry refs #10190
• src/hg/makeDb/doc/xenTro7.txt
  • lines changed 30, context: html, text, full: html, text
    done with genscan and genbank refs #9868
• src/hg/makeDb/trackDb/alpaca/vicPac2/trackDb.ra
  • lines changed 21, context: html, text, full: html, text
    setting default visibilities refs #10833
• src/hg/makeDb/trackDb/sheep/oviAri3/trackDb.ra
  • lines changed 18, context: html, text, full: html, text
    setting default visibilities refs #9409
• src/hg/makeDb/trackDb/tagTypes.tab
  • lines changed 1, context: html, text, full: html, text
    adding joinedRmsk to allow maxWindowToDraw type refs #9741
• src/hg/makeDb/trackDb/trackDb.ra
  • lines changed 23, context: html, text, full: html, text
    removing extra blanks at the end of lines refs #10272
• src/hg/utils/automation/findEnsFtpNames.sh
  • lines changed 3, context: html, text, full: html, text
    tweaking the processing of the gtf FTP output refs #11114
• src/hg/utils/automation/unplacedScaffolds.pl
  • lines changed 4, context: html, text, full: html, text
    add twoBitDup checking refs #10272
• src/hg/utils/phyloTrees/primates.txt
  • lines changed 7, context: html, text, full: html, text
    adding macFas crab-eating macaque and chlSab green monkey refs #10272
• src/hg/utils/phyloTrees/vertebrates.txt
  • lines changed 3, context: html, text, full: html, text
    adding araMac Scarlet Macaw refs #10272
• src/userApps/README
  • lines changed 1, context: html, text, full: html, text
    the git fetch command now uses the beta branch not the HEAD refs #9149
• src/utils/ncbi/cytoBandVerify.pl
  • lines changed 18, context: html, text, full: html, text
    improve processing of the cytoBand.bed file refs #10290