Commits for hiram

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

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