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Commits on Jul 11, 2013
  1. do not cache sequences until needed for the first time. also keep nam…

    glennhickey committed Jul 11, 2013
    …es and coordinates in separate caches
  2. increase version in README

    glennhickey committed Jul 11, 2013
  3. Change how sequences are stored. Keep only indexes and not lenghts on…

    glennhickey committed Jul 11, 2013
    … disk and move names into a separate array. Version updated to 2 to reflect lack of backward compatibility
  4. undo last change where we removed all the .o s since it turns out the…

    glennhickey committed Jul 11, 2013
    …yre important for gdb. now we just remove them before making a library to serve the original porpose of not adding cruft from executables
  5. Revert "add rm *.o to all the makefiles to make sure we dont suck in …

    glennhickey committed Jul 11, 2013
    …extra object files when making library archives"
    
    This reverts commit a2b26ed.
  6. disable flip code

    glennhickey committed Jul 11, 2013
Commits on Jul 10, 2013
  1. lower default chunk of lods from 1000 to 200. add option to scripts a…

    glennhickey committed Jul 10, 2013
    …nd tools to specifiy chunk
  2. fix error in sed command

    glennhickey committed Jul 10, 2013
  3. switch to aggregate mode. add 2nd line remover for maf. seems root is…

    glennhickey committed Jul 10, 2013
    …sue may have beeno nonbinary trees
  4. make

    glennhickey committed Jul 10, 2013
    Merge remote-tracking branch 'origin/development' into phyloP
  5. fix some bugs

    glennhickey committed Jul 10, 2013
  6. add rm *.o to all the makefiles to make sure we dont suck in extra ob…

    glennhickey committed Jul 10, 2013
    …ject files when making library archives
Commits on Jul 9, 2013
  1. add wiglle scanner

    glennhickey committed Jul 9, 2013
Commits on Jul 8, 2013
  1. fix typo

    glennhickey committed Jul 8, 2013
  2. move phast include directory ahead of kent include to avoid conflict …

    glennhickey committed Jul 8, 2013
    …with gff.h when building halPhyloP
Commits on Jul 5, 2013
  1. overhaul liftover especially block logic. also fix psl. add psl valid…

    glennhickey committed Jul 5, 2013
    …ator that will throw exception or assert if it sees a problem
Commits on Jul 4, 2013