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Commits on Jul 18, 2013
  1. fix typos in udc blocks

    committed Jul 17, 2013
  2. add trial of forked prefetch

    committed Jul 17, 2013
Commits on Jul 17, 2013
  1. @ngannguyen
  2. @ngannguyen
Commits on Jul 16, 2013
  1. add lodchunk option

    committed Jul 16, 2013
  2. add clearcache option to columniterators tosite method to guarantee t…

    committed Jul 16, 2013
    …hat it lands on the desired column even in already visited. update hallodgraph to use this option
  3. dont print empty sequences

    committed Jul 16, 2013
Commits on Jul 15, 2013
  1. read in _totalSequenceLength from the sequence array if the DNA array…

    committed Jul 15, 2013
    … is empty. we want this to be valid even when the DNA is not stored to be consistent with last version
  2. add some asserts

    committed Jul 15, 2013
  3. fix bug in tosite where somehow the reference genome was incorrectly …

    committed Jul 15, 2013
    …determined in weird cases
  4. use columniterators tosite method to move around instead of creating …

    committed Jul 15, 2013
    …new one each time. not sure why this was taken out before. . hopefully i dont break anything
  5. remove some cruft

    committed Jul 15, 2013
  6. ensure that all zero length sequences get added to both the position …

    committed Jul 15, 2013
    …and the name cache (by storing them outside map)
Commits on Jul 12, 2013
  1. fix sonlib build dependency

    committed Jul 12, 2013
Commits on Jul 11, 2013
  1. @ngannguyen
  2. do not cache sequences until needed for the first time. also keep nam…

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

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

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

    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
  6. Revert "add rm *.o to all the makefiles to make sure we dont suck in …

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

    committed Jul 11, 2013
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