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Commits on Aug 6, 2010
  1. Added variable read length support to Pyper.

    Pyper slice iterator now distinguishes between reads that actually overlap with the target segment and ones that merely start at an index that should include overlaps if the reads are long enough.
    Todo (Maybe):
    Remove Caper "intersection" functionality from the engine. Rather, a Pyper style slice iterator will be implemented as a wrapper over the engine, but in C++.
  2. Further simplified the container such that it always just retrieves t…

    …he reads that overlap a given slice (inclusive)
Commits on Aug 5, 2010
  1. Reworked (hyper-simplified) the mappinginterval object so that it can…

    … be iterated over a single read at a time.
    See the tests and to see how it works.
Commits on Jul 14, 2010
Commits on Jul 13, 2010
  1. @ctb
  2. @ctb

    changed .pyx dependencies

    ctb authored
  3. @ctb
  4. @ctb
Commits on Jul 9, 2010
  1. Updated NOTES

  2. Finished adding the iterator tests.

    Not perfectly thrilled with some of the functionality (the returning of ival stop/start values) so
    the interface is still probably a little bit fluid.
    Next is some bench-marking to see where we are with iteration, compared to samtools
  3. Fixed an out of bounds error, where an empty array wasn't being prope…

    Rosangela Canino-Koning authored
    …rly interpreted.
Commits on Jul 8, 2010
  1. Removed extraneous .dll and .ilk files that shouldn't be distributed.

    Rosangela Canino-Koning authored
  2. Updated .gitignore

  3. Updated .gitignore and NOTES

  4. Re-added basic Caper tests, which now pass. Hooray!

    Next, it's readding the Pygr bridge tests.w
Commits on Jul 7, 2010
  1. Commented out all the debug statements. Will totally remove them when…

    Rosangela Canino-Koning authored
    … I finish up the test code.
  2. Fixed damned bug.

    Rosangela Canino-Koning authored
    What a delightful one. What it boils down to is that gcc initializes your member variables (ints, in particular) for you, to
    -1. I had a typo in an if statement comparing against mIndex (my member variable) rather than aIndex (my parameter).
    Further, there was an error with how I was handling End values. My default starting index was -1, the same as my End flag index, creating a meaning collision. Poop. So, I fixed that. Who knows what the repercussions would have been otherwise.
    That kind of thing is just bad design, and I'll need to go back and fix it in the future.
  3. Aha! That's a weird behaviour difference between when constructors ar…

    Rosangela Canino-Koning authored
    …e called by visual studio vs gcc.
    Seems the gcc behaviour is correct. When I init an iterator, CALL THE FUCKING CONSTRUCTOR.
    The only reason VS seemed to be behaving correctly (not reallocating the cache) was because
    it wasn't calling the constructor. Who knows why?
  4. debug messages

    Rosangela Canino-Koning authored
  5. More debug.

    Rosangela Canino-Koning authored
  6. More debug

    Rosangela Canino-Koning authored
  7. Redoing debug statements (thinning the herd)

    Rosangela Canino-Koning authored
  8. Even more debugging statements. This is getting ridiculous.

    Rosangela Canino-Koning authored
  9. Even more debugging messages.

    Rosangela Canino-Koning authored
  10. More debugging statements.

    Rosangela Canino-Koning authored
  11. Oops.

    Rosangela Canino-Koning authored
  12. Re-did commenting out of extraneous destructor (wtf?)

    Rosangela Canino-Koning authored
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