Making trunk directory

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Importing everything

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Forgot the cookbook package. Fixed bitset.pyx (still in progress) so that it builds.

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"bed_merge_overlapping" merges all overlapping intervals in a bed file. It uses projection onto a bitset
like featureBits, but the bitset is broken up into bins which makes things much faster for smaller data
sets.

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(1) corrected reverse_complement (2) brought axt support up-to-snuff with maf (3) which necessitated changes to maf and core (4) added stubs for lav

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stub module that eventually will read/write LAV format alignment blocks with same interface as maf.py and axt.py

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Fixed off by one error in intervals.Intersecter
Added a function to BinnedBitSet for counting the number of set bits in a ranges

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Added a script for extracting the regions covered (in the reference species)
by all other species in an alignment.

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C implementation of binned bitsets.

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Fixed a bug in count_range for BinnedBitset
Added bed_coverage, bed_intersect, and bed_merge_overlapping (all using binned bitsets)

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Another bug fix for counting in binned bitsets
bed_intersect now allows specifying a number of bases to overlap.

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Added species_to_lengths argument to Alignment constructor.

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Allow bed_merge_overlapping to take input from both stdin and files

Import and other fixes for python 2.3 compatibility

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More import fixes

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completion of yesterday's correction;  incorporating other 'lost' changes (which consists only of a comment)

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Added tests for Bitset and BinnedBitset covering set/clear, setrange, countrange, next_set/next_clear

Added a hacky test runner that adds the build directories to the pythonpath. Long term this should read possible tests from a file, and allow a command line for just running some tests.

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Undo path change, need to make this more easily configurable

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Binned bitsets now use two sentinals, ALL_ONE for bins containing all ones and ALL_ZERO for bins containing all zeros. Boolean operations (and, or, not) implemented (with tests).

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changed import of interval_index_file

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changed import paths to bx...

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