Commits

Author Commit Message Labels Comments Date
Bob Harris
moved test data for bx.seq tests to common area
Bob Harris
moved test data for bx.seq tests to common area
Bob Harris
moved test data for bx.seq tests to common area
Bob Harris
moved test data for bx.seq tests to common area
Ian Schenk
intervals.io now throws a ParseError is start > end. This should avoid seg faults with bitsets too.
Bob Harris
moving test data for bx.seq tests to common area
Ian Schenk
Moved things around, restored random.py's name.
Ian Schenk
Changes to quicksect - test now works. Moving out of this directory in the next commit.
Ian Schenk
Minor typo in quicksect.
Ian Schenk
Fixed join, added quicksect, which is faster than intersecter, uses the same or less memory, and is a little more flexible with what you give it.
James Taylor
Forgot to change class name in maf_thread_for_species.py
James Taylor
Require at least python2.4 to setup.
James Taylor
Commenting out tests for bzip2 / lzop since they currently depend on specific files. They *should* generate some data on the fly to test with.
James Taylor
Make thread not modify the passed in MAF.
James Taylor
Offset calculation in interval_index_file was broken. Don't use the version from the last three weeks (or any indexes created with it)
James Taylor
Minor fixes.
Bob Harris
improved memory utilization for long fetches
James Taylor
Alignment chopping
James Taylor
Various fixes from Bob, Thanks!
James Taylor
Several changes to how binning works in interval_index_file. First, the maximum has been increased (to 4096*1024*1024, bigger than the 32bit integer we use to actaully store the positions can hold, thus MAX is actually 2**31). Second, the number of levels of bins to use is determined from the max size passed to create the index. Thus, where small intervals (e.g. contigs) previously the smallest number of bins one could use had to include space for all the …
Ian Schenk
Fixed potential for divide by zero error in coverage operation.
Bob Harris
added qdna (partial) write capability; writing codebooks is still not supported (due to laziness)
Ian Schenk
operations shouldn't be referencing file anymore since they use the reader.
Ian Schenk
concat had a bug where if the first input didn't return any intervals the rest of the output would end up mangled.
Bob Harris
removed outdated warning
Bob Harris
corrected import statement
James Taylor
Support for q rows.
James Taylor
Fixes.
James Taylor
Fixing up "tell" for seeklzop.
James Taylor
maf build index fixes.
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