Fix conditional compilation issue in Hashbits counting logic. (Still need to test this more.)
Prevent shared compression libs from building. (Increase portability and decrease build time.)
(Thanks to Greg Edvenson for reporting a bzip2 shared lib build problem on MacOS X.)
Merge branch 'bleeding-edge' from 'ged-lab/khmer'.
Blindly attempt to get the thread ID for Mac OS X and other platforms unknown.
removed score
Rip out remnants of threadedParsers and OMP stuff from core implementation.
Remove KHMER_THREADED conditional compilation from core implementation.
added tests for graph alignment
Reduce default read buffer memory and apply default everywhere relevant.
Set thread-safety on everywhere. (Finish removing 'KHMER_THREADED' conditional compilation.)
Remove all compilation and linking flags related to OMP, except in the tests where they are used.
Disable execution tracing by default.
Hackishly fix a thread-deadlock bug by periodically issuing memory barriers in the busy waiters used for synchronization. (Bug generally appearied when execution tracing is disabled.)
(Note: Still need to think about causality of bug and possibly a different synchronization scheme.)
Disable execution tracing by default.
Hackishly fix a thread-deadlock bug by periodically issuing memory barriers in the busy waiters used for synchronization. (Bug generally appeared when execution tracing was disabled.)
(Note: Still need to think about causality of bug and possibly a different synchronization scheme.)
Merge branch 'mt-reader' of github.com:spartanem/khmer into mt-reader
updated ec.py
Notes to self.
Include <cstdint> from 'khmer.hh'.
Simplify 'khmer_config.hh' by removing map as storage.
Remove methods which are no longer relevant from 'khmer_config.hh'.
Remove nosetests and wrapper methods which correspond to deleted methods.
Ignore Vim backup files in 'python' directory.
Refactor sloppy hash counting support into the Hashtable base class.
Ignore Vim backup files in the 'tests' directory.
Fix all errors and warnings for Cython builds.
Pass most tests with Cythoned build.
(Note: The Cythoned code appears to have a memory leak or, at least, be a larger memory hog. Need to investigate.)