…p_filtering' branch.

…r Hashbits.

Add KHMER_THREADED macro for conditional compilation with multi-threading support.
Wrap serial and parallel parsers in a namespace so that they can coexist (for easier porting).

…confused when linking it into a driver program.

…ones for debugging purposes. Fix bug with 'seq' variable not being declared thread-private.

…will build properly.

Allow 'load_graph' to test counting hashes or hashbits.
Add parallel reading support to 'consume_fasta' in 'hashtable.cc'.
Replace a constant literal with a named constant for parallel read chunk size.
Prevent build of incomplete driver program 'consume_prof'.

… modify.

Add TAU profiling support to Makefile.
Rename 'test.cc' to 'ktable_test.cc' so that the 'test' target doesn't confuse 'make'.

Add flag to compile code with extra sanity checking (with about a 15% to 20% performance loss).
Create high performance macro version of the 'toupper' function and use for normalization.
Use quicker code when extra sanity checking disabled: reduce number of calls to the 'toupper' function.

…c operations.

(EXPERIMENTAL) Allow slightly sloppy high counts in multi-threaded operation.
Reduce MAX_COUNT threshold for counting hash bins to accomodate some slop from multiple threads crossing the threshold.

…ogram.

Create Python wrapper for 'khmer:: Config'.
Create methods to get and set the number of threads in the configuration interface.
Create methods to get hash bin counting thresholds in the configuration interface.
Only allow number of threads to be set when codes are built with 'KHMER_THREADED' defined.
Note: C++ API allows multiple config objects (with one active at any given time), but Python wrapper effectively works with a singleton for now. The bookkeeping required to keep the wrapper objects synchronized with the underlying API does not seem worth the dubious benefit of multiple config objects at this time.

Tweak Python wrapper slightly for more cosmetic output in interpreter.
Ensure that driver programs are linked with khmer_config.o.

Refine interaction between lib/Makefile and the build of the bundled zlib.
Dynamically generate python/setup.py according to user-tweakable knobs which are set. (Automatically maintains consistency with what is built in lib.)

… version control.

Breakout the automatic generation of setup.py into a separate make rule.

Update Python wrapper and tests accordingly.

… force. (I.e., beware of consuming lowercase characters.)

…-level makefile.

…directory.

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.

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.)

…port clock_gettime(2).

…Parser.

Create '_parse_read' methods for FastaParser and FastqParser classes.
Clean up 'test-Parser.cc'.
(Still need to test FASTQ parser, but refactored FASTA parser works for 1 thread, at least.)

…refactoring/generalization.)

…n sublcass there as well.

Create config interfaces for tuning the trace levels of the input buffer manager and the reads parsers.

Fix bug which masks a deeper bug (unfixed).
(Bug: Exception not being thrown for all bad parses which are expected to be good parses.)
(Deeper Bug: Setaside buffer not being set before it is needed. Causes some data to be skipped which leads to bad parses.)
(Note: Will probably switch to using copyaside buffers instead of setaside buffers to fix deeper bug.)
(Note: Copyaside buffers will also make async input easier to implement.)

…arser test driver program.

Finish disconnecting old parsers from everything.
Fix bug in tests of khmer Config object, where values were not being reset after tests.
Fix bug in parsing, stemming from segment start being detected per line rather than per record.

…counting.

…with the get_median_count move into Hashtable.

Conflicts:
	lib/Makefile
	lib/hashbits.cc
	lib/hashtable.cc
	lib/hashtable.hh