Quick test of code review functionality using a a file that I committed.
Testing GitHub/Lighthouse integation. [#15 state:resolved]
Testing GitHub/Lighthouse integation. [#1 state:resolved]
Testing GitHub/Lighthouse integation. [#1 state:resolved]
Remove test file.
Import Tim Brom's SMP FAST{A,Q} parsers from his 'smp_filtering' branch.
Import Tim Brom's Makefile for the SMP FAST{A,Q} parsers from his 'smp_filtering' branch.
Integrate multi-threaded parsers into FASTA consume-and-tag method for 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).
Fix parallel build dependency issue in top-level Makefile.
Remove 'main' function from 'parsers.cc' so that linker does not get confused when linking it into a driver program.
Break large critical section in 'consume_fasta_and_tag' into smaller ones for debugging purposes. Fix bug with 'seq' variable not being declared thread-private.
Add 'load_graph' driver program for testing parallelized FASTA consumer.
Import 'primes.hh' from Tim Brom's branch so that his driver program will build properly.
Improve build support for driver programs.
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'.
Restructure Makefile slightly for improved consistency and ability to modify.
Add TAU profiling support to Makefile.
Rename 'test.cc' to 'ktable_test.cc' so that the 'test' target doesn't confuse 'make'.
Normalize reads (convert to all uppercase chars) before verifying them.
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.
Break down critical sections into smaller critical sections and atomic 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.
Add support for writing out a hashtable to the 'load_graph' driver program.
Merge branch 'refactor' into mt-reader
Improve output of 'load_graph' driver program.