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Update bleeding-edge with get_median_count changes to Hashtable & Mac OS X dylib "fixes" #4
Commits on Jan 30, 2012
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Quick test of code review functionality using a a file that I committed.
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Testing GitHub/Lighthouse integation. [#15 state:resolved]
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Testing GitHub/Lighthouse integation. [#1 state:resolved]
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Testing GitHub/Lighthouse integation. [#1 state:resolved]
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Commits on Feb 1, 2012
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Import Tim Brom's SMP FAST{A,Q} parsers from his 'smp_filtering' branch.
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Import Tim Brom's Makefile for the SMP FAST{A,Q} parsers from his 'sm…
…p_filtering' branch.
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Commits on Feb 2, 2012
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Integrate multi-threaded parsers into FASTA consume-and-tag method fo…
…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).
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Commits on Feb 3, 2012
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Fix parallel build dependency issue in top-level Makefile.
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Commits on Feb 7, 2012
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Remove 'main' function from 'parsers.cc' so that linker does not get …
…confused when linking it into a driver program.
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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.
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Add 'load_graph' driver program for testing parallelized FASTA consumer.
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Import 'primes.hh' from Tim Brom's branch so that his driver program …
…will build properly.
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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'.
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Commits on Feb 8, 2012
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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'.
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Commits on Feb 13, 2012
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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.
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Commits on Feb 16, 2012
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Break down critical sections into smaller critical sections and atomi…
…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.
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Add support for writing out a hashtable to the 'load_graph' driver pr…
…ogram.
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Merge branch 'refactor' into mt-reader
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Commits on Feb 21, 2012
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Improve output of 'load_graph' driver program.
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Commits on Feb 28, 2012
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Create configuration interface, 'khmer:: Config', in C++ API.
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.
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Commits on Mar 1, 2012
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Create tests for khmer:: Config.
Tweak Python wrapper slightly for more cosmetic output in interpreter. Ensure that driver programs are linked with khmer_config.o.
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Commits on Mar 2, 2012
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Hoist user-tweakable knobs from lib/Makefile to Makefile.
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.)
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No longer track and ignore automatically generated python/setup.py in…
… version control. Breakout the automatic generation of setup.py into a separate make rule.
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Merge branch 'refactor' into mt-reader
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Add 'has_extra_sanity_checks' method to 'khmer:: Config'.
Update Python wrapper and tests accordingly.
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Fix tests to accomodate the case where extra sanity checks are not in…
… force. (I.e., beware of consuming lowercase characters.)
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Properly cleanup Python wrapper directory when clean invoked from top…
…-level makefile.
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Place test output in a temp directory rather than in the soruce data …
…directory.
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Commits on Mar 5, 2012
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Fix read validation code. Reject sequences with 'n' as well as 'N'.
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Commits on Mar 9, 2012
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Fix bug where invalid read would be skipped if encountered at EOF.
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Ignore failure of attempt to use 'setup.py' to clean the build, if it…
… has not been generated. (Handle multiple successive cleanings without breaking.)
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Fix previous bug fix of parser code.
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Commits on Mar 12, 2012
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Parse argument of 'set_number_of_threads' as signed rather than unsig…
…ned int so that attempts to set negative numbers of threads can be caught and handled properly.
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Fix bug in thread-safe readmask setter.
(Doh! It helps to use the atomic operation you intended (compare-and-swap) rather than the one your fingers actually wrote (add).) (Adding 0 to a variable having a value of 1 is not the same as setting that variable to 0. :-) The entire automated test suite now passes with the threaded code.
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Cleanup of OMP parallel parameters declaration.
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Bug fix to multi-threaded parser. Only assert that a valid read name …
…was found if not at end of file. (Technically, one could question rather this should be an assert or whether it should throw an exception.)
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Commits on Mar 13, 2012
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Use config interface to get size of sloppy hash bins in kmer-counting…
… logic.
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Commits on Mar 14, 2012
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Replace some coarse-grained critical sections with fine-grained atomi…
…c operations. Fuse testing for and setting kmer presence bits in Bloom filter hash tables into a single function for reasons of hopefully-improved efficiency and adding thread safety. Cleanup and simplify declaration of OpenMP parallel region in 'consume_fasta_and_tag'. Note: More performance testing and tuning must still be done. Some pieces of code related to this have been left in, wrapped in conditional compilation constructs.
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Commits on Mar 15, 2012
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Change hash bin sloppiness formula in config interface.
Update tests of config interface accordingly.
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Commits on Mar 21, 2012
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WARNING: This is a broken commit. Everything builds with the Python C…
… API or with Cython, but not everything tests out. Merge branch 'merge_cython' into mt-reader Conflicts: lib/parsers.cc lib/parsers.hh python/Makefile python/setup.py.in
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Rename _khmermodule.cc.orig back to _khmermodule.cc.
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Commits on Mar 22, 2012
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Hack support for Config interface into Cython.
NOTE: The 'get_config' method is not quite right, due to the way Cython handles C++ references.
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Commits on Mar 26, 2012
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Comment out test corresponding to 'collect_high_abundance_kmers', whi…
…ch is disabled in Cython interface.
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Commits on Mar 27, 2012
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Undo breakage caused by importing 'new_counting_hash' as 'new_hashtab…
…le' in Cython merge.
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Clean up directories from tests which abort abnormally.
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Commits on Mar 28, 2012
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Handle differences between CPython API and Cython interfaces with a c…
…rude try-except hack during imports.
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Merge branch 'master' into mt-reader
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Merge branch 'qp_refactor' into mt-reader
NOTE: The 'test_count_overlap_cpp' test may be broken. Rest of commit should be good though. Conflicts: lib/hashbits.cc lib/hashbits.hh tests/test_scripts.py
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Commits on Apr 2, 2012
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Merge branch 'qp_refactor' into mt-reader
Note: All tests now pass. However, one test requires 'matplotlib' (which requires 'NumPy'). We may wish to make the execution of this test depedent on the availability of 'matplotlib' on the user's system or else make 'matplotlib' a prerequistite for the 'khmer' package. Conflicts: tests/test_scripts.py
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Commits on Apr 4, 2012
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Create config API controls for whether threading is used when parsing…
… reads files and the stride length to be used by threaded reads parsers.
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Add Cython wrappings for expanded config interface.
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Commits on Apr 5, 2012
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Add bzip2 library to khmer build process. (Not used anywhere yet, tho…
…ugh.) Rework 'lib/Makefile' for a simpler zlib dependency graph.
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Rename 'zlib-1.2.3' directory to 'zlib' for brevity of compilation li…
…nes. Make changes associated with the rename. Improve the setup.py template to be more readable and hackable.
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Ignore generated files in lib/bzip2 directory.
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Merge branch 'master' into mergethon
Resolve conflicts. Conflicts: lib/Makefile lib/hashtable.cc lib/hashtable.hh
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Add back change from Titus accidentally removed during merge.
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Commits on Apr 14, 2012
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Create stream readers for new parser architecture. Create test harnes…
…s for new stream readers.
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Commits on Apr 24, 2012
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Update 'lib/.gitignore'. Remove accidentally committed executable.
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Initial implementation of cache manager to interface with stream read…
…ers. Note: This commit includes a bug when appending a wrapped-around ssegment to a psegment. Note: This implementation is not efficient across multiple NUMA nodes. Needs to be rewritten so that cache segments are allocated separately on demand rather than as part of one large pool which will be biased to the physical memory of the master thread.
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Commits on Apr 26, 2012
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New implementation of cache manager code. Should be much more NUMA-fr…
…iendly and also does not have any bugs I am aware of from thinking about the code. Now on to finding and fixing those of which I am not aware....
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Commits on Apr 28, 2012
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Capture per-thread timing data for the various wait loops and reading…
… from the stream.
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Commits on May 7, 2012
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Create tester for cache manager used by the reads parsers.
Instrument cache manager debug tracing and performance measurement logic. Fix enough logic bugs for multi-threaded tests to successfully complete.
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Fix a bug where a solo cache manager thread could lock itself out.
Fix a bug where a byte reader function could be using the wrong cache segment size.
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Write cache manager performance metrics to a trace file. (Note: Shoul…
…d probably store in a metrics object instead.)
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Commits on May 9, 2012
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Create FASTA parser. Minor tweaks elsewhere in the read_parsers code.…
… Still need to test.
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Commits on May 10, 2012
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Create performance metrics objects. Apply them to stream readers and …
…cache managers. (Still need to test.)
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Commits on May 12, 2012
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Create TraceLogger class. Use TraceLogger instances to trace executio…
…n of cache manager segments. (Note: Still need to test.)
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Commits on May 15, 2012
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Improve cache segment allocation logic.
Add performance metrics and execution tracing to the parser interface. (Still need to test.)
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Commits on May 16, 2012
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Fix dependency issue in 'lib/Makefile' where test program .o files wo…
…uld not be regenerated on change of a header which the corresponding source used.
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Create test harness for reconstructed parser infrastructure.
Fix bug where data was being lost if a cache segment fill occurred in the midst of copying memory to a parser buffer.
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Commits on May 17, 2012
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Bug fix. In CPython API, register the type of khmer Config objects as…
… being the Python built-in 'type'. Having a metaclass allows the object attributes to be listed and type to be determined. (Imagine that....)
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Delete 'get_byte' method from CacheManager.
Add parameter for tracking segment and setaside buffer boundaries to 'get_bytes' method in CacheManager. Temporarily add deeper tracing to parser for debugging purposes. Fix bug which caused overlapping reads and a segmentation fault from an invalid split position.
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Commits on May 19, 2012
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Fix bug where the sequence line appender logic was not checking wheth…
…er a fil l segment boundary had been crossed.
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Commits on May 21, 2012
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Fix bug where a read was being skipped because the completed state wa…
…s being flagged prematurely (before the parser buffer was fully consumed).
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Commits on May 22, 2012
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Refine tracer output to be more useful for hunting what is hopefully …
…the final parser bug.
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Commits on May 23, 2012
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Improve cache manager and read parser diagnostics for bug hunting.
Fix bug where first seqment fill would make a setaside buffer of size 0, causing fill segment 1 to erroneously believe that it did not have an extension. (I.e., fix an off-by-one error.)
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Commits on May 24, 2012
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Another one-line change to fix a bug where the cache manager's 'copy_…
…bytes' function was not checking if a cache segment was still valid and was recopying bytes from the start of the segment after the cursor was reset to there during a segment maintenance in which the segment was invalidated (due to end of stream being reached). (No more known bugs in the cache manager and parser logic as of this commit.)
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Cleanup of cache manager- and parser-related code.
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Merge branch 'master' into mergethon
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Merge branch 'mt-reader' into mergethon
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Merge branch 'master' into bleeding-edge
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Commits on Jun 5, 2012
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Improve maintainability of test driver programs in 'lib' directory.
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Set the default trace level to be 'TLVL_NONE' rather than 0, which is…
… 'TLVL_ALL'. Shuffle some includes from the read parsers implementation file to the read parsers header file.
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Reduce verbosity of the test driver for the rewritten FASTA parser.
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Commits on Jun 6, 2012
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Refactor TraceLogger class into a separate set of files.
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Commits on Jun 22, 2012
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Merge in Titus' changes to ged-lab:master.
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Merge branch 'refactor' into bleeding-edge
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Commits on Jun 25, 2012
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Merge branch 'refactor' into bleeding-edge
Fix from QP to remove dependency upon the 'matplotlib' package. Conflicts: tests/test_scripts.py
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Fix return type scoping issue identified by more recent version of GCC.
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Commits on Jun 28, 2012
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Integrate rewritten parser logic into counting hashes. (Still need to…
… fix a possible bug, but code executes without crashing.)
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Merge branch 'bleeding-edge' into mt-reader
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Compile without internal tracer logic for a speedup, if desired.
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Fix some linking problems in Python wrapper.
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Commits on Jul 3, 2012
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Do not open or close trace files if 'WITH_INTERNAL_TRACING' is not de…
…fined.
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Add macro for switching between original parser and new parser for te…
…sting purposes. (The hashtables produced by the original parser and single-threaded operation of the new parser are currently indentical, btw.)
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Commits on Jul 20, 2012
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Create intelligent hashtable differ. (Still need to add support for b…
…igcounts and for sloppy counting.)
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Commits on Jul 26, 2012
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Allow truncation of saturated bins in hash table differencer.
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Commits on Jul 27, 2012
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Rip readmask functionality out of 'consume_fasta'.
Delete 'consume_fasta_build_readmask' method and interfaces to it. Update test suite accordingly.
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Commits on Jul 31, 2012
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Add Hasher helper class to Hashtable.
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Make separate category for auxiliary programs such as 'ht-diff' and m…
…ake sure that programs in this category are deleted when the 'clean' target is invoked.
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Convert from using old single-threaded parser as the default to using…
… the new threadsafe parser as the default. Remove OMP dependencies from 'lib/hashtable.cc'. Cleanup some disabled debugging logic no longer used. Add per-thread execution tracing to 'consume_fasta' method. Initialize read and k-mer counters in Python wrappers prior to passing them to 'consume_fasta'. (This is needed for threadsafe counting.)
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Commits on Aug 9, 2012
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Extend Read struct to accommodate members found in Screed read records.
Rename the 'seq' member of the Read struct 'sequence' and update sources accordingly.
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Wrap Read and ReadParser objects in CPython. (Still need to do Cython…
… and write tests.)
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Commits on Aug 14, 2012
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Cython wrappers for IParser and Read objects. (Still need to expose t…
…o 'khmer' module and write tests.)
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Commits on Aug 15, 2012
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Import wrapped Read and IParser classes into 'khmer' module. (Incompl…
…ete. Still need to clean up some.)
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Commits on Oct 10, 2012
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Manual merge from 'master' branch.
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Commits on Oct 22, 2012
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Merge from 'bleeding-edge' branch of 'ged-lab' repo.
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Improve efficiency of copy from cache segment into line buffer.
(Thanks to Eric Norige for noticing this. Somehow I overlooked it....)
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Allow 'HashTable' objects to be used by multiple threads.
Use multiple threads in the 'HashTable' test driver.
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Partial brain dump about future directions.
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Prep input streams with posix_fadvise(2).
(TODO: Add O_DIRECT support for raw streams from regular files.) (Could've sworn that I had already started that task previously....)
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Commits on Oct 23, 2012
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Add O_DIRECT support to RawStreamReader with aligned memory where nee…
…ded.
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Merge from branch 'bleeding-edge' in 'ged-lab' repo.
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Refactor IPerformanceMetrics to separate files.
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Commits on Oct 24, 2012
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Stake out places to gather timing data.
Clean up code: tighten down a conditional compilation, remove a stray OMP directive. Improve performance: precalculate MAX_COUNT and MAX_BIGCOUNT and store with HashTable object.
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Commits on Oct 25, 2012
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Create HashTablePerformanceMetrics.
Improve efficiency of DNA string validator.
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Commits on Oct 28, 2012
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Add conditional compilation of performance metrics.
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Commits on Oct 30, 2012
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Ignore error if 'zlib' directory already clean and the automatically-…
…generated makefile is missing.
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Add cache size adjuster to multi-threaded hash table tester.
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Add '-pg' flag during linking when 'gprof' profiling is enabled.
(Bug: Threads hang if the code is not built with internal tracing enabled. Need to fix.)
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Commits on Nov 7, 2012
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Quicker toupper for sequence normalization.
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Ignore log files generated while running tests with tracing enabled.
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Commits on Nov 8, 2012
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Merge with 'master' branch from 'ged-lab/khmer'.
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Merge with branch 'bleeding-edge' from 'ged-lab/khmer'.
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Reduce overhead by changing some defaults.
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Commits on Nov 9, 2012
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Merge pull request #3 from edvenson/5a42baae16a2db9c9f94a1463abe8b84b…
…dbf46e6 changes from os x build experience
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Commits on Nov 12, 2012
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Merge branch 'master' from 'ged-lab/khmer'.
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Merge branch 'bleeding-edge' from 'ged-lab/khmer'.
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Add TODO item about hunting for more memory leaks.
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Conditionally compile an attempt to open with O_DIRECT for Linux only.
(Thanks to Greg Edvenson for catching this.)
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Fix conditional compilation issue in Hashbits counting logic. (Still …
…need to test this more.)
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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.)
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Merge branch 'bleeding-edge' from 'ged-lab/khmer'.
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Blindly attempt to get the thread ID for Mac OS X and other platforms…
… unknown.
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Commits on Nov 13, 2012
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Rip out remnants of threadedParsers and OMP stuff from core implement…
…ation.
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Remove KHMER_THREADED conditional compilation from core implementation.
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Reduce default read buffer memory and apply default everywhere relevant.
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Set thread-safety on everywhere. (Finish removing 'KHMER_THREADED' co…
…nditional compilation.) Remove all compilation and linking flags related to OMP, except in the tests where they are used.
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Commits on Nov 14, 2012
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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.)
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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.)
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Merge branch 'mt-reader' of github.com:spartanem/khmer into mt-reader
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Commits on Nov 15, 2012
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Commits on Nov 16, 2012
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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.
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Ignore Vim backup files in 'python' directory.
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Refactor sloppy hash counting support into the Hashtable base class.
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Ignore Vim backup files in the 'tests' directory.
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Commits on Nov 17, 2012
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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.)
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Commits on Nov 19, 2012
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Remove unneeded 'consume_genome' code and script.
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Zero performance metrics stopwatches on platforms which might not sup…
…port clock_gettime(2).
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Factor 'ThreadIDMap' into separate files.
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Commits on Nov 20, 2012
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Generalize and refactor 'get_next_read' logic. Hoist to base class: I…
…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.)
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Commits on Nov 21, 2012
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Add source code as Makefile dependencies for tester programs.
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Fix bug in multi-threaded FASTA/FASTQ parsing. (Introduced by recent …
…refactoring/generalization.)
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Hoist inclusion of <exception> to 'khmer.hh'. Place a common exceptio…
…n sublcass there as well. Create config interfaces for tuning the trace levels of the input buffer manager and the reads parsers.
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Commits on Nov 22, 2012
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Add some additional execution tracing to input buffer manager.
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.)
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Conditionally compile the writing of per-thread summary logs in C++ p…
…arser test driver program.
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Replace setaside buffering with copyaside buffering.
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.
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Commits on Nov 28, 2012
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Add thread-safety to 'bigcount' overflow bins for Bloom filter k-mer …
…counting.
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Initialize k-mer counter spinlocks to 0 for 'bigcounts'.
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Commits on Nov 30, 2012
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Allow number of threads to be chosen from 'load-into-counting' script.
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Commits on Dec 1, 2012
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Use chosen number of threads from 'load-into-counting' script.
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Update documentation on load-into-counting script.
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Commits on Jan 25, 2013
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Eric McDonald committed
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Commits on Feb 2, 2013
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Merge branch 'master' into bleeding-edge. This updates bleeding-edge …
…with the get_median_count move into Hashtable. Conflicts: lib/Makefile lib/hashbits.cc lib/hashtable.cc lib/hashtable.hh
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