| 2007-05-04 |
Michael Coleman | bug fix: don't merge spectrum 0002.0002.1 from different...
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commit | commitdiff | tree |
| 2007-05-03 |
Michael Coleman | zap NOTHROW in C++ code; no apparent speedup
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commit | commitdiff | tree |
| 2007-05-03 |
Michael Coleman | update README and TODO
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commit | commitdiff | tree |
| 2007-05-03 |
Michael Coleman | rename XTP to GLP
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commit | commitdiff | tree |
| 2007-05-03 |
Michael Coleman | zap a bit of dead code; cleanups; update TODO list
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commit | commitdiff | tree |
| 2007-05-03 |
Michael Coleman | update sloccount stats: slightly smaller since redesign (!)
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commit | commitdiff | tree |
| 2007-05-02 |
Michael Coleman | update TODO list
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commit | commitdiff | tree |
| 2007-05-02 |
Michael Coleman | minor bug fix: assertion was tripping because it was...
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commit | commitdiff | tree |
| 2007-05-02 |
Michael Coleman | Add cleavage params, minor cleanups
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commit | commitdiff | tree |
| 2007-05-02 |
Michael Coleman | update mass tracing--now works for basic cases
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commit | commitdiff | tree |
| 2007-05-02 |
Michael Coleman | greylag-sge-slice: rearrange code
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commit | commitdiff | tree |
| 2007-05-02 |
Michael Coleman | greylag-process lockfile bug fix, plus use new greylag...
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commit | commitdiff | tree |
| 2007-05-01 |
Michael Coleman | update TODO list
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commit | commitdiff | tree |
| 2007-04-30 |
Michael Coleman | Add peak cache, for speed. (buys 14% improvement-...
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commit | commitdiff | tree |
| 2007-04-30 |
Michael Coleman | Inline update_p_mass (simpler and faster)
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commit | commitdiff | tree |
| 2007-04-30 |
Michael Coleman | Re-enable specific cleavage; code cleanup
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commit | commitdiff | tree |
| 2007-04-30 |
Michael Coleman | greylag-grind: add 'enable_pca_mods' parameter
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commit | commitdiff | tree |
| 2007-04-30 |
Michael Coleman | split search_peptide from search_run (non-specific...
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commit | commitdiff | tree |
| 2007-04-29 |
Michael Coleman | opt: minor deSTL optimization (mass ladder as double...
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commit | commitdiff | tree |
| 2007-04-29 |
Michael Coleman | opt: minor deSTL optimization (theoretical ladders)
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commit | commitdiff | tree |
| 2007-04-29 |
Michael Coleman | opt: minor deSTL optimization in score_spectrum (3...
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commit | commitdiff | tree |
| 2007-04-29 |
Michael Coleman | opt: minor deSTL optimization in score_spectrum (2)
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commit | commitdiff | tree |
| 2007-04-28 |
Michael Coleman | opt: minor deSTL optimization in score_spectrum
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commit | commitdiff | tree |
| 2007-04-26 |
Michael Coleman | greylag-process: default to 1100 parts (good for our...
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commit | commitdiff | tree |
| 2007-04-26 |
Michael Coleman | update TODO list
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commit | commitdiff | tree |
| 2007-04-26 |
Michael Coleman | Bug fixes: deterministic order of H lines, greylag...
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commit | commitdiff | tree |
| 2007-04-26 |
Michael Coleman | Update greylag-solo and tests, plus bug fixes.
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commit | commitdiff | tree |
| 2007-04-25 |
Michael Coleman | minor test fix; update TODO list
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commit | commitdiff | tree |
| 2007-04-25 |
Michael Coleman | update TODO list
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commit | commitdiff | tree |
| 2007-04-25 |
Michael Coleman | optimizations and minor cleanups
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commit | commitdiff | tree |
| 2007-04-24 |
Michael Coleman | greylag-merge: add --files-on-stdin flag, to handle...
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commit | commitdiff | tree |
| 2007-04-24 |
Michael Coleman | greylag-process: don't rely on qsub status--check output...
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commit | commitdiff | tree |
| 2007-04-24 |
Michael Coleman | greylag-process: explicitly specify shell
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commit | commitdiff | tree |
| 2007-04-24 |
Michael Coleman | Use greylag-python as the python interpreter.
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commit | commitdiff | tree |
| 2007-04-24 |
Michael Coleman | Cleanups: dead code removal/etc.
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commit | commitdiff | tree |
| 2007-04-23 |
Michael Coleman | update TODO list
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commit | commitdiff | tree |
| 2007-04-23 |
Michael Coleman | greylag-grind: no-spectra bug fix; *.gwr filename convention
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commit | commitdiff | tree |
| 2007-04-23 |
Michael Coleman | greylag-merge: fixed false warnings on varying metadata
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commit | commitdiff | tree |
| 2007-04-23 |
Michael Coleman | greylag-process now works
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commit | commitdiff | tree |
| 2007-04-23 |
Michael Coleman | Explicitly run scripts with command 'python2.5'
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commit | commitdiff | tree |
| 2007-04-23 |
Michael Coleman | Use "configuration file" instead of "parameter file".
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commit | commitdiff | tree |
| 2007-04-23 |
Michael Coleman | Update install target with new scripts (and "_" naming)
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commit | commitdiff | tree |
| 2007-04-23 |
Michael Coleman | Add greylag_merge. Changes to result pickle format...
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commit | commitdiff | tree |
| 2007-04-21 |
Michael Coleman | Zap .bz2 compression
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commit | commitdiff | tree |
| 2007-04-21 |
Michael Coleman | Update some unit tests.
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commit | commitdiff | tree |
| 2007-04-21 |
Michael Coleman | Rename python scripts to make them importable.
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commit | commitdiff | tree |
| 2007-04-21 |
Michael Coleman | Eliminate spectra w/candidates statistic.
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commit | commitdiff | tree |
| 2007-04-20 |
Michael Coleman | add proper duplicate peptide merging to -grind; plus...
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commit | commitdiff | tree |
| 2007-04-20 |
Michael Coleman | Check sequence db locus name uniqueness
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commit | commitdiff | tree |
| 2007-04-20 |
Michael Coleman | Add basic consistency check for spectrum indices
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commit | commitdiff | tree |
| 2007-04-20 |
Michael Coleman | Change parent tolerance to mz units (scaling by charge)
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commit | commitdiff | tree |
| 2007-04-20 |
Michael Coleman | update TODO list
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commit | commitdiff | tree |
| 2007-04-19 |
Michael Coleman | greylag-sqt: order output by spec number, plus bug...
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commit | commitdiff | tree |
| 2007-04-19 |
Michael Coleman | Merge redundant peptides, in a hacky way.
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commit | commitdiff | tree |
| 2007-04-19 |
Michael Coleman | Rudimentary SQT file generation works; plus other fixes...
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commit | commitdiff | tree |
| 2007-04-18 |
Michael Coleman | basic search runs (w/pickle output only)
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commit | commitdiff | tree |
| 2007-04-13 |
Michael Coleman | filtering bug fixes; basic filtering now works
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commit | commitdiff | tree |
| 2007-04-13 |
Michael Coleman | do MyriMatch-style filtering; add min/max parent mass...
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commit | commitdiff | tree |
| 2007-04-11 |
Michael Coleman | revamped param file; spectrum slice reading; spec index...
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commit | commitdiff | tree |
| 2007-04-10 |
Michael Coleman | rename uniprocess search program to greylag-grind
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commit | commitdiff | tree |
| 2007-04-10 |
Michael Coleman | greylag-index-spectra: check for spectrum name order...
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commit | commitdiff | tree |
| 2007-04-10 |
Michael Coleman | greylag: add --version flag
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commit | commitdiff | tree |
| 2007-04-10 |
Michael Coleman | new command greylag-index-spectra (trivial ms2 offset...
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commit | commitdiff | tree |
| 2007-04-09 |
Michael Coleman | begin redesign after reading Tabb et al paper re Myrimatch
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commit | commitdiff | tree |
| 2007-04-09 |
Michael Coleman | use pid in profile filenames, so multiple profiles...
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commit | commitdiff | tree |
| 2007-03-09 |
Michael Coleman | Fix printf vs size_t portability buglet.
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commit | commitdiff | tree |
| 2007-03-09 |
Michael Coleman | Assume 'greylag' in $PATH, rather than explicitly naming
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commit | commitdiff | tree |
| 2007-03-09 |
Michael Coleman | Makefile fixups: -fPIC, install greylag-mp, etc
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commit | commitdiff | tree |
| 2007-03-09 |
Michael Coleman | Choose default output filename based on parameter filename.
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commit | commitdiff | tree |
| 2007-03-09 |
Michael Coleman | Add yeast database for testing, and some tests.
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commit | commitdiff | tree |
| 2007-03-09 |
Michael Coleman | Add -P option to override XML parameters on command...
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commit | commitdiff | tree |
| 2007-03-09 |
Michael Coleman | add yeast database
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commit | commitdiff | tree |
| 2007-03-09 |
Michael Coleman | Add greylag-mp framework and a few tests.
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commit | commitdiff | tree |
| 2007-03-09 |
Michael Coleman | Disallow '%' in --part-prefix.
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commit | commitdiff | tree |
| 2007-03-08 |
Michael Coleman | New script greylag-mp.py: simple multiprocessing wrapper
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commit | commitdiff | tree |
| 2007-03-08 |
Michael Coleman | Add test input files, plus ok results
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commit | commitdiff | tree |
| 2007-03-08 |
Michael Coleman | Add better error checking of ms2 input, plus more tests.
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commit | commitdiff | tree |
| 2007-03-08 |
Michael Coleman | test: Implement combination test framework
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commit | commitdiff | tree |
| 2007-03-08 |
Michael Coleman | Makefile: remove some test tmp files, change nose flags
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commit | commitdiff | tree |
| 2007-03-08 |
Michael Coleman | Add more tests (cgreylag spectrum functions, small...
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commit | commitdiff | tree |
| 2007-03-08 |
Michael Coleman | greylag.py: Don't exit on error unless we're __main__
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commit | commitdiff | tree |
| 2007-03-08 |
Michael Coleman | whitespace cleanups
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commit | commitdiff | tree |
| 2007-03-06 |
Michael Coleman | Use contextlib.closing to close zopen handles
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commit | commitdiff | tree |
| 2007-03-06 |
Michael Coleman | Add basic unit test suite, plus minor bugfixes
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commit | commitdiff | tree |
| 2007-03-05 |
Michael Coleman | Merge branch 'python2.5' into tests
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commit | commitdiff | tree |
| 2007-03-05 |
Michael Coleman | pass program args via main(), for ease of testing
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commit | commitdiff | tree |
| 2007-03-05 |
Michael Coleman | rename Makefile 'test' target to 'check', per GNU
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commit | commitdiff | tree |
| 2007-03-05 |
Michael Coleman | Use with+contextlib to close lists of open files
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commit | commitdiff | tree |
| 2007-03-04 |
Michael Coleman | Add basic doctests, plus Makefile 'test' target
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commit | commitdiff | tree |
| 2007-03-03 |
Michael Coleman | remove unneeded logging shutdown call, syntax cleanup
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commit | commitdiff | tree |
| 2007-03-03 |
Michael Coleman | Use new python2.5 features (with, defaultdict, etc)
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commit | commitdiff | tree |
| 2007-03-03 |
Michael Coleman | .gitignore: *.pyc, *.pyo
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commit | commitdiff | tree |
| 2007-03-02 |
Michael Coleman | Upgrade to Python 2.5 (now required)
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commit | commitdiff | tree |
| 2007-03-01 |
Michael Coleman | add .gitignore; minor TODO update
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commit | commitdiff | tree |
| 2007-02-27 |
Michael Coleman | source code cleanups (remove keywords, bad whitespace)
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commit | commitdiff | tree |
| 2007-01-26 |
Michael Coleman | checkpoint
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commit | commitdiff | tree |
| 2007-01-25 |
Michael Coleman | checkpoint
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commit | commitdiff | tree |
| 2007-01-23 |
Michael Coleman | checkpoint, in midst of moving peptide loop inward
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commit | commitdiff | tree |
| 2007-01-23 |
Michael Coleman | added --estimate, better running status, fixes
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commit | commitdiff | tree |
| 2007-01-19 |
Michael Coleman | basic fx, now dbg
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commit | commitdiff | tree |
