| 2007-06-12 |
Michael Coleman | sqt-filter: add temporary --laf argument to filter...
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commit | commitdiff | tree |
| 2007-05-15 |
Michael Coleman | fix FDR/FPR confusion, additional debug lines
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commit | commitdiff | tree |
| 2007-05-10 |
Michael Coleman | omit/default unneeded fields in glw files
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commit | commitdiff | tree |
| 2007-05-09 |
Michael Coleman | don't gzip glw files--it's slower (at least in Python)
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commit | commitdiff | tree |
| 2007-05-08 |
Michael Coleman | sqt-filter: always warn if we couldn't calculate a...
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commit | commitdiff | tree |
| 2007-05-08 |
Michael Coleman | sqt-filter: implement --mark, --reset-marks; plus bug...
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commit | commitdiff | tree |
| 2007-05-07 |
Michael Coleman | use cPickle 'fast' flag to reduce space/time for glw...
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commit | commitdiff | tree |
| 2007-05-07 |
Michael Coleman | update TODO list
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commit | commitdiff | tree |
| 2007-05-07 |
Michael Coleman | sqt-filter: only print stats on --verbose
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commit | commitdiff | tree |
| 2007-05-07 |
Michael Coleman | sqt-filter: rearrange and clean up code
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commit | commitdiff | tree |
| 2007-05-07 |
Michael Coleman | sqt-filter: filter SQT files by FPR (incomplete version)
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commit | commitdiff | tree |
| 2007-05-04 |
Michael Coleman | change filename suffix gwr -> glw; adjust SGE virtual_free...
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commit | commitdiff | tree |
| 2007-05-04 |
Michael Coleman | update TODO list
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commit | commitdiff | tree |
| 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 |
| 2007-05-02 |
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 |
| 2007-05-01 |
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 |
| 2007-04-26 |
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 |
| 2007-04-25 |
Michael Coleman | minor test fix; update TODO list
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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 |
| 2007-04-23 |
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 |
| 2007-04-20 |
Michael Coleman | add proper duplicate peptide merging to -grind; plus...
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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 |
| 2007-04-13 |
Michael Coleman | filtering bug fixes; basic filtering now works
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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 |
| 2007-03-06 |
Michael Coleman | Use contextlib.closing to close zopen handles
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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 |
| 2007-03-02 |
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 |
| 2007-01-19 |
Michael Coleman | checkpoint
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commit | commitdiff | tree |
| 2007-01-18 |
Michael Coleman | checkpoint
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commit | commitdiff | tree |
| 2007-01-17 |
Michael Coleman | checkpoint
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commit | commitdiff | tree |
| 2007-01-17 |
Michael Coleman | checkpoint
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commit | commitdiff | tree |
| 2007-01-16 |
Michael Coleman | checkpoint
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commit | commitdiff | tree |
| 2007-01-12 |
Michael Coleman | checkpoint
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commit | commitdiff | tree |
| 2007-01-11 |
Michael Coleman | checkpoint
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commit | commitdiff | tree |
| 2007-01-10 |
Michael Coleman | checkpoint
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commit | commitdiff | tree |
| 2007-01-09 |
Michael Coleman | new mod parsing, reformat, etc
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commit | commitdiff | tree |
| 2007-01-08 |
Michael Coleman | Rearrange code
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commit | commitdiff | tree |
| 2006-12-27 |
Michael Coleman | inversion branch
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commit | commitdiff | tree |
| 2006-12-27 |
Michael Coleman | checkpoint prior to inversion branch
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commit | commitdiff | tree |
| 2006-12-13 |
Michael Coleman | pychecker fixes, target
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commit | commitdiff | tree |
| 2006-12-05 |
Michael Coleman | add COPYING and --copyright flag
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commit | commitdiff | tree |
| 2006-11-03 |
Michael Coleman | checkpoint after talk
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commit | commitdiff | tree |
| 2006-10-26 |
Michael Coleman | faster peptide generation working (?)
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commit | commitdiff | tree |
| 2006-10-26 |
Michael Coleman | checkpoint, faster peptide generation almost working
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commit | commitdiff | tree |
| 2006-10-25 |
Michael Coleman | checkpoint
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commit | commitdiff | tree |
| 2006-10-24 |
Michael Coleman | checkpoint
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commit | commitdiff | tree |
| 2006-10-19 |
Michael Coleman | this version tests well against xt on a real example
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commit | commitdiff | tree |
| 2006-10-19 |
Michael Coleman | checkpoint, parts bug fixed?
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commit | commitdiff | tree |
| 2006-10-18 |
Michael Coleman | checkpoint
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commit | commitdiff | tree |
| 2006-10-17 |
Michael Coleman | checkpoint, protein_expect bug present?
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commit | commitdiff | tree |
| 2006-10-16 |
Michael Coleman | split mass speedup
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commit | commitdiff | tree |
