| 2008-04-28 |
Michael Coleman | validate: add --no-saturation flag, back to binary...
|
commit | commitdiff | tree |
| 2008-04-22 |
Michael Coleman | Merge branch 'bug-mark-fp'
|
commit | commitdiff | tree |
| 2008-04-22 |
Michael Coleman | validate: minor improvement to FDR adjustment
|
commit | commitdiff | tree |
| 2008-04-18 |
Michael Coleman | fix: keep track of match mods instead of using delta...
|
commit | commitdiff | tree |
| 2008-04-18 |
Michael Coleman | doc: clarify correctness goal
|
commit | commitdiff | tree |
| 2008-04-18 |
Michael Coleman | Merge commit 'val-pr^'
|
commit | commitdiff | tree |
| 2008-04-17 |
Michael Coleman | update Debian/Ubuntu package dependency doc
|
commit | commitdiff | tree |
| 2008-04-15 |
Michael Coleman | fix read/write of pickles in binary mode
|
commit | commitdiff | tree |
| 2008-04-15 |
Michael Coleman | greylag-validate: adjust precision of float output
|
commit | commitdiff | tree |
| 2008-04-15 |
Michael Coleman | Merge branch 'val-pr'
|
commit | commitdiff | tree |
| 2008-04-14 |
Michael Coleman | greylag-validate: fix delta bug, mv to generators,...
|
commit | commitdiff | tree |
| 2008-04-11 |
Michael Coleman | add TOO doc on mod combination generation, depth limit
|
commit | commitdiff | tree |
| 2008-04-07 |
Michael Coleman | trivial reformat
|
commit | commitdiff | tree |
| 2008-04-07 |
Michael Coleman | fix: clear previous state in initialize_spectrum_parameters
|
commit | commitdiff | tree |
| 2008-04-07 |
Michael Coleman | add parameter 'mass_regime_debug_delta' (debugging...
|
commit | commitdiff | tree |
| 2008-04-02 |
Michael Coleman | documentation fixes
|
commit | commitdiff | tree |
| 2008-03-26 |
Michael Coleman | read/write pickle files in binary mode
|
commit | commitdiff | tree |
| 2008-03-25 |
Michael Coleman | greylag-chase: abort on no listeners
|
commit | commitdiff | tree |
| 2008-03-21 |
Michael Coleman | disable gc, kills greylag-sqt/merge performance
|
commit | commitdiff | tree |
| 2008-03-21 |
Michael Coleman | allow greylag-validate to run without being "installed"
|
commit | commitdiff | tree |
| 2008-03-20 |
Michael Coleman | Makefile: add install_scripts target
|
commit | commitdiff | tree |
| 2008-03-19 |
Michael Coleman | greylag-sqt: emit better legacy SQT headers, to support...
|
commit | commitdiff | tree |
| 2008-03-19 |
Michael Coleman | fix omission of sqt header lines
|
commit | commitdiff | tree |
| 2008-03-19 |
Michael Coleman | fix greylag-sqt to handle unmarked mods
|
commit | commitdiff | tree |
| 2008-03-18 |
Michael Coleman | add --kill flag to greylag-validate
|
commit | commitdiff | tree |
| 2008-03-18 |
Michael Coleman | new "rally" master/slave parallel search architecture
|
commit | commitdiff | tree |
| 2008-02-29 |
Michael Coleman | incomplete cut at documentation, plus small test cases
|
commit | commitdiff | tree |
| 2008-01-30 |
Michael Coleman | Minor cosmetic changes. Some compile flag cleanups.
|
commit | commitdiff | tree |
| 2008-01-14 |
Michael Coleman | change 'grind' -> 'chase'
|
commit | commitdiff | tree |
| 2007-12-07 |
Michael Coleman | Install to our 64-bit directory by default.
|
commit | commitdiff | tree |
| 2007-12-07 |
Michael Coleman | Switch to GPLv3 and fix up copyright notices a bit.
|
commit | commitdiff | tree |
| 2007-12-07 |
Michael Coleman | Output flanking peptide residues (A.BCD.E instead of...
|
commit | commitdiff | tree |
| 2007-12-06 |
Michael Coleman | Add grind --skip-if-done flag.
|
commit | commitdiff | tree |
| 2007-11-27 |
Michael Coleman | Add --minimum-trypticity flag, replacing --laf (peptide...
|
commit | commitdiff | tree |
| 2007-11-26 |
Michael Coleman | trivial cleanup
|
commit | commitdiff | tree |
| 2007-06-13 |
Michael Coleman | add greylag-validate (derived from sqt_filter.py)
|
commit | commitdiff | tree |
| 2007-06-12 |
Michael Coleman | sqt-filter: add temporary --laf argument to filter...
|
commit | commitdiff | tree |
| 2007-05-15 |
Michael Coleman | fix FDR/FPR confusion, additional debug lines
|
commit | commitdiff | tree |
| 2007-05-10 |
Michael Coleman | omit/default unneeded fields in glw files
|
commit | commitdiff | tree |
| 2007-05-09 |
Michael Coleman | don't gzip glw files--it's slower (at least in Python)
|
commit | commitdiff | tree |
| 2007-05-08 |
Michael Coleman | sqt-filter: always warn if we couldn't calculate a...
|
commit | commitdiff | tree |
| 2007-05-08 |
Michael Coleman | sqt-filter: implement --mark, --reset-marks; plus bug...
|
commit | commitdiff | tree |
| 2007-05-07 |
Michael Coleman | use cPickle 'fast' flag to reduce space/time for glw...
|
commit | commitdiff | tree |
| 2007-05-07 |
Michael Coleman | update TODO list
|
commit | commitdiff | tree |
| 2007-05-07 |
Michael Coleman | sqt-filter: only print stats on --verbose
|
commit | commitdiff | tree |
| 2007-05-07 |
Michael Coleman | sqt-filter: rearrange and clean up code
|
commit | commitdiff | tree |
| 2007-05-07 |
Michael Coleman | sqt-filter: filter SQT files by FPR (incomplete version)
|
commit | commitdiff | tree |
| 2007-05-04 |
Michael Coleman | change filename suffix gwr -> glw; adjust SGE virtual_free...
|
commit | commitdiff | tree |
| 2007-05-04 |
Michael Coleman | update TODO list
|
commit | commitdiff | tree |
| 2007-05-04 |
Michael Coleman | bug fix: don't merge spectrum 0002.0002.1 from different...
|
commit | commitdiff | tree |
| 2007-05-03 |
Michael Coleman | zap NOTHROW in C++ code; no apparent speedup
|
commit | commitdiff | tree |
| 2007-05-02 |
Michael Coleman | update TODO list
|
commit | commitdiff | tree |
| 2007-05-02 |
Michael Coleman | minor bug fix: assertion was tripping because it was...
|
commit | commitdiff | tree |
| 2007-05-02 |
Michael Coleman | Add cleavage params, minor cleanups
|
commit | commitdiff | tree |
| 2007-05-01 |
Michael Coleman | update TODO list
|
commit | commitdiff | tree |
| 2007-04-30 |
Michael Coleman | Add peak cache, for speed. (buys 14% improvement-...
|
commit | commitdiff | tree |
| 2007-04-30 |
Michael Coleman | Inline update_p_mass (simpler and faster)
|
commit | commitdiff | tree |
| 2007-04-30 |
Michael Coleman | Re-enable specific cleavage; code cleanup
|
commit | commitdiff | tree |
| 2007-04-30 |
Michael Coleman | greylag-grind: add 'enable_pca_mods' parameter
|
commit | commitdiff | tree |
| 2007-04-30 |
Michael Coleman | split search_peptide from search_run (non-specific...
|
commit | commitdiff | tree |
| 2007-04-26 |
Michael Coleman | greylag-process: default to 1100 parts (good for our...
|
commit | commitdiff | tree |
| 2007-04-26 |
Michael Coleman | update TODO list
|
commit | commitdiff | tree |
| 2007-04-26 |
Michael Coleman | Bug fixes: deterministic order of H lines, greylag...
|
commit | commitdiff | tree |
| 2007-04-25 |
Michael Coleman | minor test fix; update TODO list
|
commit | commitdiff | tree |
| 2007-04-24 |
Michael Coleman | greylag-merge: add --files-on-stdin flag, to handle...
|
commit | commitdiff | tree |
| 2007-04-24 |
Michael Coleman | greylag-process: don't rely on qsub status--check output...
|
commit | commitdiff | tree |
| 2007-04-24 |
Michael Coleman | greylag-process: explicitly specify shell
|
commit | commitdiff | tree |
| 2007-04-24 |
Michael Coleman | Use greylag-python as the python interpreter.
|
commit | commitdiff | tree |
| 2007-04-23 |
Michael Coleman | update TODO list
|
commit | commitdiff | tree |
| 2007-04-23 |
Michael Coleman | greylag-grind: no-spectra bug fix; *.gwr filename convention
|
commit | commitdiff | tree |
| 2007-04-23 |
Michael Coleman | greylag-merge: fixed false warnings on varying metadata
|
commit | commitdiff | tree |
| 2007-04-23 |
Michael Coleman | greylag-process now works
|
commit | commitdiff | tree |
| 2007-04-23 |
Michael Coleman | Explicitly run scripts with command 'python2.5'
|
commit | commitdiff | tree |
| 2007-04-23 |
Michael Coleman | Use "configuration file" instead of "parameter file".
|
commit | commitdiff | tree |
| 2007-04-20 |
Michael Coleman | add proper duplicate peptide merging to -grind; plus...
|
commit | commitdiff | tree |
| 2007-04-19 |
Michael Coleman | greylag-sqt: order output by spec number, plus bug...
|
commit | commitdiff | tree |
| 2007-04-19 |
Michael Coleman | Merge redundant peptides, in a hacky way.
|
commit | commitdiff | tree |
| 2007-04-13 |
Michael Coleman | filtering bug fixes; basic filtering now works
|
commit | commitdiff | tree |
| 2007-04-11 |
Michael Coleman | revamped param file; spectrum slice reading; spec index...
|
commit | commitdiff | tree |
| 2007-04-10 |
Michael Coleman | rename uniprocess search program to greylag-grind
|
commit | commitdiff | tree |
| 2007-04-10 |
Michael Coleman | greylag-index-spectra: check for spectrum name order...
|
commit | commitdiff | tree |
| 2007-04-10 |
Michael Coleman | greylag: add --version flag
|
commit | commitdiff | tree |
| 2007-04-10 |
Michael Coleman | new command greylag-index-spectra (trivial ms2 offset...
|
commit | commitdiff | tree |
| 2007-04-09 |
Michael Coleman | begin redesign after reading Tabb et al paper re Myrimatch
|
commit | commitdiff | tree |
| 2007-04-09 |
Michael Coleman | use pid in profile filenames, so multiple profiles...
|
commit | commitdiff | tree |
| 2007-03-09 |
Michael Coleman | Fix printf vs size_t portability buglet.
|
commit | commitdiff | tree |
| 2007-03-09 |
Michael Coleman | Assume 'greylag' in $PATH, rather than explicitly naming
|
commit | commitdiff | tree |
| 2007-03-09 |
Michael Coleman | Makefile fixups: -fPIC, install greylag-mp, etc
|
commit | commitdiff | tree |
| 2007-03-09 |
Michael Coleman | Choose default output filename based on parameter filename.
|
commit | commitdiff | tree |
| 2007-03-09 |
Michael Coleman | Add yeast database for testing, and some tests.
|
commit | commitdiff | tree |
| 2007-03-09 |
Michael Coleman | Add -P option to override XML parameters on command...
|
commit | commitdiff | tree |
| 2007-03-09 |
Michael Coleman | add yeast database
|
commit | commitdiff | tree |
| 2007-03-09 |
Michael Coleman | Add greylag-mp framework and a few tests.
|
commit | commitdiff | tree |
| 2007-03-09 |
Michael Coleman | Disallow '%' in --part-prefix.
|
commit | commitdiff | tree |
| 2007-03-08 |
Michael Coleman | New script greylag-mp.py: simple multiprocessing wrapper
|
commit | commitdiff | tree |
| 2007-03-08 |
Michael Coleman | Add test input files, plus ok results
|
commit | commitdiff | tree |
| 2007-03-08 |
Michael Coleman | Add better error checking of ms2 input, plus more tests.
|
commit | commitdiff | tree |
| 2007-03-08 |
Michael Coleman | test: Implement combination test framework
|
commit | commitdiff | tree |
| 2007-03-08 |
Michael Coleman | Makefile: remove some test tmp files, change nose flags
|
commit | commitdiff | tree |
| 2007-03-06 |
Michael Coleman | Use contextlib.closing to close zopen handles
|
commit | commitdiff | tree |
