| 2008-05-22 |
Michael Coleman | shuffle: add copyright, minor code cleanups
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commit | commitdiff | tree |
| 2008-05-22 |
Michael Coleman | shuffle: add basic Markov shuffle, other minor cleanups
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commit | commitdiff | tree |
| 2008-05-21 |
Michael Coleman | shuffle: use common fasta reader, upcase sequences...
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commit | commitdiff | tree |
| 2008-05-20 |
Michael Coleman | validate: choose the better charge for multiple charge...
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commit | commitdiff | tree |
| 2008-05-20 |
Michael Coleman | validate: fix bug in predicted mass parsing
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commit | commitdiff | tree |
| 2008-05-13 |
Michael Coleman | glw file cleanups: identify spectra by filename/spectrum...
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commit | commitdiff | tree |
| 2008-05-06 |
Michael Coleman | rally: limit open file count
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commit | commitdiff | tree |
| 2008-05-06 |
Michael Coleman | stream processing of spectra
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commit | commitdiff | tree |
| 2008-04-30 |
Michael Coleman | validate: bug fix (listify generator)
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commit | commitdiff | tree |
| 2008-04-30 |
Michael Coleman | validate: fix bug in histogram code (mass_delta, not...
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commit | commitdiff | tree |
| 2008-04-30 |
Michael Coleman | Merge branches 'hist' and 'doc'
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commit | commitdiff | tree |
| 2008-04-30 |
Michael Coleman | add more doc test cases, minor code rearrangement
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commit | commitdiff | tree |
| 2008-04-30 |
Michael Coleman | validate: add mass error histogram option
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commit | commitdiff | tree |
| 2008-04-30 |
Michael Coleman | validate: handle isoleucine/leucine aliasing
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commit | commitdiff | tree |
| 2008-04-30 |
Michael Coleman | fix typo
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commit | commitdiff | tree |
| 2008-04-29 |
Michael Coleman | Merge branch 'n-terminal'
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commit | commitdiff | tree |
| 2008-04-29 |
Michael Coleman | validate: disable maximum-sp-rank filter by default
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commit | commitdiff | tree |
| 2008-04-29 |
Michael Coleman | bump version
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commit | commitdiff | tree |
| 2008-04-29 |
Michael Coleman | validate: rearrange log messages
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commit | commitdiff | tree |
| 2008-04-28 |
Michael Coleman | validate: fix bug (empty output sqt file not deleted)
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commit | commitdiff | tree |
| 2008-04-28 |
Michael Coleman | validate: fix filename bug
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commit | commitdiff | tree |
| 2008-04-28 |
Michael Coleman | validate: add --no-saturation flag, back to binary...
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commit | commitdiff | tree |
| 2008-04-22 |
Michael Coleman | enable potential peptide terminal modifications
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commit | commitdiff | tree |
| 2008-04-22 |
Michael Coleman | Merge branch 'bug-mark-fp'
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commit | commitdiff | tree |
| 2008-04-22 |
Michael Coleman | validate: minor improvement to FDR adjustment
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commit | commitdiff | tree |
| 2008-04-18 |
Michael Coleman | fix: keep track of match mods instead of using delta...
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commit | commitdiff | tree |
| 2008-04-18 |
Michael Coleman | doc: clarify correctness goal
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commit | commitdiff | tree |
| 2008-04-18 |
Michael Coleman | Merge commit 'val-pr^'
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commit | commitdiff | tree |
| 2008-04-17 |
Michael Coleman | update Debian/Ubuntu package dependency doc
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commit | commitdiff | tree |
| 2008-04-15 |
Michael Coleman | fix read/write of pickles in binary mode
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commit | commitdiff | tree |
| 2008-04-15 |
Michael Coleman | greylag-validate: adjust precision of float output
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commit | commitdiff | tree |
| 2008-04-15 |
Michael Coleman | Merge branch 'val-pr'
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commit | commitdiff | tree |
| 2008-04-14 |
Michael Coleman | greylag-validate: fix delta bug, mv to generators,...
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commit | commitdiff | tree |
| 2008-04-11 |
Michael Coleman | add TOO doc on mod combination generation, depth limit
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commit | commitdiff | tree |
| 2008-04-07 |
Michael Coleman | trivial reformat
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commit | commitdiff | tree |
| 2008-04-07 |
Michael Coleman | fix: clear previous state in initialize_spectrum_parameters
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commit | commitdiff | tree |
| 2008-04-07 |
Michael Coleman | add parameter 'mass_regime_debug_delta' (debugging...
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commit | commitdiff | tree |
| 2008-04-02 |
Michael Coleman | documentation fixes
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commit | commitdiff | tree |
| 2008-03-26 |
Michael Coleman | read/write pickle files in binary mode
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commit | commitdiff | tree |
| 2008-03-25 |
Michael Coleman | greylag-chase: abort on no listeners
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commit | commitdiff | tree |
| 2008-03-21 |
Michael Coleman | disable gc, kills greylag-sqt/merge performance
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commit | commitdiff | tree |
| 2008-03-21 |
Michael Coleman | allow greylag-validate to run without being "installed"
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commit | commitdiff | tree |
| 2008-03-20 |
Michael Coleman | Makefile: add install_scripts target
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commit | commitdiff | tree |
| 2008-03-19 |
Michael Coleman | greylag-sqt: emit better legacy SQT headers, to support...
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commit | commitdiff | tree |
| 2008-03-19 |
Michael Coleman | fix omission of sqt header lines
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commit | commitdiff | tree |
| 2008-03-19 |
Michael Coleman | fix greylag-sqt to handle unmarked mods
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commit | commitdiff | tree |
| 2008-03-18 |
Michael Coleman | add --kill flag to greylag-validate
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commit | commitdiff | tree |
| 2008-03-18 |
Michael Coleman | new "rally" master/slave parallel search architecture
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commit | commitdiff | tree |
| 2008-02-29 |
Michael Coleman | incomplete cut at documentation, plus small test cases
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commit | commitdiff | tree |
| 2008-01-30 |
Michael Coleman | Minor cosmetic changes. Some compile flag cleanups.
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commit | commitdiff | tree |
| 2008-01-14 |
Michael Coleman | change 'grind' -> 'chase'
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commit | commitdiff | tree |
| 2007-12-07 |
Michael Coleman | Install to our 64-bit directory by default.
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commit | commitdiff | tree |
| 2007-12-07 |
Michael Coleman | Switch to GPLv3 and fix up copyright notices a bit.
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commit | commitdiff | tree |
| 2007-12-07 |
Michael Coleman | Output flanking peptide residues (A.BCD.E instead of...
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commit | commitdiff | tree |
| 2007-12-06 |
Michael Coleman | Add grind --skip-if-done flag.
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commit | commitdiff | tree |
| 2007-11-27 |
Michael Coleman | Add --minimum-trypticity flag, replacing --laf (peptide...
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commit | commitdiff | tree |
| 2007-11-26 |
Michael Coleman | trivial cleanup
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commit | commitdiff | tree |
| 2007-06-13 |
Michael Coleman | add greylag-validate (derived from sqt_filter.py)
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commit | commitdiff | tree |
| 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 |
