| 2008-05-29 |
Michael Coleman | Merge commit 'v0.1.2'
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commit | commitdiff | tree |
| 2008-05-29 |
Michael Coleman | document release steps
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commit | commitdiff | tree |
| 2008-05-29 |
Michael Coleman | update todo list
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commit | commitdiff | tree |
| 2008-05-29 |
Michael Coleman | bump version, update release notes
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commit | commitdiff | tree |
| 2008-05-28 |
Michael Coleman | update release notes
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commit | commitdiff | tree |
| 2008-05-28 |
Michael Coleman | doc rearrangement, add install doc and example, beta...
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commit | commitdiff | tree |
| 2008-05-22 |
Michael Coleman | add greylag-flatten-fasta, fix bugs in fasta reader
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commit | commitdiff | tree |
| 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 |
| 2008-05-10 |
Michael Coleman | Merge branch 'slowbisect'
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commit | commitdiff | tree |
| 2008-05-10 |
Michael Coleman | fix: continue handling candidate spectra after tie
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commit | commitdiff | tree |
| 2008-05-10 |
Michael Coleman | add chase_error (better error messages to user), hex...
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commit | commitdiff | tree |
| 2008-05-09 |
Michael Coleman | fix: continue handling candidate spectra after tie
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commit | commitdiff | tree |
| 2008-05-09 |
Michael Coleman | fix logging statement
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commit | commitdiff | tree |
| 2008-05-07 |
Michael Coleman | minor logging cleanups, close a file
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commit | commitdiff | tree |
| 2008-05-07 |
Michael Coleman | Merge branches 'chase-noasync' and 'sp-streaming'
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commit | commitdiff | tree |
| 2008-05-07 |
Michael Coleman | chase: switch asyncore implementation to socket/generator
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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 |
| 2008-04-29 |
Michael Coleman | validate: switch to proper logging
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commit | commitdiff | tree |
| 2008-04-29 |
Michael Coleman | validate: automatic saturation fall-back
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commit | commitdiff | tree |
| 2008-04-29 |
Michael Coleman | validate: add maximum Sp rank limit, make FDR adjustment...
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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 |
| 2008-04-27 |
Michael Coleman | validate: prefix saturation, --output-peptides, adjust...
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commit | commitdiff | tree |
| 2008-04-26 |
Michael Coleman | validate: add min spectra per locus and saturation...
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commit | commitdiff | tree |
| 2008-04-24 |
Michael Coleman | validate: reorg code preparing for pr filter, saturation
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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 |
| 2008-01-18 |
Michael Coleman | cosmetic cleanups: better messages, var name changes...
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commit | commitdiff | tree |
| 2008-01-18 |
Michael Coleman | buglet fix: $0 might include whole absolute path
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commit | commitdiff | tree |
| 2008-01-18 |
Michael Coleman | buglet fix: undefined var on single input glw file
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commit | commitdiff | tree |
| 2008-01-17 |
Michael Coleman | Don't use the fileinput module to read FASTA files...
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commit | commitdiff | tree |
| 2008-01-17 |
Michael Coleman | get rid of multipart options for --work-slice and ...
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commit | commitdiff | tree |
| 2008-01-14 |
Michael Coleman | change 'grind' -> 'chase'
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commit | commitdiff | tree |
| 2008-01-14 |
Michael Coleman | minor cleanups
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commit | commitdiff | tree |
| 2008-01-12 |
Michael Coleman | zap 'greylag-python' in favor of just 'python'
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commit | commitdiff | tree |
| 2008-01-10 |
Michael Coleman | minor wording fixes
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commit | commitdiff | tree |
| 2007-12-08 |
Michael Coleman | Add methox test case.
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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 |
| 2007-12-05 |
Michael Coleman | use greylag.q queue and default to 3000 parts
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commit | commitdiff | tree |
| 2007-12-05 |
Michael Coleman | Implement --list-peptides option.
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commit | commitdiff | tree |
| 2007-11-28 |
Michael Coleman | greylag-solo: if we're testing, call the corresponding...
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commit | commitdiff | tree |
| 2007-11-28 |
Michael Coleman | minor code reorg (use new Python if/else operator)
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commit | commitdiff | tree |
| 2007-11-28 |
Michael Coleman | bug fix: parent mass delta wasn't being added in for...
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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 |
| 2007-11-27 |
Michael Coleman | Merged sqt-filter into greylag-validate. This version...
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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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