| 2008-05-10 |
Michael Coleman | fix: continue handling candidate spectra after tie
|
commit | commitdiff | tree |
| 2008-05-09 |
Michael Coleman | fix logging statement
|
commit | commitdiff | tree |
| 2008-05-07 |
Michael Coleman | minor logging cleanups, close a file
|
commit | commitdiff | tree |
| 2008-05-07 |
Michael Coleman | Merge branches 'chase-noasync' and 'sp-streaming'
|
commit | commitdiff | tree |
| 2008-05-07 |
Michael Coleman | chase: switch asyncore implementation to socket/generator
|
commit | commitdiff | tree |
| 2008-05-06 |
Michael Coleman | rally: limit open file count
|
commit | commitdiff | tree |
| 2008-05-06 |
Michael Coleman | stream processing of spectra
|
commit | commitdiff | tree |
| 2008-04-30 |
Michael Coleman | validate: bug fix (listify generator)
|
commit | commitdiff | tree |
| 2008-04-30 |
Michael Coleman | validate: fix bug in histogram code (mass_delta, not...
|
commit | commitdiff | tree |
| 2008-04-30 |
Michael Coleman | Merge branches 'hist' and 'doc'
|
commit | commitdiff | tree |
| 2008-04-30 |
Michael Coleman | add more doc test cases, minor code rearrangement
|
commit | commitdiff | tree |
| 2008-04-30 |
Michael Coleman | validate: add mass error histogram option
|
commit | commitdiff | tree |
| 2008-04-30 |
Michael Coleman | validate: handle isoleucine/leucine aliasing
|
commit | commitdiff | tree |
| 2008-04-30 |
Michael Coleman | fix typo
|
commit | commitdiff | tree |
| 2008-04-29 |
Michael Coleman | Merge branch 'n-terminal'
|
commit | commitdiff | tree |
| 2008-04-29 |
Michael Coleman | validate: disable maximum-sp-rank filter by default
|
commit | commitdiff | tree |
| 2008-04-29 |
Michael Coleman | bump version
|
commit | commitdiff | tree |
| 2008-04-29 |
Michael Coleman | validate: rearrange log messages
|
commit | commitdiff | tree |
| 2008-04-29 |
Michael Coleman | validate: switch to proper logging
|
commit | commitdiff | tree |
| 2008-04-29 |
Michael Coleman | validate: automatic saturation fall-back
|
commit | commitdiff | tree |
| 2008-04-29 |
Michael Coleman | validate: add maximum Sp rank limit, make FDR adjustment...
|
commit | commitdiff | tree |
| 2008-04-28 |
Michael Coleman | validate: fix bug (empty output sqt file not deleted)
|
commit | commitdiff | tree |
| 2008-04-28 |
Michael Coleman | validate: fix filename bug
|
commit | commitdiff | tree |
| 2008-04-28 |
Michael Coleman | validate: add --no-saturation flag, back to binary...
|
commit | commitdiff | tree |
| 2008-04-27 |
Michael Coleman | validate: prefix saturation, --output-peptides, adjust...
|
commit | commitdiff | tree |
| 2008-04-26 |
Michael Coleman | validate: add min spectra per locus and saturation...
|
commit | commitdiff | tree |
| 2008-04-24 |
Michael Coleman | validate: reorg code preparing for pr filter, saturation
|
commit | commitdiff | tree |
| 2008-04-22 |
Michael Coleman | enable potential peptide terminal modifications
|
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 |
| 2008-04-22 |
Mike Coleman | validate: FDR adjustment, fix marking of bad charges
|
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 |
| 2008-01-18 |
Michael Coleman | cosmetic cleanups: better messages, var name changes...
|
commit | commitdiff | tree |
| 2008-01-18 |
Michael Coleman | buglet fix: $0 might include whole absolute path
|
commit | commitdiff | tree |
| 2008-01-18 |
Michael Coleman | buglet fix: undefined var on single input glw file
|
commit | commitdiff | tree |
| 2008-01-17 |
Michael Coleman | Don't use the fileinput module to read FASTA files...
|
commit | commitdiff | tree |
| 2008-01-17 |
Michael Coleman | get rid of multipart options for --work-slice and ...
|
commit | commitdiff | tree |
| 2008-01-14 |
Michael Coleman | change 'grind' -> 'chase'
|
commit | commitdiff | tree |
| 2008-01-14 |
Michael Coleman | minor cleanups
|
commit | commitdiff | tree |
| 2008-01-12 |
Michael Coleman | zap 'greylag-python' in favor of just 'python'
|
commit | commitdiff | tree |
| 2008-01-10 |
Michael Coleman | minor wording fixes
|
commit | commitdiff | tree |
| 2007-12-08 |
Michael Coleman | Add methox test case.
|
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 |
| 2007-12-05 |
Michael Coleman | use greylag.q queue and default to 3000 parts
|
commit | commitdiff | tree |
| 2007-12-05 |
Michael Coleman | Implement --list-peptides option.
|
commit | commitdiff | tree |
| 2007-11-28 |
Michael Coleman | greylag-solo: if we're testing, call the corresponding...
|
commit | commitdiff | tree |
| 2007-11-28 |
Michael Coleman | minor code reorg (use new Python if/else operator)
|
commit | commitdiff | tree |
| 2007-11-28 |
Michael Coleman | bug fix: parent mass delta wasn't being added in for...
|
commit | commitdiff | tree |
| 2007-11-27 |
Michael Coleman | Add --minimum-trypticity flag, replacing --laf (peptide...
|
commit | commitdiff | tree |
| 2007-11-27 |
Michael Coleman | Merged sqt-filter into greylag-validate. This version...
|
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 |
| 2007-05-03 |
Michael Coleman | update README and TODO
|
commit | commitdiff | tree |
| 2007-05-03 |
Michael Coleman | rename XTP to GLP
|
commit | commitdiff | tree |
| 2007-05-03 |
Michael Coleman | zap a bit of dead code; cleanups; update TODO list
|
commit | commitdiff | tree |
| 2007-05-03 |
Michael Coleman | update sloccount stats: slightly smaller since redesign (!)
|
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 |
