| 2008-09-12 |
Michael Coleman | bump version and add new release notes
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commit | commitdiff | tree |
| 2008-09-12 |
Michael Coleman | doc: security caveat, performance equivalence, minor...
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commit | commitdiff | tree |
| 2008-09-11 |
Michael Coleman | install greylag-call-proteins
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commit | commitdiff | tree |
| 2008-09-11 |
Michael Coleman | minor change to match MyriMatch scoring better
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commit | commitdiff | tree |
| 2008-09-11 |
Michael Coleman | add (temporary?) debugging code for peak scoring, etc
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commit | commitdiff | tree |
| 2008-09-11 |
Michael Coleman | rally: batch size changes (use larger batches)
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commit | commitdiff | tree |
| 2008-09-11 |
Michael Coleman | chase: add DIE command, for debugging/etc
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commit | commitdiff | tree |
| 2008-09-11 |
Michael Coleman | validate: default to no peptide saturation
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commit | commitdiff | tree |
| 2008-09-09 |
Michael Coleman | rally: change default for 'maximum_missed_cleavage_sites...
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commit | commitdiff | tree |
| 2008-09-09 |
Michael Coleman | validate: disable remove_charge_aliases for now
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commit | commitdiff | tree |
| 2008-09-04 |
Michael Coleman | score: fix bug in peak scoring (plus cleanup)
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commit | commitdiff | tree |
| 2008-09-04 |
Michael Coleman | score: generate N b and y ions, instead of N-1
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commit | commitdiff | tree |
| 2008-09-04 |
Michael Coleman | peak TIC filter: don't break ties, just keep them all
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commit | commitdiff | tree |
| 2008-09-04 |
Michael Coleman | chase: fix bug in residue statistics
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commit | commitdiff | tree |
| 2008-09-02 |
Michael Coleman | greylag_call_proteins: parsimoniously assign peptides...
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commit | commitdiff | tree |
| 2008-09-02 |
Michael Coleman | validate: --minimum-sp-length filter, 'both' -> 'decoy...
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commit | commitdiff | tree |
| 2008-09-02 |
Michael Coleman | doc: minor changes to performance example
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commit | commitdiff | tree |
| 2008-08-26 |
Michael Coleman | validate: add --minimum-unmodified-proportion filter
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commit | commitdiff | tree |
| 2008-08-26 |
Michael Coleman | sqt: bugfix: handle static terminii output
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commit | commitdiff | tree |
| 2008-08-26 |
Michael Coleman | shuffle: add --decoy-count option--multiple decoys...
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commit | commitdiff | tree |
| 2008-08-15 |
Michael Coleman | validate: warn on same spectrum at multiple charges
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commit | commitdiff | tree |
| 2008-08-15 |
Michael Coleman | validate: disable prefix saturation
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commit | commitdiff | tree |
| 2008-08-14 |
Michael Coleman | validate: saturate on unstripped peptides (instead...
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commit | commitdiff | tree |
| 2008-08-14 |
Michael Coleman | validate: properly keep/omit candidate matches by mass...
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commit | commitdiff | tree |
| 2008-08-13 |
Michael Coleman | rally: use a batch size of one spectrum
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commit | commitdiff | tree |
| 2008-08-13 |
Michael Coleman | sqt: fix bug in merging of modifications having same...
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commit | commitdiff | tree |
| 2008-08-08 |
Michael Coleman | Merge branch 'merge-fix'
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commit | commitdiff | tree |
| 2008-08-07 |
Michael Coleman | validate: warn if no decoys seen in input (-> bogus...
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commit | commitdiff | tree |
| 2008-08-07 |
Michael Coleman | sqt: use score for SpScore, too, for backward compatibility
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commit | commitdiff | tree |
| 2008-08-07 |
Michael Coleman | doc: add some profiling statistics to front page
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commit | commitdiff | tree |
| 2008-08-07 |
Michael Coleman | sqt: emit backward-compatible 'DiffMod' lines for terminal...
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commit | commitdiff | tree |
| 2008-08-07 |
Michael Coleman | chase: fix to allow --profile to dump correctly on...
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commit | commitdiff | tree |
| 2008-08-06 |
Michael Coleman | sqt: fix bug in --enhanced output
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commit | commitdiff | tree |
| 2008-08-06 |
Michael Coleman | merge: check that output file is not in inputs
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commit | commitdiff | tree |
| 2008-07-23 |
Michael Coleman | merge: zap --files-on-stdin flag (unneeded)
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commit | commitdiff | tree |
| 2008-07-09 |
Michael Coleman | Merge branch 'bootstrap'
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commit | commitdiff | tree |
| 2008-07-09 |
Michael Coleman | validate: handle precursor error option correctly
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commit | commitdiff | tree |
| 2008-06-24 |
Michael Coleman | validate: add --bootstrap (generates single FDR data...
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commit | commitdiff | tree |
| 2008-06-20 |
Michael Coleman | validate: mass filter by M line (not working?)
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commit | commitdiff | tree |
| 2008-06-20 |
Michael Coleman | validate: add --exact-ptms flag
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commit | commitdiff | tree |
| 2008-06-19 |
Michael Coleman | validate: prefer closest mass for multiple modification...
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commit | commitdiff | tree |
| 2008-06-18 |
Michael Coleman | Merge branch 'fix' into orbi
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commit | commitdiff | tree |
| 2008-06-18 |
Michael Coleman | validate: add mass error filter flags
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commit | commitdiff | tree |
| 2008-06-18 |
Michael Coleman | validate: add --mass-error-histogram-bin-width option
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commit | commitdiff | tree |
| 2008-06-18 |
Michael Coleman | validate: add --mass-error-histogram-bin-width option
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commit | commitdiff | tree |
| 2008-06-16 |
Michael Coleman | theory: validation algorithm, technological alternatives
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commit | commitdiff | tree |
| 2008-06-16 |
Michael Coleman | minor cleanups: option metavars, release checklist...
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commit | commitdiff | tree |
| 2008-05-29 |
Michael Coleman | minor release cleanups
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commit | commitdiff | tree |
| 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 |
