github.com/OpenMS/OpenMS commits | Ecosyste.ms: OpenCollective

fix: format assigned to sequences_file

5219c59723264af3d7b7bcf58077e7c995879064 authored almost 5 years ago by M Bernt <[email protected]>

[FIX] make decharger safe for eval order of string manip. stmts

589a8d56514a850829e2d2aff1764e6d2929f0bd authored almost 5 years ago by Julianus Pfeuffer <[email protected]>

Added some if-defined statements around Cmake vars that one might want to set from outside

199d2768be639a51b1c313c0e937440e5cb58c7b authored almost 5 years ago by jpfeuffer <[email protected]>

Update contrib for vs2019

8accd5bc7962c9071bd01c8803bce27b7ed570f8 authored almost 5 years ago by Julianus Pfeuffer <[email protected]>

Update fix_dependencies.rb

2055bfe3529e2a1ae86002853df3bb6c1ad03a06 authored almost 5 years ago by jpfeuffer <[email protected]>

rename comet pin_out tsv (#4438)

4e1e10e40e6e060885e6e54cc7b56e134412cb90 authored almost 5 years ago by M Bernt <[email protected]>

[FIX] fixes underflow (segfault) (#4435)

746ed76cd62a7412eb498a4eadfba129ca342d41 authored almost 5 years ago by Hannes Roest <[email protected]>

[FEATURE] test MSNumpress raw

3dac1547133ffcb8a6dee619f88df9b3756d7ff2 authored almost 5 years ago by Hannes Roest <[email protected]>

[FIX] PrecursorPurity not thread safe yet, keep it single threaded (#4431)

* [FIX] PrecursorPurity not thread safe yet, keep it single threaded

* [FIX] thread safe Prec...

c8e6c324ecc3e84b6490cf42dde9e8d76f8a8ba5 authored almost 5 years ago by Eugen Netz <[email protected]>

Merge pull request #4432 from cbielow/fix_mzXML_forMaxQuant

mzXML: add more attributes which are optional in mzXML but required for MaxQuant

64269cf128bbe222d69f8c70a2e25fd0f6d81472 authored almost 5 years ago by Chris Bielow <[email protected]>

fix atomic compile error & fix scan index

b8aeee4acfd13ab4b3de75a3adb4b9023f20c657 authored almost 5 years ago by Chris Bielow <[email protected]>

check if spec is sorted before using 1st and last peak for m/z low and high.

fe71160efcfd3645bd752b585013ffe8e47a10a7 authored almost 5 years ago by Chris Bielow <[email protected]>

update test

aeb84383bd82e8b65464771d5c76a65cab1c8d34 authored almost 5 years ago by Chris Bielow <[email protected]>

update MQcompat mode

ccf75b52e9a046029fda04cba7fc8efaf0854a58 authored almost 5 years ago by Chris Bielow <[email protected]>

add more attributes which are optional in mzXML but required for MaxQuant

f19f194bfb62fa3cbaa7c57c361f7905c2546492 authored almost 5 years ago by Chris Bielow <[email protected]>

[FIX] OpenPepXL: sort spectra by RT after parallel preprocessing (#4427)

78ade64624e446d55536528a462ea9e15bf52647 authored almost 5 years ago by Eugen Netz <[email protected]>

add missing argument

might fix: https://github.com/OpenMS/OpenMS/issues/4428

1eb621be596579119f541c128c668395abdf1b24 authored almost 5 years ago by M Bernt <[email protected]>

modified the code due to the quant work

1cf0c482d90a5da1d313c83bd8d33854bfc35ca4 authored almost 5 years ago by JeeK <[email protected]>

CVInspector: the mapping_file argument is mandatory

a38a2bf5f685ba7ef3556f53d0cc14c1a4003994 authored almost 5 years ago by M Bernt <[email protected]>

fix typo

08a521e5605b2b9c52fcb610475c4ef1a9d38451 authored almost 5 years ago by M Bernt <[email protected]>

restore .tab extension for temporary files

1763f79fc5b11d3ee5d4d9f2e45c92bb297656a8 authored almost 5 years ago by M Bernt <[email protected]>

Merge pull request #4424 from cbielow/fix_mzXML_forMaxQuant

Fix mz xml for max quant

d86cc483929c61b631c2501688de8a6d374493aa authored almost 5 years ago by Chris Bielow <[email protected]>

Merge pull request #4422 from jpfeuffer/fix/clangc17streampos

[FIX] Clang and C17 stream_pos

0d2b5af2878f1a646d513d610543d58122c6e89a authored almost 5 years ago by Chris Bielow <[email protected]>

Had problems with unresponsive threadpools when using imap right away

3f31d5241add8940e35718c0fff9782ca75ab329 authored almost 5 years ago by jpfeuffer <[email protected]>

Merge pull request #4415 from enetz/feature/OPXL_opt

[FEATURE] OpenPepXL score and runtime optimization

dd18b9e4ceeb15782f93735a87bd686fdbd0cbe9 authored almost 5 years ago by Eugen Netz <[email protected]>

Merge pull request #4409 from enetz/feature/parallelized_precursor_purity

[FEATURE] parallelized PrecursorPurity and spectrum preprocessing in OpenPepXL

f49dc83fae6d13cfd2ebbd9458fa33fe989532b8 authored almost 5 years ago by Eugen Netz <[email protected]>

fix our old mzXML files (where activation method might have gone missing)

c83503293b2bb714229c1077248be97df0bfd167 authored almost 5 years ago by Chris Bielow <[email protected]>

add activationMethod to Precursor when reading mzXML (#4423)

7a6d0ccc57724bbad2766b199d6d92c74e23f0c8 authored almost 5 years ago by Chris Bielow <[email protected]>

add activationMethod to Precursor when reading mzXML

bb461c8d4089cc2a1b3e772258a4a4309cb43ef4 authored almost 5 years ago by Chris Bielow <[email protected]>

[FIX] Clang and C17 stream_pos

0c275649112e6045b51d9dcd21bc78d6d4755619 authored almost 5 years ago by Julianus Pfeuffer <[email protected]>

[FIX] added critical section to parallel loop

094d5fb86b8867bcd20eb2eb58ec640bb08bc1f5 authored almost 5 years ago by enetz <[email protected]>

Make difference between Qt GUI/noGUI dependencies in examples

bcee938423da70ba833c2ba7f8f1cef80fde2cf9 authored almost 5 years ago by jpfeuffer <[email protected]>

[INTERNAL] use pdqsort_branchless with a branchless comparator

4fdfcf3a5d94dc565f5efec65f531d65442eb574 authored almost 5 years ago by enetz <[email protected]>

[TEST] added test cases to PrecursorPurity class test

45ed843a61d6aa78d217970f93b37ba5404195f8 authored almost 5 years ago by enetz <[email protected]>

[FIX] PrecursorPurity skips PeakMaps with non-existent or non-unique NativeIDs

e7d9b761f3343d0de4743098c251fe135760604c authored almost 5 years ago by enetz <[email protected]>

[INTERNAL] removed inline operators from non-trivial functions

6a08304660718a21d6e658e44e5cbab301348bc6 authored almost 5 years ago by enetz <[email protected]>

[INTERNAL] removed redundant inline operators

43af9c431b389d79c0256135510ea5871271cdd8 authored almost 5 years ago by enetz <[email protected]>

Merge branch 'develop' of https://github.com/OpenMS/OpenMS into feature/OPXL_opt

Conflicts:
src/tests/topp/OpenPepXL_output.idXML
src/tests/topp/OpenPepXL_output.mzid
src/tes...

c3c63e3ccf9972958ed3081086d25bfbc5e35da5 authored almost 5 years ago by enetz <[email protected]>

Feature/parallel tagger (#4413)

* [FEATURE] Prallellized Sequence Tagging

* [FEATURE] OpenPepXLLF: using Tagger and more effi...

cb99c8f8ed9741d7d060ce067888481e692dac3f authored almost 5 years ago by Eugen Netz <[email protected]>

[TEST] added additional cases to PrecursorPurity class test

c3e2f8c7a08160b0829d8fc7ed1858488def89ed authored almost 5 years ago by enetz <[email protected]>

[INTERNAL] made PrecursorPurity a bit more robust

d7389968f7096985081f6886d4f6ac134125be4c authored almost 5 years ago by enetz <[email protected]>

[INTERNAL] removed unused variable

07134286f6b6cf7d51942a6e9dc786bed12e24da authored almost 5 years ago by enetz <[email protected]>

[INTERNAL, PYOPENMS] fixed constructor in python bindings

415ac459f36c135ebafd4a1c4167dc8351fa1e24 authored almost 5 years ago by enetz <[email protected]>

[INTERNAL] using a lambda comparator

d85e128ee572d9bc066f7c6b894e64ee0ee45d2d authored almost 5 years ago by enetz <[email protected]>

Merge branch 'id-file-format' of https://github.com/hendrikweisser/OpenMS into id-file-format

4dfa9a958672e7bb115def1ea7e9f8888a397a35 authored almost 5 years ago by Hendrik Weisser <[email protected]>

[API] IdentificationData: new class storing input files, incl. primary run and experimental design information

3fd8a31fb3ebd60c8bc9c8182f201c6d9a74ce2d authored almost 5 years ago by Hendrik Weisser <[email protected]>

SpectraSTSearchAdapter: xls -> tsv

24fb245a5c1b924147b43668dc388bbb47056e71 authored almost 5 years ago by M Bernt <[email protected]>

PercolatorAdapter: rename tab to tsv

6d827a1d9f086aee4c09546c98ccdcf46e32a6c5 authored almost 5 years ago by M Bernt <[email protected]>

[FIX] use boost pdqsort only with boost 1.67 or higher

24d3c65a018b88d88b0f066f7a5794c6db563f37 authored almost 5 years ago by enetz <[email protected]>

[INTERNAL] SimpleTSGXLMS: using emplace_back to add peaks

a1c5f6c571b976bd84dd9e5a1f750a37a284b851 authored almost 5 years ago by enetz <[email protected]>

[FEATURE] SimpleTSGXLMS: simplification and optimization

This class is the main bottleneck in OpenPepXL runtime.

eb5bb2dd8320ed94334221cec95a99f2b5cc2b4c authored almost 5 years ago by enetz <[email protected]>

[TEST] updated OpenPepXL test files

5a80de74f7bc49e7688e588f3c8cb785f41e5105 authored almost 5 years ago by enetz <[email protected]>

[FEATURE] some optimization of OpenPepXL

removed mostly useless peak types
parallellized a post-processing section
reserved vector sizes ...

0fc414d45f8b1bc52039def151c70607c2a4b88f authored almost 5 years ago by enetz <[email protected]>

[TEST, COMMENT] added benchmarks for spectrum generation runtime

7b484165276273339c24f92644ce8a5f68ad28f8 authored almost 5 years ago by enetz <[email protected]>

[FIX] fixed a numerical issue in XQuestScores

ca1c49c91352113f747ab3c283b29f87203ffaeb authored almost 5 years ago by enetz <[email protected]>

[INTERNAL] added inlines in SimpleTSGXLMS

9c6fc09d6f7235cc92f5802832d3799441d091d2 authored almost 5 years ago by enetz <[email protected]>

[FIX] use references in Comparator

e0f54fb34795dd7bc394b53a5d27718de9962787 authored almost 5 years ago by enetz <[email protected]>

[FIX] PrecursorPurity: removed unused attribute

0f6f1784b05aa62f862a2aa1e1678d2f3802885a authored almost 5 years ago by enetz <[email protected]>

[API] IdentificationData: new class storing input files, incl. primary run and experimental design information

3f28a51b44000fb3b8e4beac0ddcc9e7fed3e558 authored almost 5 years ago by Hendrik Weisser <[email protected]>

[FEATURE] added 'empty' function to IdentificationData; changed storage of data queries to enable updates to them

cdc17f77d65d83f9dcdb4c2bb3b260045ece05b6 authored almost 5 years ago by Hendrik Weisser <[email protected]>

[FIX] SQLite file format for ID data (OMSFile): fix SQL statement

dff3c03b8dabf3ba2f266cff7e84bd31cd170da8 authored almost 5 years ago by Hendrik Weisser <[email protected]>

[FIX] SQLite file format for ID data (OMSFile): fix SQL statement

0f8dc540021c0382db105dc1d43abbc51a81dfe5 authored almost 5 years ago by Hendrik Weisser <[email protected]>

[FEATURE] MapAlignerIdentification: store data processing step in .oms files

afd0352b3de12ebbadee38cec9b519eb57115692 authored almost 5 years ago by Hendrik Weisser <[email protected]>

Merge branch 'develop' of https://github.com/OpenMS/OpenMS into feature/parallelized_precursor_purity

Conflicts:
src/openms/source/ANALYSIS/XLMS/OpenPepXLAlgorithm.cpp
src/openms/source/ANALYSIS/X...

3bd727c9fc0d5b7cff74c793f5306b5802af6d53 authored almost 5 years ago by enetz <[email protected]>

Merge pull request #4410 from enetz/feature/OPXL_PPHR

[FEATURE] Using PeakPickerHiRes in auto mode for preprocessing in OpenPepXL

ce53d13da1fc6f499f4cb0eb7de28a0bdb6e8740 authored almost 5 years ago by Timo Sachsenberg <[email protected]>

[PYOPENMS] fixed OPXLSpectrumProcessingAlgorithms python bindings

0dc34a4581ede525fcf493817082c8ffda98e145 authored almost 5 years ago by enetz <[email protected]>

[INTERNAL] OpenPepXL: removed unused ifdefs and debug output

5b51ba02236ab953799f191d3d121b59e7968d61 authored almost 5 years ago by enetz <[email protected]>

[INTERNAL] got rid of unused macros and ifdefs

00f91e972ea7549036896229229442b8ec9e33b6 authored almost 5 years ago by enetz <[email protected]>

Merge branch 'feature/parallelized_precursor_purity' of https://github.com/enetz/OpenMS into feature/parallelized_precursor_purity

2b7eb8c7f73c4814485d495f8ced1894b980fc4e authored almost 5 years ago by enetz <[email protected]>

[PYOPENMS] commented out broken python binding

aa421b58a3c6fa60d2d3847ef7dc2cddf1d86b44 authored almost 5 years ago by enetz <[email protected]>

[FIX] OpenPepXL: removed useless progress output

0484701f8c0fa37dfbf9a162b22140e8db8fdea3 authored almost 5 years ago by enetz <[email protected]>

[FEATURE] OpenPepXL: using PeakPickerHiRes in auto mode for spectrum preprocessing

2019aa715f13ab70bc89d2446b0e27e9c54939de authored almost 5 years ago by enetz <[email protected]>

[FIX] removed unused variable in OpenPepXLLF

b954a7b2d76cdd3d00f92a371cb0d05d1fac03e9 authored almost 5 years ago by Eugen Netz <[email protected]>

[FIX] removed unused variable in OpenPepXL

3484f62beee210a29dc21bf544d4d9710273d33f authored almost 5 years ago by Eugen Netz <[email protected]>

[COMMENT] removed dead code

3f9f76428282263ac4b18d29f0b53416875d8645 authored almost 5 years ago by enetz <[email protected]>

[FEATURE] adapted use of PrecursorPurity in OpenPepXL and parallelized spectrum preprocessing

10da74ef9c207547bce6918096b1c0a40d19a093 authored almost 5 years ago by enetz <[email protected]>

[PYOPENMS] updated PrecursorPurity python bindings

43211d4de5ee7fe7cbe45bd04a9d83b1c9d606ad authored almost 5 years ago by enetz <[email protected]>

[FEATURE] parallelized PrecursorPurity class

12ca5a3bdbdcf1200ecee84c59fe04a4c8f74000 authored almost 5 years ago by enetz <[email protected]>

[FIX] updated RNPxlSearch to new PrecursorPurity behaviour

ee69f169da6a61d9f777c3dc65d9e17a91f60db0 authored almost 5 years ago by enetz <[email protected]>

[NOP] RNPxlSearch: removed whitespace

72d12e875184136496384272f14178848314c555 authored almost 5 years ago by enetz <[email protected]>

Merge branch 'develop' into feature/chrom_by_id

9ffba1ab385712821089747619c2ebdce61c822f authored almost 5 years ago by Timo Sachsenberg <[email protected]>

Merge pull request #4379 from jpfeuffer/feature/compileFeatureCXXstd

[FEATURE] use compile feature instead of fixed CXX standard to require only a minimum

b5a78f1262ef4a132cab920eecd43602e19500f9 authored almost 5 years ago by Timo Sachsenberg <[email protected]>

Fix bug for jenkins builder

af8a11e1cb873b90622df3c3dfe00eb4baecc379 authored almost 5 years ago by JeeK <[email protected]>

Merge pull request #4403 from AnthonyOfSeattle/fix_ascore_scoring

Fix AScore Scoring

2d8e4b8771bda2ef14b0e84f0fa387948cbd2135 authored almost 5 years ago by Timo Sachsenberg <[email protected]>

Merge pull request #4405 from OpenMS/jpfeuffer-patch-4

Default from -Weverything to -Wall and -Wextra

ad523f60d6b649a9014c470b4bf7d210d0262e08 authored almost 5 years ago by Timo Sachsenberg <[email protected]>

Default from -Weverything to -Wall and -Wextra

The conda builds with clang are almost impossible to read.
It is actually not even recommended ...

34069af46a813863ff37383f5715f4fbd6251f0c authored almost 5 years ago by jpfeuffer <[email protected]>

Fix weighted average in AScore

This commit fixes the denominator in a weighted average to make it
correct. Tests were added to ...

46c563a76b05d8f8060c0c317046ff8cc3d8ec8e authored almost 5 years ago by Anthony Valente <[email protected]>

Add method to calculate probability of a peak match based on mass tolerance and units

92767f3875189127cf37e6db4d9900765563b992 authored almost 5 years ago by Anthony Valente <[email protected]>

Merge pull request #4398 from jpfeuffer/fix/macFixes

[Fix] mac fixes

38489c526d885a53f5de6f77caf70b1205a13019 authored almost 5 years ago by jpfeuffer <[email protected]>

remove static in cpp

b1431047d151c8dfb91e637b97eb5f5b16d2b606 authored almost 5 years ago by Julianus Pfeuffer <[email protected]>

Another wrong singleton in RibonucleotideDB.

34de1af1b78bfd277ed692717bf61da0d8d17211 authored almost 5 years ago by Julianus Pfeuffer <[email protected]>

Fix bug on DBSearchDeconvMass_masslist

6ee6f1dbc8dc306e312fcd870bba929c30a173a5 authored almost 5 years ago by JeeK <[email protected]>

Wrongly placed class namespace and defaults.

6f131cc1cc8c1b237c9db36d2e127b2a1e6780b3 authored almost 5 years ago by Julianus Pfeuffer <[email protected]>

ModDb is non-const

b38600c1529bc02cd7375a0b0d1c2f913d2ebbf1 authored almost 5 years ago by Julianus Pfeuffer <[email protected]>

Merge pull request #4394 from poshul/PeakHeightMassTrace

Peak height mass trace

0c84b9a4b987015d0f193408318a2625678eb963 authored almost 5 years ago by Timo Sachsenberg <[email protected]>

Remove copy of fix.sh

Should not be necessary anymore.

194a12e0250aa40dc8a1ff66b607d57c532d90f3 authored almost 5 years ago by Oliver Alka <[email protected]>

Merge pull request #4397 from OpenMS/jpfeuffer-patch-3

[FIX] findExecutable should skip directories in Env with same name

2f9b01ae4de5cac1968d86f8fe283d704bd4c4a8 authored almost 5 years ago by jpfeuffer <[email protected]>

[FIX] also fix ModificationsDB singleton.

81a7e517f0bbcd513e72c9b26b95a8deb7325c2f authored almost 5 years ago by Julianus Pfeuffer <[email protected]>

Remove unused variable.

dde3c74b7303277a5ad6f3b298e5a2a7b317463b authored almost 5 years ago by Builder <[email protected]>

Restore MassTraceDetection from origin/develop, then add mass_error_da

a9cee418b97712399c16f728570e9e2ce80e2c93 authored almost 5 years ago by JeeK <[email protected]>