github.com/OpenMS/OpenMS-1 commits | Ecosyste.ms: OpenCollective

Update src/openms/include/OpenMS/FILTERING/SMOOTHING/SavitzkyGolayFilter.h

ae56072fb098026a42ab51665a38c771a32504ce authored about 2 years ago by Chris Bielow <[email protected]>

Update src/openms/include/OpenMS/FILTERING/SMOOTHING/SavitzkyGolayFilter.h

8c2f224641b887e7aa06539c60196ded1f50e06e authored about 2 years ago by Chris Bielow <[email protected]>

Update src/openms/include/OpenMS/FILTERING/SMOOTHING/SavitzkyGolayFilter.h

872cbea8e355bc4bb46582a70ce6d65a86bce3a5 authored about 2 years ago by Chris Bielow <[email protected]>

store num peaks mv loading msp file

81a2e61694dffd9935a12ef46ee9ae4d6a2b717e authored about 2 years ago by axelwalter <[email protected]>

update Name regex

e763ccb981fec362fec7c3c9811c04147a7d1727 authored about 2 years ago by axelwalter <[email protected]>

update RT and point regex

6d4052d270c6489e1a2a030fba600d340ea46bd1 authored about 2 years ago by axelwalter <[email protected]>

bug fixing for jenkins build

8bba14abbac2980dff066dfc4d7f19abbe61ddf8 authored about 2 years ago by JeeH-K <[email protected]>

Merge remote-tracking branch 'origin/develop' into feature/FLASHDeconv

07c8bca483aa9e843fe302f353d0bf563603508c authored about 2 years ago by JeeH-K <[email protected]>

Build version 02082022 - min charge bug fixed

f8be7e9ae2c5944310d81c9ecad12e393ed6c654 authored about 2 years ago by kyowonjeong <[email protected]>

add Scan_ID mv from mgf file

4e125e631989414143a0677fc614662ab92576d8 authored about 2 years ago by axelwalter <[email protected]>

Build version 02082022 - min charge bug fixed

7e98ba800317acfc0eb8680c0c2ed31595ddfb0f authored about 2 years ago by kyowonjeong <[email protected]>

Build version 01082022

623447fb5c6ce04869553dc06e87c23a0b755ba0 authored about 2 years ago by kyowonjeong <[email protected]>

FLASHIda exclusion testing

12401ddcefbb5d7f197baabbbe766e10b85e37e6 authored about 2 years ago by kyowonjeong <[email protected]>

Charge decoy annotation bug fixed..

e0af9b878668afd2d06ca6e8c178005f5273e9cc authored about 2 years ago by kyowonjeong <[email protected]>

Clear bug fixed. Write detail now report -3 to max+3 isotopes. iso da distance was considered in peakgroup peak recruiting

bc7263d2fe29cece2f9a61aa2c3df6e91188f187 authored about 2 years ago by kyowonjeong <[email protected]>

Merge branch 'maxquant-output' of https://github.com/vrossow/OpenMS into maxquant-output

66a69a598cc838ad1747b5ee5f384d56bb15d760 authored about 2 years ago by beschorneh32 <[email protected]>

implemented suggestions from the review

e638914b074c330f16114da15217576ff56078e6 authored about 2 years ago by beschorneh32 <[email protected]>

Removed parameters and added noisy peak output for detailed output. Memory efficiency improved.

89499459cb7bfe704e791851c0bff8cf37c9fc0f authored about 2 years ago by kyowonjeong <[email protected]>

Removed parameters and added noisy peak output for detailed output. Memory efficiency improved.

2eeb05e1b8ca0c184d575da07ad7c354bc0edb1e authored about 2 years ago by kyowonjeong <[email protected]>

[TEST] Add tests to SwathMapMassCorrection

Rather than testing the entire OpenSwathWorkflow it is sufficient to
just test correctMz and cor...

08863c2dc1dc7a0a05f4775dad13d646ed2b12eb authored about 2 years ago by Joshua <[email protected]>

remove outdated comment

68b04efd384e3095b63d57e8ecc2c06ea35f623c authored about 2 years ago by Chris Bielow <[email protected]>

fix compile error

44f630ff8a13614afc8c884756fcbb15c50525cd authored about 2 years ago by bielow <[email protected]>

fix some frequent warnings

d7880ac7b2a0aec2972dc6626f76272a1b3583d1 authored about 2 years ago by bielow <[email protected]>

Merge branch 'develop' into ConsoleFun

a5ec0fbdf43ba30d485dc608e72498cf1f02daab authored about 2 years ago by Timo Sachsenberg <[email protected]>

remove Windows CRLF...

28c4e3345e1f8af5c6bd08254648969e56e7ac2c authored about 2 years ago by bielow <[email protected]>

Merge pull request #6278 from OpenMS/fix/compile

fix compile bug

a16568db230876c1e475a73da9b89d5d55e5ebf6 authored about 2 years ago by Timo Sachsenberg <[email protected]>

Merge branch 'develop' into feature/FLASHDeconvOnly

90253d8a13cd960b24c59b3722141e4b2290b0f1 authored about 2 years ago by JihyungKim <[email protected]>

add missing include

62d82d65d74f06dadeb4d49e396337ccca092e24 authored about 2 years ago by bielow <[email protected]>

fixes

4d4d2361751d22c83acafab67eb2312d07f62cec authored about 2 years ago by bielow <[email protected]>

MGF file import new meta values

a1cb38c53abf81820bd94adf06f7cd67868fa4e2 authored about 2 years ago by axelwalter <[email protected]>

fix another unused variable test

ce813530a7a206bab6f9bc24011776f663705a1c authored about 2 years ago by Timo Sachsenberg <[email protected]>

Timo Jihyung comments addressed

b71da28eb11c3ac713546448f2c66b66be004159 authored about 2 years ago by kyowonjeong <[email protected]>

Timo Jihyung comments addreassed

810ef29722ca7db2bbb9059072663997ef7c2c29 authored about 2 years ago by kyowonjeong <[email protected]>

remove unused functions (not for FLASHDeconvOnly)

697403eec0a76f709cc211332ff3d4fd1b9ab0a6 authored about 2 years ago by JeeH-K <[email protected]>

Decoy testing.

f6e65af76dff57c059f32f109b2f4709dd077570 authored about 2 years ago by kyowonjeong <[email protected]>

Update DimMapper.h

9988496ece1e2f0793c80cea18e34abe847a64d4 authored about 2 years ago by Timo Sachsenberg <[email protected]>

FLASHDeconv Only decoy removed with the current version!!

b3b923f190c6892f6e45b3b5ad56cf01ae048d59 authored about 2 years ago by kyowonjeong <[email protected]>

Update DimMapper.h

01daa7d36b1d40fab1c860570070510667757ecc authored about 2 years ago by Timo Sachsenberg <[email protected]>

remove unused method parameter names

3c67d4d141608672f05872f24295fb1f534018a7 authored about 2 years ago by Timo Sachsenberg <[email protected]>

fix compile bug

d1e54885afee35f307850d5dab764ea437da874d authored about 2 years ago by Timo Sachsenberg <[email protected]>

Chris comment has been addressed 3.

5f0bbaf55ebb88a751b047ffc547800fc700c7d3 authored about 2 years ago by kyowonjeong <[email protected]>

Merge remote-tracking branch 'origin/feature/FLASHDeconv' into feature/FLASHDeconvOnly

48152adb7e037b2888b46743fa90cc2d834d6099 authored about 2 years ago by JeeH-K <[email protected]>

Chris comment has been addressed 2.

a5738bbb5b05546a0f29972c42e95b7b6db7796b authored about 2 years ago by kyowonjeong <[email protected]>

Merge pull request #6273 from jpfeuffer/nose2pytest

Switch from nose to pytest

1506bb36aede11e68a038e541b658f61d8cd8c07 authored about 2 years ago by Timo Sachsenberg <[email protected]>

fix UTILS;

add tests;
fix small bugs

9e4a67472e32d28bea69efa1e8113af640ef719d authored about 2 years ago by bielow <[email protected]>

Chris comment has been addressed.

fd9fb35a99798ee2b00712783933139a68a5dc3e authored about 2 years ago by kyowonjeong <[email protected]>

remove unused file

d47a9832d2e1138d03392c5b1f5d4b0eb7008199 authored about 2 years ago by JeeH-K <[email protected]>

add MSPGenericFile

2a6fcf7a7906c97d93362e3b18bcdd9329d34cf3 authored about 2 years ago by Timo Sachsenberg <[email protected]>

revert to the ugly hack.

6cc781903f4bff99116e10ff337e9e01212adad6 authored about 2 years ago by Julianus Pfeuffer <[email protected]>

update peakgroup_test based on the changes

2080bbe5828c5899ef86088b007e4fb7e5c8886d authored about 2 years ago by JeeH-K <[email protected]>

update peakgroup_test based on the changes

eb886bacf7edb55851339016bbac0b31b6dd98d2 authored about 2 years ago by JeeH-K <[email protected]>

Merge remote-tracking branch 'origin/feature/FLASHDeconv' into feature/FLASHDeconvOnly

# Conflicts:
# doc/doxygen/public/TOPP.doxygen
# src/openms/include/OpenMS/ANALYSIS/TOPDOWN/FLAS...

eb8fe86917418a22056da774967a152aefdbc40a authored about 2 years ago by JeeH-K <[email protected]>

fixing year number, typo and tests

8a1a30e42134e1ed039139e81db0d456de7206c8 authored about 2 years ago by JeeH-K <[email protected]>

change messages

61d85286af520e792b007d1450f54f1a29f598ef authored about 2 years ago by Julianus Pfeuffer <[email protected]>

Switch from nose to pytest

dfe38c6a6125a2aea0be754ece5568add6748e00 authored about 2 years ago by Julianus Pfeuffer <[email protected]>

coloring usage

fc632b90058d9976b0dee2e15237d478f4a66ca0 authored about 2 years ago by bielow <[email protected]>

Merge branch 'develop' into feature/flashdeconv

3b2c12d905cac4521f7bf762a348ae47baf6f2a1 authored about 2 years ago by JeeH-K <[email protected]>

more fixes

d5b5365de8eb9b754a271eb04edcc7dfd87f5e45 authored about 2 years ago by bielow <[email protected]>

Merge branch 'develop' into feature/FLASHDeconvOnly

5441ac80a7dda65167e64945816474bc4c173d81 authored about 2 years ago by Timo Sachsenberg <[email protected]>

Merge pull request #6271 from axelwalter/feature/GNPSMetaValues-index

[Feature] Index column for GNPS meta value file

c93665ba0f9cfe42c1e33dbcdf3ff914ae16ac6d authored about 2 years ago by Timo Sachsenberg <[email protected]>

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

cedf36f0d30f66a95762be64a62456308c4df4b3 authored about 2 years ago by bielow <[email protected]>

fix log functions

9aeaa89e93da11b10bc36cb04affc4a3cbe0bc51 authored about 2 years ago by bielow <[email protected]>

[FIX] CorrectMZ support for PASEF data

Change CorrectMZ function to be similar to correctIM() such that in
PASEF data, precursors are e...

7a6b444b4f2fc88976a7eaddc207fa1f758706f8 authored about 2 years ago by Joshua <[email protected]>

a first version ...

e4980a0fcd2f5dee09408395094fb49cc320ed1f authored about 2 years ago by bielow <[email protected]>

[NOP] fix spacing

72b68966855e26d0f1ef1cdbfe2b2ad8776565e1 authored about 2 years ago by Joshua <[email protected]>

Merge branch 'develop' into feature/OswImCalibOutput

5f63055c84ccba7bacd5b4fa3246723fc8dec8ba authored about 2 years ago by Timo Sachsenberg <[email protected]>

indent in header row

815d71fc4564bde675eb4c62ea92d4ac63cb2b30 authored about 2 years ago by axelwalter <[email protected]>

update GNPSExport test

1fc0d7407578a1b9624df5b749ed25a6bd0412c8 authored about 2 years ago by axelwalter <[email protected]>

add index column for meta value file

163eaed41e2fa2c0a538949e3b6d2fc0ddc37598 authored about 2 years ago by axelwalter <[email protected]>

[TEST] OpenSwathDecoyTest_5

add to test to ensure decoys of different charge states and same
sequence are not excluded.

b06a19d18d9afb75c2a68e79ea8809e46d19e5e0 authored about 2 years ago by Joshua <[email protected]>

[FIX] OpenSwathDecoy exclude too many peptides bug

Previously I added a function to ensure OpenSwathDecoy generator does
not add decoys that are al...

b5658824c8182a0490e2844623bd633edc1c1c24 authored about 2 years ago by Joshua <[email protected]>

[TEST] add test for PASEF IM irt calibration

Append to OpenSwathWorkflow_23 test to also test that pasef windows can be
correctly assigned in...

5c8402a1f388027563910a5b62e7f6e78d3b4375 authored about 2 years ago by Joshua <[email protected]>

[NOP] format changes for PR

5a66d1356c20a00d0127f721fe366bf73d3779f2 authored about 2 years ago by Joshua <[email protected]>

log sirius stdout for SiriusAdapter tests

2b367eb0c93130fd32fc82dba61d802e9fc33c3c authored about 2 years ago by axelwalter <[email protected]>

merged develop and resolved conflict in SiriusAdapterAlgorithm.cpp

5bd65a4cc36f30af22a6b2719cdd6d4a0705c5aa authored about 2 years ago by axelwalter <[email protected]>

update changelog

54be3454b6c382f52ae300bfdf8df8c716db7487 authored about 2 years ago by Joshua <[email protected]>

[TEST] fix tests with new output

replace output files for tests which now include the new delta_im
parameters

ebff85461cadd75b181e68a6d6ac2ae88b59e639 authored about 2 years ago by Joshua <[email protected]>

Add extra IM output to OSW

add output of delta im (both MS1 and MS2 level) and add IM for both MS1
and MS2

10475cc620935614e25d040cab48627c1af09ede authored about 2 years ago by Joshua <[email protected]>

[FIX] fix swath tests for calibrate IM

2bd0dc66f2f28304359ea3cceb06bfacb93d2e74 authored about 2 years ago by Joshua <[email protected]>

[FIX] IM calibration with PASEF data

Previously IM calibration not working with PASEF data, code thought it
was sonar data. Added fun...

e51f1eb5fbfd58fc5efaaa322e670d34df91850f authored about 2 years ago by Joshua <[email protected]>

[FEATURE] PASEF picking for iRT calibration

Allow iRT peptides to be picked from the SWATH which they are most
centered around with their io...

e5ab3cc16c1d7ad3b63d2846365c561a30cfaf06 authored about 2 years ago by Joshua <[email protected]>

Merge pull request #6265 from tillenglert/fix/MSFragger_PEPmodel_Support

Fix/MSFragger_PEPModel_Support

031a36f3790a8a2fcd9818a2f9414e58bfe720c9 authored about 2 years ago by Julianus Pfeuffer <[email protected]>

Added myself to the Author list

204bb9e25dadd83bd9b4b2ec0459180444390a24 authored about 2 years ago by tillenglert <[email protected]>

fixed downstream support for MSFragger idXML, when using the PEP tool

edb2006aacd33d6c1fff3d72a834812ddefc045f authored about 2 years ago by tillenglert <[email protected]>

Merge branch 'OpenMS:develop' into maxquant-output

ce1a004456f20ed359c944d633ec5a22d413ca88 authored about 2 years ago by Virginia Rossow <[email protected]>

Build version

08e532cb86d443db5153ec9ee7f8265dcc299eac authored about 2 years ago by kyowonjeong <[email protected]>

Bugs in decoy scannumber fixed. Reintroduced charge score threshold of 0.7. Should make a parameter for this

cfde822a6d3846346947ae19885c8390ffc8e35d authored over 2 years ago by kyowonjeong <[email protected]>

small fixes

789ee0c23947708851950d2c279ec6fe167f6dbb authored over 2 years ago by bielow <[email protected]>

fix tutorial

9683e4b1df0956d1ef089f8df7e2a1c4338851d6 authored over 2 years ago by bielow <[email protected]>

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

# Conflicts:
# contrib
# src/openms/include/OpenMS/KERNEL/DimMapper.h
# src/openms/include/OpenM...

712c663f9d557f7f82e49c31483e4cef337dd551 authored over 2 years ago by bielow <[email protected]>

Update binaries_lnx.ini

re-remove myrimatch binary

2a9ca82b1f043bd930865ea0ee0bf010fb752f73 authored over 2 years ago by Samuel Wein <[email protected]>

Update binaries_win.ini

re-remove myrimatch

e44038a5f8d630e230b9ef35279cde25689d65c8 authored over 2 years ago by Samuel Wein <[email protected]>

Merge pull request #6230 from OpenMS/remove_crux

Crux related parts have been removed. Tested in M1 arm64 machine.

1744153f0ce0faf816ab7760a4c8d96384a932a8 authored over 2 years ago by Samuel Wein <[email protected]>

Merge remote-tracking branch 'upstream/develop' into HEAD

309183a8ff0f3db9ca4fb17dcd54ec11abfc7334 authored over 2 years ago by Samuel Wein <[email protected]>

Merge pull request #6257 from cbielow/prepTV

More preparations for TOPPView refactor

be9861f50ac9c3c68a399bbf83d8d5bc771a8128 authored over 2 years ago by Timo Sachsenberg <[email protected]>

Also expose peptide identification meta values (first one) attached to consensus/feature (#6256)

* add methods to extract peptide id meta values

* export consensus feature meta values of fir...

e1bd67c71643e974841847f2a3214e75e34cc9eb authored over 2 years ago by Timo Sachsenberg <[email protected]>

Crux related parts have been removed. Tested in M1 arm64 machine. Jihyung's comments have beend addressed : revoke pepXML_v122.xsd and just edit "new" for OpenMS 3.0 in CHANGELOG

6b5f08de100ecaf6116a04c7ab8e98972981460f authored over 2 years ago by kyowonjeong <[email protected]>

minor variable name fix

102cc66972faa2688c8b39b68cddffa7d3e1927c authored over 2 years ago by bielow <[email protected]>

fix gcc compile error

5c45589c09c65c050f85f2b5d0c62b43107ffe49 authored over 2 years ago by bielow <[email protected]>

Merge branch 'develop' into feature/FLASHDeconv

6947bc453343724effbe5b0642f6db2ee9ef1dd0 authored over 2 years ago by JeeH-K <[email protected]>