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

make writing of protein quants dependent on mzTab meta info

380516006d6f7bd08a797768e4c92b0da4dbb165 authored over 4 years ago by Julianus Pfeuffer <[email protected]>

Merge branch 'mapalignerident-force' into idfile-integration

93d9ad0b686befd0145a22a99c305e3371aab29c authored over 4 years ago by Hendrik Weisser <[email protected]>

[TEST] updated tests to change in 'force' TOPP parameter description

281398a33cb30dfc291cf4e9aec40054a744ffe5 authored over 4 years ago by Hendrik Weisser <[email protected]>

[FEATURE] MapAlignerIdentification: support 'force' flag to continue processing despite missing data

121ae795d9b70ed90f04269e0cb917bb1763c2f7 authored over 4 years ago by Hendrik Weisser <[email protected]>

[DOC] small documentation improvements

44ed098526817b889fbe12306e160295192ee54d authored over 4 years ago by Hendrik Weisser <[email protected]>

[FIX] mzTab with protein groups. use last entry instead of first. Do not duplicate inference protein run if already present.

c7941d0e3495a4c16da3ff04090adcdd97211fb0 authored over 4 years ago by Julianus Pfeuffer <[email protected]>

Promex output done

62674dbb6ded749095e8daa88fedb78db934ee4a authored over 4 years ago by kyowonjeong <[email protected]>

[FIX] NucleicAcidSearchEngine: fixed export of results to idXML/mzTab when pre-digested input is used

933ad2b27d3401a9f1d0db0890191426cd1a0139 authored over 4 years ago by Hendrik Weisser <[email protected]>

[TEST] added test case for NucleicAcidSearchEngine with pre-digested input

cdc93005c1f0ddeff3f2fcdb25818f78b2f43d3a authored over 4 years ago by Hendrik Weisser <[email protected]>

[Feature] add protein group support to consensusXML

cd243afa84f16531eaccc84ff59310f60cebb793 authored over 4 years ago by Julianus Pfeuffer <[email protected]>

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

2f26dce851fe6d0e9a4d13fc69e234e2f9fc9a82 authored over 4 years ago by kyowonjeong <[email protected]>

Promex output started

3a7d88d6b2bc14022727fc2f7b91a36fb7e24a14 authored over 4 years ago by kyowonjeong <[email protected]>

added more test stubs

8a44b59015dd04c4fdbda1421e398c9f3da6779b authored over 4 years ago by Timo Sachsenberg <[email protected]>

Merge pull request #4626 from jpfeuffer/fix/HashGridFind

[FIX] implement HashGrid.find to avoid "at" with exceptions

d5551985fb458b39b43a9089f7551cbb4ea23898 authored over 4 years ago by jpfeuffer <[email protected]>

[FIX] implement HashGrid.find to avoid "at" with exceptions

0a47c0842f5a6a2977f56570d3c268676eb013d6 authored over 4 years ago by Julianus Pfeuffer <[email protected]>

[IO] NucleicAcidSearchEngine: added option to re-use digestion data from a previous run (not yet tested)

b2b5ebe5fe892349ef6c9e44e88bc7615b737e8b authored over 4 years ago by Hendrik Weisser <[email protected]>

[COMMENT] removed outdated comments; minor clean-up

462a131e13ad177c2ffacd60a1f5f0fd5e31e420 authored over 4 years ago by Hendrik Weisser <[email protected]>

[API] added option to set log type in c'tor of class 'OMSFile'

615154cb7e608a12441439ada2498c4ebf339da0 authored over 4 years ago by Hendrik Weisser <[email protected]>

fix gcc4.8 compile error...

207d4552870397ca16ff73eabadd872f41675d45 authored over 4 years ago by Chris Bielow <[email protected]>

pyopenms default build type = release

7fb73bff137a3cfb1cdfc2107c0c7f4be2ad2f39 authored over 4 years ago by jpfeuffer <[email protected]>

Set Release as default build type

b1f0fd71ca1d0e418977d85a8986028c2bda37d2 authored over 4 years ago by jpfeuffer <[email protected]>

[DOC] extended documentation of experimental design

34192a2d637a04d6fcf057d111e54d433f0d1258 authored over 4 years ago by Timo Sachsenberg <[email protected]>

Merge pull request #4621 from timosachsenberg/fix/luciphor

map spectra to ids by native ids in Luciphor

aac987c731647b371f45c576a958f600b4e134e4 authored over 4 years ago by Timo Sachsenberg <[email protected]>

[FIX,TEST] fixed test of IDMerger with .oms files

7775024346a29d09b2f417aa79e536156206622b authored over 4 years ago by Hendrik Weisser <[email protected]>

Revert "[FEATURE] add SQLite to list of known file formats"

This reverts commit 3df8e4d640c1da6cef53b7f7e20548cda1b33c26.

Reason: conflict between SQLite (...

0bbdd8ad3c62c70f13f79cf71236a778f1c7ba78 authored over 4 years ago by Hendrik Weisser <[email protected]>

[TEST] added test case for IDMerger with .oms files

f32f0ba66a9a8ce1419be260e18d8056639d17f7 authored over 4 years ago by Hendrik Weisser <[email protected]>

[FEATURE] add SQLite to list of known file formats

3df8e4d640c1da6cef53b7f7e20548cda1b33c26 authored over 4 years ago by Hendrik Weisser <[email protected]>

Merge pull request #4620 from OpenMS/feature/comet_peptide_length

added minimum and maximum peptide length to comet adapter

79d3416a63f82440ca534c2079c009eb193b2f57 authored over 4 years ago by Timo Sachsenberg <[email protected]>

Merge pull request #4590 from timosachsenberg/feature/SSE

expose scaling parameters in SimpleSVM and add decoy generation in SSE

88adb36512a228bfd6ea9d57041a61c5633c4b1e authored over 4 years ago by Timo Sachsenberg <[email protected]>

Update CometAdapter.cpp

54b824b417bad0a9fec27270349c004901373ac0 authored over 4 years ago by Timo Sachsenberg <[email protected]>

[FEATURE] IdentificationDataConverter (export): sort peptide IDs by RT for increased reproducibility

ba11214e1e146d94763e4136b14618691147dbc2 authored over 4 years ago by Hendrik Weisser <[email protected]>

some GCC compiler forbid sharing of constants

... so I remove that restriction

ee44553dab49827426440e48f688447778afd843 authored over 4 years ago by Timo Sachsenberg <[email protected]>

[FIX] IdentificationData: fixed oversight in 'merge' function (fixes export from .oms to .idXML for merge results)

62f32b00fb71b8f1d5d39bbc9cf43055d8217491 authored over 4 years ago by Hendrik Weisser <[email protected]>

map spectra to ids by native ids in Luciphor

ba75a4affbfd69ba7dd7a3eca9053bae76c14d1e authored over 4 years ago by timosachsenberg <[email protected]>

[TEST] extended IdentificationData class test (merge, copy c'tor)

095c4388b0ba3bfb3633b3677e9df031661f3a2c authored over 4 years ago by Hendrik Weisser <[email protected]>

added constants to SSE

aa64d39a4d7671902844df1910a45102cac5b930 authored over 4 years ago by timosachsenberg <[email protected]>

simplify code

34c1f8d23cc1180408ff06c2faf166dbc437140e authored over 4 years ago by Timo Sachsenberg <[email protected]>

added minimum and maximum peptide length to comet adapter

1d267625495b0631cc644d59839ad6edcab10497 authored over 4 years ago by Timo Sachsenberg <[email protected]>

Update DecoyGenerator.h

fd29f0f4a7be64f6cedaf10c6b83da91533dbe9d authored over 4 years ago by Timo Sachsenberg <[email protected]>

Merge pull request #4619 from OpenMS/fix/4614

fix crash in PeptideIndexer caused by -1 in missed cleavage

df2cd79f5d9f47b46bde086d805da8ce19fd4c71 authored over 4 years ago by Timo Sachsenberg <[email protected]>

address review comments

7cf2067ea70398a42ff6df22f23d074e18acfc71 authored over 4 years ago by Timo Sachsenberg <[email protected]>

Merge remote-tracking branch 'upstream/develop' into feature/SSE

ea0a329ba16a9009daede4ea4ef6800bafee45fd authored over 4 years ago by Timo Sachsenberg <[email protected]>

Update DecoyGenerator.pxd

50ab3505c6f61a41646da1b62ddef34d665cb31e authored over 4 years ago by Timo Sachsenberg <[email protected]>

[API] IdentificationData: added copy c'tor; some doc clean-up

288bfae76add4df32211b23000e95ae6ab3572b0 authored over 4 years ago by Hendrik Weisser <[email protected]>

Merge pull request #76 from akriese/feature_anton

[FIX] catch exceptions by reference

599929445f5156c9fbe2a5de3b1d063f5c26a8c7 authored over 4 years ago by Chris Bielow <[email protected]>

Update DecoyGenerator.pxd

90becc8df63f8403c695a6bdac080a8c8a91947b authored over 4 years ago by Timo Sachsenberg <[email protected]>

Update pyopenms-wheels.yml

4902f567b3f2f4078be68b0f649daa7a94668f1f authored over 4 years ago by jpfeuffer <[email protected]>

[FIX] IdentificationData: include 'no_checks_' flag in move c'tor, avoid compiler warning about initialization order

a990e6d9e9637a32b814254f5d8d510cf0faacbc authored over 4 years ago by Hendrik Weisser <[email protected]>

Update DecoyGenerator.h

03b5725287962813c09435be6d6e0e7eb193e0bb authored over 4 years ago by Timo Sachsenberg <[email protected]>

Merge branch 'idfile-integration' of https://github.com/hendrikweisser/OpenMS into idfile-integration

7a874dca9e4f57828f8c8657347fa00660d2dca5 authored over 4 years ago by Hendrik Weisser <[email protected]>

[API] IdentificationData: added function to merge instances; added flag to disable validity checks

f86bd3b32562e9686c3f41bfdc8d8e71287b3716 authored over 4 years ago by Hendrik Weisser <[email protected]>

[INTERNAL] renamed parameter for consistency

cb3815bcaf792027ad2fb9f80498d42a4711a4ef authored over 4 years ago by Hendrik Weisser <[email protected]>

[FIX] typo fix

31581e3ddfde2eb1ddd802192d9357ca48579ae0 authored over 4 years ago by Hendrik Weisser <[email protected]>

fix crash in PeptideIndexer caused by -1 in missed cleavage

4fedff951e62f120ffd50e5bd5dbb1dabf40d476 authored over 4 years ago by Timo Sachsenberg <[email protected]>

Update DecoyGenerator.cpp

ccfcded5d3281fcf03da4f496ff5229c2e946057 authored over 4 years ago by Timo Sachsenberg <[email protected]>

Update DecoyGenerator.cpp

8e87b7a1956876c3ec8dbff002379ca063773ddb authored over 4 years ago by Timo Sachsenberg <[email protected]>

Merge pull request #72 from taranehstrunk/testbranch

added myself as author

bdca899265de760457a4de387d34dafa97722128 authored over 4 years ago by Chris Bielow <[email protected]>

Merge pull request #73 from Felix-Droop/first_steps

Preemptively added myself as author.

7fe670ea3c09a8b9be0bb8caa7d84c8f56f8445b authored over 4 years ago by Chris Bielow <[email protected]>

Merge pull request #74 from IceFreez3r/author

Added myself as author

a38fd174673bc2f972dffb7e411b7ab421ef28b3 authored over 4 years ago by Chris Bielow <[email protected]>

create portable shuffle

03ed3e4fd2f9622cb9bc84245efc9b8b7e7b1e69 authored over 4 years ago by timosachsenberg <[email protected]>

[FIX] catch exceptions by reference

359bf588db5399eb9feee5f443c6dc210289dcbe authored over 4 years ago by akriese <[email protected]>

Added myself as author

f30d3acb92af9d1a940b2c057ea82aedf4478ed7 authored over 4 years ago by IceFreez3r <[email protected]>

Preemptively added myself as author.

d2eea6fef9c2c76eac1d36d66afc8dc0e3c761a5 authored over 4 years ago by Felix Droop <[email protected]>

added myself as author

ccd5ec6d925c8088b10220850a610a62e19e6c1a authored over 4 years ago by Taraneh Strunk <[email protected]>

Merge pull request #71 from akriese/feature_anton

add myself to author list

b32d083fb2a98c35f5e87a761bc3386f4a55be36 authored over 4 years ago by Chris Bielow <[email protected]>

add myself to author list

d57e0d9df7d5c3a7b2edb8604b0c8409e7d2a603 authored over 4 years ago by akriese <[email protected]>

[fix] replaced baseName calls with completeBaseName when getting the layer name. Now files with internal . are treated properly

7e73335b459788ca6e7d12d099ad841db0d51a07 authored over 4 years ago by Samuel Wein <[email protected]>

[PARAM] IDMerger: removed support for 'add_to' parameter when merging .oms files

ff3d673685a02dd4c25f4ecb70bede9e38a397b5 authored over 4 years ago by Hendrik Weisser <[email protected]>

[IO] support for .oms input/output files in IDMerger (work in progress)

bd817e736b1a769ad7ba6f09cd2aaa5b706aaa88 authored over 4 years ago by Hendrik Weisser <[email protected]>

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

691cef217ab6e4601a9b04be17d40e5a02e11231 authored over 4 years ago by Chris Bielow <[email protected]>

Update pyopenms-wheels.yml

7db2930f284377cea5e122095b4c33cb528d3b84 authored over 4 years ago by jpfeuffer <[email protected]>

Merge pull request #4609 from OpenMS/feature/update3rdparty

update THIRDPARTY

98a21ea6994926f1be6db069c622bf3eb57e2628 authored over 4 years ago by jpfeuffer <[email protected]>

fix cpplint

5ed662eabe5a8dcbc1980a1e6f882cb001ac1b3d authored over 4 years ago by Chris Bielow <[email protected]>

Merge pull request #4608 from jpfeuffer/feature/mergeIdx

[Feature] use merge idx to keep track of primaryRuns in Consenus/IDMerger

0f0582293a01f27b8d3707dea1c7c949b5f437c6 authored over 4 years ago by Timo Sachsenberg <[email protected]>

portable shuffle

922448264c25014a4bc094bd69c7fd4a66ac810f authored over 4 years ago by timosachsenberg <[email protected]>

more test fixes. sort output. ignore version. update test input.

ac9e622ca62e98ac1b3b5ab8970b3c9994b0cc6a authored over 4 years ago by Julianus Pfeuffer <[email protected]>

Merge branch 'feat_QC_labeled' of https://github.com/cbielow/OpenMS into feat_QC_labeled

416ba5a683694b1b6c0077e3fecbac5b7924e256 authored over 4 years ago by Chris Bielow <[email protected]>

fix tests

051acdfdbd8a77d40bdfc48bdf71871c7e709fc1 authored over 4 years ago by Chris Bielow <[email protected]>

[FEATURE] Nightly pyopenms wheel through GitHub Actions (#4587)

* Create pyomslnxwheel.yml

* Update pyomslnxwheel.yml

* fix and upload

* fix indent?

* sourc...

268a11b1c7bf159f3231b30e548fac044b2a8fd7 authored over 4 years ago by jpfeuffer <[email protected]>

Merge pull request #4613 from cbielow/feat_ReleaseVersion

change OpenMS version to 2.6-pre (for nightly installers)

58479edf64cd4a3fd2dd3904c746bbd5bfc79b93 authored over 4 years ago by jpfeuffer <[email protected]>

Update Manual.tex

a7c6772b5f057c36cf9be9cf344fc27d70af7554 authored over 4 years ago by jpfeuffer <[email protected]>

Update INIUpdater_1_noupdate.toppas

5452476729484ec44707dbf7fd4ab78317e9b994 authored over 4 years ago by jpfeuffer <[email protected]>

Merge branch 'develop' into feat_QC_labeled

0ddf80d78b01f23da4a5d6937b63c71975d179b1 authored over 4 years ago by Chris Bielow <[email protected]>

fix tests

97caf5471e84ca25d0d06a6ba27043ed1659be94 authored over 4 years ago by Chris Bielow <[email protected]>

more test fixes. sort output. ignore version. update test input.

23c2ca20a8fd47fa46ec0053ce38a074d8bb1e01 authored over 4 years ago by Julianus Pfeuffer <[email protected]>

Merge branch 'feat_ReleaseVersion' of https://github.com/cbielow/OpenMS into feat_ReleaseVersion

d6e7f2114d6693079c0401b6dd1909292e0c54ef authored over 4 years ago by Chris Bielow <[email protected]>

update script to 2.6

ad2bdc022fe05e3d79a46c87ef053bccb3fbe2e1 authored over 4 years ago by Chris Bielow <[email protected]>

fix codefactor warning

336aa0b842e949fb765780667a4b91b575b8f00d authored over 4 years ago by Chris Bielow <[email protected]>

fix tests

8f4d692395dc05b49d4f36b8968933c693c6e6d2 authored over 4 years ago by Chris Bielow <[email protected]>

fix test

effb300ff24f60d2ee865c96e9ae1e3babc17752 authored over 4 years ago by jpfeuffer <[email protected]>

Update DecoyGenerator.cpp

1ae52822461d708a4c0a9b71847b642cc600ef02 authored over 4 years ago by Timo Sachsenberg <[email protected]>

change OpenMS version to 2.6-pre (for nightly installers)

d36938cadee0517c222777a88d852f1e7803d94d authored over 4 years ago by Chris Bielow <[email protected]>

attempt to use boost random_shuffle

e298d7e2d179105983f3ba71a74a8d59bf6a617a authored over 4 years ago by Timo Sachsenberg <[email protected]>

try to fix test on windows

66c7a5cc677c0aca9f55c67e0ae295b61261aa03 authored over 4 years ago by Timo Sachsenberg <[email protected]>

fix class tests

781a30f4f7e483a109508753075c75008b237a7f authored over 4 years ago by Julianus Pfeuffer <[email protected]>

Update CMakeLists.txt

caba0f29950f27b0390ccdd95dc5c5b6842bf7aa authored over 4 years ago by Timo Sachsenberg <[email protected]>

fix dependent tools and test data.

3c5a6e5a2d73163e231af8aa7d011eaa612667cb authored over 4 years ago by Julianus Pfeuffer <[email protected]>

header hygiene. fixes and test fixes

07eca1aa4626f19e51692c4c979bb1fe6d588c9d authored over 4 years ago by Julianus Pfeuffer <[email protected]>

whitelist search path

a96759869a8100ae98187fb63b8170dffd57d562 authored over 4 years ago by Timo Sachsenberg <[email protected]>

Merge remote-tracking branch 'origin/develop' into feature/update3rdparty

e01f9f8bc5628873384c15c191edf62e72654153 authored over 4 years ago by Timo Sachsenberg <[email protected]>