OpenMS/OpenMS issues and pull requests

#6032 - SiriusAdapter issue (sirius invocation failed)

Issue - State: closed - Opened by eeko-kon over 2 years ago - 6 comments

#6028 - Use new ID data structures in FeatureFinderIdentification (and ProteomicsLFQ)

Pull Request - State: open - Opened by hendrikweisser over 2 years ago - 1 comment
Labels: wontfix

#6019 - Feature id promotion

Pull Request - State: open - Opened by poshul over 2 years ago - 11 comments
Labels: wontfix

#6003 - Deprecated (doxygen) Doc pages notice does not work

Issue - State: closed - Opened by jpfeuffer over 2 years ago - 5 comments
Labels: Documentation, Website, good first issue, first-timers-only, sprint candidate

#5956 - Feature/isotope class

Pull Request - State: open - Opened by hroest over 2 years ago - 3 comments
Labels: ready-post-release

#5893 - [FEATURE] TSG option to add internal ions

Pull Request - State: open - Opened by timosachsenberg over 2 years ago - 3 comments
Labels: wontfix

#5847 - Installer packages too large

Issue - State: open - Opened by jpfeuffer over 2 years ago - 4 comments
Labels: BinaryPackages, Build System

#5836 - Combine PSMFeatureExtractor and Percolator in PercolatorAdapter

Issue - State: open - Opened by jpfeuffer over 2 years ago - 3 comments
Labels: Hacktoberfest, usability, sprint candidate

#5829 - [FEATURE] prepare for ion mobility support in FFCentroid

Pull Request - State: open - Opened by hroest over 2 years ago - 3 comments

#5740 - [BUILD] Try to silence NPY Deprecated warnings in pyopenms

Pull Request - State: closed - Opened by jpfeuffer over 2 years ago - 7 comments
Labels: NoJenkins

#5736 - How to create MassTrace objects with pyopenms

Issue - State: closed - Opened by jtprince over 2 years ago - 6 comments

#5708 - pass calling process environment to children

Pull Request - State: closed - Opened by timosachsenberg almost 3 years ago - 4 comments

#5692 - FLASHIda

Pull Request - State: closed - Opened by JeeH-K almost 3 years ago - 1 comment
Labels: wontfix

#5689 - Added new features in SpectraMerger

Pull Request - State: closed - Opened by JeeH-K almost 3 years ago - 4 comments

#5687 - PeakPickerHiRes fails with leading flank peaks

Issue - State: open - Opened by hroest almost 3 years ago - 7 comments
Labels: defect, critical

#5680 - Clang tidy performance type-promotion-in-math-fn,move-const-arg,unnecessary-copy-initialization

Pull Request - State: closed - Opened by timosachsenberg almost 3 years ago - 2 comments

#5669 - Wrapping new IdentificationData in pyopenms

Issue - State: open - Opened by timosachsenberg almost 3 years ago - 3 comments

#5660 - Patch/use td library

Pull Request - State: closed - Opened by SGSSGene almost 3 years ago - 6 comments
Labels: wontfix

#5645 - PeakTypeEstimator fails for timsTOF profile data

Issue - State: open - Opened by hroest almost 3 years ago - 1 comment
Labels: defect, major

#5639 - Add MZMLb support

Issue - State: open - Opened by poshul almost 3 years ago - 4 comments
Labels: enhancement, major, File Format

#5637 - How to extract DIA MS2 consensus features for ClusterMassTraces

Issue - State: open - Opened by yyi17 almost 3 years ago - 3 comments
Labels: Documentation

#5636 - Pyopenms actions. Mismatch between building and testing versions

Issue - State: open - Opened by jpfeuffer almost 3 years ago - 2 comments
Labels: pyOpenMS, CI

#5621 - Add some std::moves to SpectrumMerger

Issue - State: closed - Opened by jpfeuffer almost 3 years ago
Labels: Performance, Hacktoberfest, good first issue, first-timers-only

#5618 - ConsensusID failure because MS run path not interpreted from MSFragger idXML

Issue - State: closed - Opened by zhuchcn almost 3 years ago - 2 comments

#5613 - Split up OpenMS library

Pull Request - State: closed - Opened by hroest almost 3 years ago - 3 comments
Labels: wontfix

#5568 - Linux dependency missing for KNIME nodes 2.7.0

Issue - State: closed - Opened by julianu about 3 years ago - 9 comments
Labels: BinaryPackages, critical, KNIME

#5523 - validate experimental design

Pull Request - State: closed - Opened by timosachsenberg about 3 years ago - 8 comments
Labels: wontfix

#5436 - libicu has no rpath (anymore?) on linux

Issue - State: open - Opened by jpfeuffer about 3 years ago - 13 comments
Labels: BinaryPackages, Build System, critical, KNIME

#5376 - [Feature] AccurateMassSearch sqlite support

Pull Request - State: open - Opened by jpfeuffer over 3 years ago - 7 comments
Labels: wontfix

#5334 - add internal ions and n terminal losses

Pull Request - State: closed - Opened by timosachsenberg over 3 years ago - 3 comments
Labels: wontfix

#5307 - ID score switcher error

Issue - State: closed - Opened by Maithy15 over 3 years ago - 28 comments

#5290 - fixed some AddressSanitizer errors (mainly for demonstration purposes)

Pull Request - State: closed - Opened by timosachsenberg over 3 years ago

#5195 - Update Docs + Readme + Website with new C std and min. compilers

Issue - State: open - Opened by jpfeuffer over 3 years ago - 3 comments
Labels: major, Documentation

#5168 - OpenSwathWorkflow crashes

Issue - State: closed - Opened by sjr24 over 3 years ago - 6 comments

#5149 - Update Comet and support all our enzymes

Issue - State: open - Opened by jpfeuffer over 3 years ago - 2 comments
Labels: major

#4912 - Release automation

Issue - State: open - Opened by jpfeuffer about 4 years ago - 5 comments
Labels: enhancement, task, good first issue, first-timers-only

#4901 - [FEATURE] added CV terms for spectral counting / label-free abundances

Pull Request - State: open - Opened by timosachsenberg about 4 years ago - 4 comments
Labels: wontfix

#4842 - Ion mobility support in OpenMS

Issue - State: open - Opened by hroest about 4 years ago - 4 comments
Labels: Projects

#4833 - Error Reporting in DataValue.cpp

Issue - State: open - Opened by ekawaler about 4 years ago - 3 comments
Labels: enhancement, major

#4824 - MzTab for TMT

Issue - State: open - Opened by jpfeuffer about 4 years ago
Labels: enhancement, major

#4600 - [Feature] Include calculation of QC parameters in ProteomicsLFQ tool

Pull Request - State: open - Opened by jpfeuffer over 4 years ago - 10 comments
Labels: wontfix

#4291 - Build pyOpenMS with static QT to avoid version mismatches with e.g. Spyder/pyQT (especially on Win)

Issue - State: open - Opened by timosachsenberg almost 5 years ago - 19 comments
Labels: defect, pyOpenMS

#4240 - SpectraST unix binary problem

Issue - State: open - Opened by Leon-Bichmann about 5 years ago - 26 comments
Labels: defect, major

#4215 - OpenMS assumes strict hierarchy of MS levels in mzML?

Issue - State: open - Opened by jpfeuffer about 5 years ago - 7 comments
Labels: critical

#4152 - Update Comet version and auto-determine version

Issue - State: open - Opened by jpfeuffer over 5 years ago - 2 comments
Labels: enhancement, major, Hacktoberfest

#3856 - Bioconda thirdparty packages

Issue - State: closed - Opened by Leon-Bichmann almost 6 years ago - 7 comments
Labels: enhancement, BinaryPackages

#3685 - how to download the example file in http://www.peptideatlas.org/PASS/PASS00779

Issue - State: closed - Opened by mantouRobot about 6 years ago - 4 comments
Labels: question

#3501 - XML Reader performance

Issue - State: closed - Opened by hroest over 6 years ago - 3 comments
Labels: enhancement, Performance

#3319 - Use dynamic contrib libraries as default?

Issue - State: open - Opened by hroest over 6 years ago - 6 comments
Labels: question, major, Build System, contrib, defaults

#3255 - [REVIEW] Consistent search engine adapter interfaces

Issue - State: open - Opened by jpfeuffer over 6 years ago - 9 comments
Labels: major, TOPP, task, Hacktoberfest, OpenMS Dev Meeting

#2958 - MetaProSIP Report inconsistent value for low RIA peptides?

Issue - State: closed - Opened by timosachsenberg almost 7 years ago - 7 comments
Labels: defect, major

#2673 - Fast base64 encoding

Issue - State: closed - Opened by hroest over 7 years ago - 2 comments
Labels: question, task, Performance

#2593 - Invalid mzIdentML created from idXML with missing proteins

Issue - State: open - Opened by hendrikweisser over 7 years ago - 1 comment
Labels: defect, major

#2557 - Error handling spaces in paths in the course of a workflow

Issue - State: open - Opened by jpfeuffer over 7 years ago
Labels: defect, major, unconfirmed

#1915 - MSGFPlusAdapter - self-defined mods not passed on to the search result

Issue - State: open - Opened by lars20070 over 8 years ago - 13 comments
Labels: defect, major, TOPP

#1252 - FileInfo: memory usage reported correctly?

Issue - State: closed - Opened by hendrikweisser over 9 years ago - 7 comments
Labels: enhancement, major

#1053 - enable ubsan

Issue - State: closed - Opened by hroest almost 10 years ago - 4 comments
Labels: enhancement, major, Build System, CI, beginner tasks

#1049 - EGHTraceFitter sigma bug

Issue - State: closed - Opened by WMGoBuffs almost 10 years ago - 3 comments
Labels: defect, major

#907 - Show precursor charge in Scan View panel

Issue - State: closed - Opened by lars20070 about 10 years ago - 4 comments
Labels: TOPPView, task, minor

#731 - MyriMatch adapter - N-terminal modifications

Issue - State: closed - Opened by hendrikweisser over 10 years ago - 3 comments
Labels: defect, major

#627 - Create image of workflow (and include it in repository) [627]

Issue - State: closed - Opened by timosachsenberg over 10 years ago - 1 comment
Labels: enhancement, major, TOPPAS

#621 - No "linked zoom" with mouse wheel [621]

Issue - State: closed - Opened by timosachsenberg over 10 years ago - 2 comments
Labels: defect, TOPPView, minor, Hacktoberfest

#619 - MSSimulator: unrealistic intensities in picked/centroided data [619]

Issue - State: closed - Opened by timosachsenberg over 10 years ago - 4 comments
Labels: defect, minor, UTILS, Hacktoberfest

#617 - MSSimulator (MS2): wrong m/z values for overlapping precursors [617]

Issue - State: closed - Opened by timosachsenberg over 10 years ago - 4 comments
Labels: defect, minor, UTILS

#615 - MSSimulator: Problems with peptide cleavage model [615]

Issue - State: closed - Opened by timosachsenberg over 10 years ago - 3 comments
Labels: defect, minor, UTILS, Documentation

#611 - Define transparent criteria for dependencies [611]

Issue - State: closed - Opened by timosachsenberg over 10 years ago - 1 comment
Labels: OpenMS - library, major, task

#604 - Improve external project examples [604]

Issue - State: open - Opened by timosachsenberg over 10 years ago - 4 comments
Labels: enhancement, Build System, minor, Documentation, good first issue, first-timers-only

#572 - --help --helphelp program options. [572]

Issue - State: closed - Opened by timosachsenberg over 10 years ago
Labels: enhancement, major, TOPP

#564 - Implementation of Low Memory algorithms for certain algorithms [564]

Issue - State: closed - Opened by timosachsenberg over 10 years ago - 2 comments
Labels: OpenMS - library, task, Hacktoberfest, Projects

#559 - Deprecate MascotAdapter? [559]

Issue - State: closed - Opened by timosachsenberg over 10 years ago - 6 comments
Labels: OpenMS - library, task, minor

#422 - Make "Save"-Dialog available via Menu/Shortcut and not only via right mouse click [422]

Issue - State: closed - Opened by timosachsenberg over 10 years ago - 2 comments
Labels: enhancement, TOPPView, minor, Hacktoberfest

#415 - Noise Simulation in MS2 [415]

Issue - State: closed - Opened by timosachsenberg over 10 years ago - 2 comments
Labels: OpenMS - library, major, task

#405 - Identification view: improve "mirror mode" [405]

Issue - State: closed - Opened by timosachsenberg over 10 years ago - 2 comments
Labels: enhancement, TOPPView, minor

#395 - Showing TOPP tools description in the GUI [395]

Issue - State: closed - Opened by timosachsenberg over 10 years ago - 2 comments
Labels: enhancement, TOPPView, minor, Hacktoberfest

#307 - Compute intensity statistics for peak maps [307]

Issue - State: closed - Opened by timosachsenberg over 10 years ago
Labels: enhancement, major, TOPP, Hacktoberfest

#290 - IdentificationView save modified ordering of columns [290]

Issue - State: closed - Opened by timosachsenberg over 10 years ago - 3 comments
Labels: enhancement, TOPPView, minor

#285 - Canceling dialog during loading of files [285]

Issue - State: closed - Opened by timosachsenberg over 10 years ago - 3 comments
Labels: enhancement, TOPPView, minor, usability

#256 - Remember settings by layer [256]

Issue - State: closed - Opened by timosachsenberg over 10 years ago - 1 comment
Labels: enhancement, TOPPView, minor

#219 - Store peak annotation/labels from 1D View [219]

Issue - State: closed - Opened by timosachsenberg over 10 years ago - 1 comment
Labels: enhancement, OpenMS - library, major, TOPPView

#190 - Position of survey scan/fragment scan context menu [190]

Issue - State: closed - Opened by timosachsenberg over 10 years ago - 2 comments
Labels: enhancement, wontfix, TOPPView, minor

#187 - Show peptide annotations for consensus maps [187]

Issue - State: closed - Opened by timosachsenberg over 10 years ago - 3 comments
Labels: enhancement, TOPPView, minor

#138 - Add feature list in place of spectra list [138]

Issue - State: closed - Opened by timosachsenberg over 10 years ago
Labels: enhancement, major, TOPPView

#79 - Update function for ControlledVocabularies?

Issue - State: closed - Opened by timosachsenberg over 10 years ago - 2 comments
Labels: enhancement, OpenMS - library, minor, beginner tasks

#52 - Integrate Logger into TOPPView [52]

Issue - State: closed - Opened by timosachsenberg over 10 years ago
Labels: major, TOPPView, task

#50 - Integrate Logger into TOPPBase and GUI apps [50]

Issue - State: closed - Opened by timosachsenberg over 10 years ago
Labels: major, TOPP, task

GitHub / OpenMS/OpenMS issues and pull requests