Abgabe MzML #164
Open
Abgabe MzML #164
Conversation
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
added 30 commits
April 14, 2025 14:32
…UE, added english comments, MzMLFile.cpp reverted, removed wordexp
BelaPfeffer
reviewed
May 16, 2025
| } | ||
|
|
||
| filter.push(*pigz_pipe); | ||
| output_stream = &filter; |
There was a problem hiding this comment.
Was genau passiert hier mit den Pointern.
.gitignore
Outdated
| src/openms_gui/OpenMS_GUI_autogen | ||
| src/openms/OpenMS_autogen | ||
| src/openms/OpenMS_autogen | ||
| files.associations: {"iosfwd": "cpp", "cctype": "cpp"} |
.vscode/settings.json
Outdated
Comment on lines
78
to
84
| "__split_buffer": "cpp", | ||
| "__string": "cpp", | ||
| "__threading_support": "cpp", | ||
| "__tuple": "cpp", | ||
| "ios": "cpp", | ||
| "locale": "cpp", | ||
| "queue": "cpp" |
|
|
||
| typedef MzMLHandlerHelper::BinaryData BinaryData; | ||
|
|
||
| bool compress_mode_ = false; |
There was a problem hiding this comment.
Gibt es einen besseren Namen und warum compress_mode_ ?
Co-authored-by: fares-kahwaji <fares.alkahwaji2002@gmail.com>
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
3 participants
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Description
The plan was to implement boost for a .gz compression for MzML files.
We changed the writeto() function in the MzMLHandler to be able to start compression, if the outputfile has the ending .gz
Boost is very slow, since it only has single threading. There is a different tool called pigz, which is capable of doing multi threading and is very fast.
We added a if else for pigz and boost, depending on what is installed on the system and kept the no compression alternative aswell.
With the -threads n (1-n threads) at the end of the run command it can be determined on how many threads will be used, this includes a dynamic compression level.
We added a new Test in MzMLFile_test to test the compression.
Current problem: Compiler cant find, some libs, need to be included in Cmake
Checklist
How can I get additional information on failed tests during CI
Click to expand
If your PR is failing you can check outIf you click in the column that lists the failed tests you will get detailed error messages.
Advanced commands (admins / reviewer only)
Click to expand
/reformat(experimental) applies the clang-format style changes as additional commit. Note: your branch must have a different name (e.g., yourrepo:feature/XYZ) than the receiving branch (e.g., OpenMS:develop). Otherwise, reformat fails to push.rebuild jenkinswill retrigger Jenkins-based CI builds