Skip to content

feat: native TSV output — bypass mzIdentML for OpenMS/Percolator pipelines #9

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
ypriverol merged 2 commits into from
Apr 15, 2026
Merged

feat: native TSV output — bypass mzIdentML for OpenMS/Percolator pipelines #9

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
ae86a1a
feat: add direct TSV output (-outputFormat tsv|mzid|both)
ypriverol Apr 14, 2026
a0a36bb
feat: include Percolator features in direct TSV output
ypriverol Apr 14, 2026
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
15 changes: 15 additions & 0 deletions src/main/java/edu/ucsd/msjava/msdbsearch/SearchParams.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -53,6 +53,7 @@ public class SearchParams {
private boolean allowDenseCentroidedPeaks;
private int minMSLevel;
private int maxMSLevel;
private int outputFormat; // 0=mzid, 1=tsv, 2=both

public SearchParams() {
}
Expand Down Expand Up @@ -232,6 +233,19 @@ public int getMaxMSLevel() {
return maxMSLevel;
}

/** 0=mzid, 1=tsv, 2=both */
public int getOutputFormat() {
return outputFormat;
}

public boolean writeMzid() {
return outputFormat == 0 || outputFormat == 2;
}

public boolean writeTsv() {
return outputFormat == 1 || outputFormat == 2;
}

/**
* Look for # in dataLine
* If present, remove that character and any comment after it
Expand Down Expand Up @@ -421,6 +435,7 @@ public String parse(ParamManager paramManager) {
}

allowDenseCentroidedPeaks = paramManager.getAllowDenseCentroidedPeaks() == 1;
outputFormat = paramManager.getOutputFormat();

IntRangeParameter msLevelParam = paramManager.getMSLevelParameter();
minMSLevel = msLevelParam.getMin();
Expand Down
Loading