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When soloOutFormatFeaturesGeneField3 is +, write GeneBiotype as FeaturesGeneField3. #2071

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When soloOutFormatFeaturesGeneField3 is +, write GeneBiotype as FeaturesGeneField3. #2071

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5 changes: 4 additions & 1 deletion source/SoloFeature_outputResults.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -35,7 +35,10 @@ void SoloFeature::outputResults(bool cellFilterYes, string outputPrefixMat)
for (uint32 ii=0; ii<Trans.nGe; ii++) {
geneStr << Trans.geID[ii] <<"\t"<< (Trans.geName[ii].empty() ? Trans.geID[ii] : Trans.geName[ii]);
if (pSolo.outFormat.featuresGeneField3!="-") {
geneStr <<'\t'<< pSolo.outFormat.featuresGeneField3;
if (pSolo.outFormat.featuresGeneField3 == "+")
geneStr <<'\t'<< (Trans.geBiotype[ii].empty() ? "MissingGeneType" : Trans.geBiotype[ii]);
else
geneStr <<'\t'<< pSolo.outFormat.featuresGeneField3;
};
geneStr << '\n';
};
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2 changes: 1 addition & 1 deletion source/parametersDefault
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Expand Up @@ -907,7 +907,7 @@ soloCellFilter CellRanger2.2 3000 0.99 10
The harcoded values are from CellRanger: 3000 0.99 10 45000 90000 500 0.01 20000 0.01 10000

soloOutFormatFeaturesGeneField3 "Gene Expression"
string(s): field 3 in the Gene features.tsv file. If "-", then no 3rd field is output.
string(s): field 3 in the Gene features.tsv file. If "+", then GeneBiotype is used. If "-", then no 3rd field is output.

soloCellReadStats None
string: Output reads statistics for each CB
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