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add gene id to dummy transcript #4

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add gene id to dummy transcript #4

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6 changes: 4 additions & 2 deletions src/main/java/com/github/kleinsamuel/gtfutils/GtfFile.java
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Original file line number Diff line number Diff line change
Expand Up @@ -557,7 +557,7 @@ private void groupFeatures() {
// generate the parent transcript if it does not exist
if (parentTranscript == null) {
GtfFeature feature = transcriptId2child.get(transcriptId).getFirst();
parentTranscript = this.generateDummyTranscriptFeature(feature);
parentTranscript = this.generateDummyTranscriptFeature(feature, parentGeneId);

this.id2transcript.put(transcriptId, parentTranscript);
}
Expand Down Expand Up @@ -598,14 +598,16 @@ private GeneFeature generateDummyGeneFeature(GtfFeature baseFeature, String pare
return new GeneFeature(geneBaseData, true);
}

private TranscriptFeature generateDummyTranscriptFeature(GtfFeature baseFeature) {
private TranscriptFeature generateDummyTranscriptFeature(GtfFeature baseFeature, String parentGeneId) {

HashMap<String, List<String>> transcriptAttributes = new HashMap<>();

for (String key : baseFeature.getBaseData().getAttributeKeys("transcript")) {
transcriptAttributes.put(key, baseFeature.getBaseData().getAttributes(key));
}

transcriptAttributes.computeIfAbsent(GtfConstants.GENE_ID_ATTRIBUTE_KEY, k -> Collections.singletonList(parentGeneId));

GtfBaseData transcriptBaseData = new GtfBaseData(baseFeature.getBaseData().getContig(),
baseFeature.getBaseData().getSource(),
GtfConfig.TYPE_TRANSCRIPT_DEFAULT, -1, -1, null,
Expand Down