From 23ab36a8b0ce72e9c14a2ef9f5befa31009df69b Mon Sep 17 00:00:00 2001
From: Manuel Holtgrewe <manuel.holtgrewe@bihealth.de>
Date: Fri, 26 Aug 2016 08:18:20 +0200
Subject: [PATCH] Fixing bug #248 for ENSEMBL that used `gene_id` for
 `gene_name`

closes #248
---
 CHANGELOG.md                                                  | 4 ++++
 .../compbio/jannovar/impl/parse/ensembl/EnsemblParser.java    | 4 +++-
 2 files changed, 7 insertions(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 5f425713f6..96ef100812 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -2,6 +2,10 @@
 
 ## develop
 
+### jannovar-core
+
+* fixing bug #248 for ENSEMBL that used `gene_id` for `gene_name`
+
 ## v0.17
 
 ### jped-cli
diff --git a/jannovar-core/src/main/java/de/charite/compbio/jannovar/impl/parse/ensembl/EnsemblParser.java b/jannovar-core/src/main/java/de/charite/compbio/jannovar/impl/parse/ensembl/EnsemblParser.java
index 51b859a1da..0fb35b2855 100644
--- a/jannovar-core/src/main/java/de/charite/compbio/jannovar/impl/parse/ensembl/EnsemblParser.java
+++ b/jannovar-core/src/main/java/de/charite/compbio/jannovar/impl/parse/ensembl/EnsemblParser.java
@@ -185,6 +185,7 @@ private Map<String, TranscriptModelBuilder> processGeneGFFRecords(ArrayList<Feat
 			final List<FeatureRecord> featureRecords = txEntry.getValue();
 
 			final FeatureRecord first = featureRecords.get(0);
+			final String geneName = first.getAttributes().get("gene_name");
 			final String geneID = first.getAttributes().get("gene_id");
 			final String txID = first.getAttributes().get("transcript_id");
 
@@ -194,7 +195,8 @@ private Map<String, TranscriptModelBuilder> processGeneGFFRecords(ArrayList<Feat
 			final Strand strand = (first.getStrand() == FeatureRecord.Strand.FORWARD) ? Strand.FWD : Strand.REV;
 			builder.setStrand(strand);
 			builder.setAccession(txID);
-			builder.setGeneSymbol(geneID);
+			builder.setGeneID(geneID);
+			builder.setGeneSymbol(geneName);
 			builder.setSequence(txID);
 
 			// Iterate over the features, interpreting "exon" and "CDS"/"stop_codon" entries