fix: move mapk1.gtf to large dir

broadinstitute · Aug 22, 2024 · ebaf095 · ebaf095
1 parent 050dc49
commit ebaf095
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Showing 4 changed files with 5 additions and 78 deletions.
diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/conversion/GtfToBed.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/conversion/GtfToBed.java
@@ -190,7 +190,7 @@ private void updateGeneEnd(GencodeGtfFeature gtfFeature) {
         // get the end value of the gene
         int geneEnd = featureInfoMap.get(gtfFeature.getGeneId()).getEnd();
 
-        // if the transcript start is greater than the gene start
+        // if the transcript end is greater than the gene end
         if (gtfFeature.getEnd() > geneEnd) {
             // set the gene end to be the transcript end
             geneEnd = gtfFeature.getEnd();
@@ -211,7 +211,6 @@ public Object onTraversalSuccess() {
         // get dictionary
         SAMSequenceDictionary sequenceDictionary = getBestAvailableSequenceDictionary();
 
-
         // create linked hash map to store sorted values of idToInfo
         LinkedHashMap<String, GtfInfo> karyotypeIdToInfo = getSortedMap(sequenceDictionary);
 

diff --git a/...test/java/org/broadinstitute/hellbender/tools/walkers/conversion/ConversionTestUtils.java b/...test/java/org/broadinstitute/hellbender/tools/walkers/conversion/ConversionTestUtils.java
@@ -13,7 +13,7 @@ public static String getDecoySampleGtf(){
     }
 
     public static String getMapk1Gtf(){
-        return getTestDataDir()+"/mapk1.gtf";
+        return GATKBaseTest.largeFileTestDir + "/gtfToBed/mapk1.gtf";
     }
 
     public static String getManyTranscriptsGtf(){
@@ -24,10 +24,6 @@ public static String getReferenceDict(){
         return getTestDataDir()+"/reference.dict";
     }
 
-//    public static String getReferenceDict(){
-//        return GATKBaseTest.publicTestDir + "large/Homo_sapiens_assembly38.dict";
-//    }
-
     public static String getDecoySamplesGeneBed(){
         return getTestDataDir() + "/decoySampleGene.bed";
     }

diff --git a/src/test/resources/large/gtfToBed/mapk1.gtf b/src/test/resources/large/gtfToBed/mapk1.gtf