fix: dictionary arg

broadinstitute · Aug 5, 2024 · 32bb1dd · 32bb1dd
1 parent 87e10bc
commit 32bb1dd
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Showing 2 changed files with 5 additions and 6 deletions.
diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/conversion/CompareGtfInfo.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/conversion/CompareGtfInfo.java
@@ -2,16 +2,14 @@
 
 import htsjdk.samtools.SAMSequenceDictionary;
 import htsjdk.samtools.util.Interval;
-import org.broadinstitute.barclay.argparser.Argument;
 import org.broadinstitute.hellbender.utils.Utils;
 
 import java.util.Comparator;
 import java.util.Map;
 
 public class CompareGtfInfo implements Comparator<Map.Entry<String, GtfInfo>> {
 
-    @Argument(shortName = "SD", fullName = "SEQUENCE_DICTIONARY", optional =  true)//TODO: figure this out
-    SAMSequenceDictionary dictionary;
+    private final SAMSequenceDictionary dictionary;
 
     CompareGtfInfo(SAMSequenceDictionary dictionary) {
         this.dictionary = dictionary;

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
@@ -1,6 +1,8 @@
 package org.broadinstitute.hellbender.tools.walkers.conversion;
 
-import htsjdk.samtools.*; //TODO: make these individual imports
+import htsjdk.samtools.SAMSequenceDictionary;
+import htsjdk.samtools.SamReader;
+import htsjdk.samtools.SamReaderFactory;
 import htsjdk.samtools.util.*;
 import htsjdk.tribble.Feature;
 import org.broadinstitute.barclay.argparser.Argument;
@@ -73,7 +75,6 @@
         programGroup = ShortVariantDiscoveryProgramGroup.class
 )
 
-//TODO: make args all caps
 public class GtfToBed extends FeatureWalker<GencodeGtfFeature> {
     public static final String SORT_BY_TRANSCRIPT_LONG_NAME = "SORT_BY_TRANSCRIPT";
     public static final String SEQUENCE_DICTIONARY_LONG_NAME = "SEQUENCE_DICTIONARY";
@@ -229,7 +230,7 @@ public Object onTraversalSuccess() {
 
     // reads the dictionary
     private SAMSequenceDictionary getSequenceDictionary(String dictionaryPath) {
-        SamReader reader = SamReaderFactory.makeDefault().open(new File(dictionaryPath)); //TODO: figure out what makeDefault() does
+        SamReader reader = SamReaderFactory.makeDefault().open(new File(dictionaryPath));
 
         return reader.getFileHeader().getSequenceDictionary();
     }