Update AbstractAlignmentMergerTest to use PicardHtsPath.

broadinstitute · May 2, 2022 · 3828906 · 3828906
1 parent f0bf3fa
commit 3828906
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Showing 3 changed files with 11 additions and 8 deletions.
diff --git a/src/main/java/picard/cmdline/argumentcollections/OptionalReferenceArgumentCollection.java b/src/main/java/picard/cmdline/argumentcollections/OptionalReferenceArgumentCollection.java
@@ -51,11 +51,12 @@ public File getReferenceFile() {
             return null;
         } else if (!REFERENCE_SEQUENCE.getScheme().equals("file")) {
             log.warn(String.format(
-                    "This tool cannot be used with non-local reference files: %s",
+                    "the reference specified by %s cannot be used as a local file object",
                     REFERENCE_SEQUENCE.getRawInputString()));
-            return null;
+            return new File(REFERENCE_SEQUENCE.getRawInputString());
+        } else {
+            return REFERENCE_SEQUENCE == null ? null : REFERENCE_SEQUENCE.toPath().toFile();
         }
-        return REFERENCE_SEQUENCE == null ? null : REFERENCE_SEQUENCE.toPath().toFile();
     }
 
     @Override

diff --git a/src/main/java/picard/cmdline/argumentcollections/RequiredReferenceArgumentCollection.java b/src/main/java/picard/cmdline/argumentcollections/RequiredReferenceArgumentCollection.java
@@ -48,11 +48,13 @@ public File getReferenceFile() {
         if (REFERENCE_SEQUENCE == null) {
             return null;
         } else if (!REFERENCE_SEQUENCE.getScheme().equals("file")) {
-                log.warn(String.format(
-                        "%s cannot bs used as a Java File object",
-                        REFERENCE_SEQUENCE.getRawInputString()));
+            log.warn(String.format(
+                    "the reference specified by %s cannot be used as a local file object",
+                    REFERENCE_SEQUENCE.getRawInputString()));
+            return new File(REFERENCE_SEQUENCE.getRawInputString());
+        } else {
+            return REFERENCE_SEQUENCE == null ? null : REFERENCE_SEQUENCE.toPath().toFile();
         }
-        return REFERENCE_SEQUENCE == null ? null : REFERENCE_SEQUENCE.toPath().toFile();
     }
 
     /**

diff --git a/src/test/java/picard/sam/AbstractAlignmentMergerTest.java b/src/test/java/picard/sam/AbstractAlignmentMergerTest.java
@@ -706,7 +706,7 @@ public void testUnmapBacterialContamination() throws IOException {
 
         //yuck!
         final RequiredReferenceArgumentCollection requiredReferenceArgumentCollection = new RequiredReferenceArgumentCollection();
-        requiredReferenceArgumentCollection.REFERENCE_SEQUENCE = new HtsPath(reference.getAbsolutePath());
+        requiredReferenceArgumentCollection.REFERENCE_SEQUENCE = new PicardHtsPath(reference.getAbsolutePath());
         mergeBamAlignment.referenceSequence = requiredReferenceArgumentCollection;
 
         final File fileMerged = newTempSamFile("merged");