Merge pull request #630 from broadinstitute/pd_blank_lines_in_listfile

Allow blank lines in a (non-BAM) list file

public/gatk-framework/src/main/java/org/broadinstitute/sting/commandline/ArgumentTypeDescriptor.java

@@ -25,7 +25,6 @@
 
 package org.broadinstitute.sting.commandline;
 
-import org.apache.commons.io.FileUtils;
 import org.apache.log4j.Logger;
 import htsjdk.tribble.Feature;
 import org.broadinstitute.sting.gatk.refdata.tracks.FeatureManager;
@@ -35,6 +34,7 @@ import org.broadinstitute.sting.utils.classloader.JVMUtils;
 import org.broadinstitute.sting.utils.exceptions.DynamicClassResolutionException;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.sting.utils.text.XReadLines;
 
 import java.io.File;
 import java.io.IOException;
@@ -477,7 +477,7 @@ public abstract class ArgumentTypeDescriptor {
         final Set<String> fileValues = new HashSet<>();
 
         // parse each line separately using the given Tags if none are provided on each line
-        for ( final String line: FileUtils.readLines(file) ) {
+        for ( final String line: new XReadLines(file) ) {
             final String[] tokens = line.split("\\s+");
             final RodBinding binding;
 

public/gatk-framework/src/test/java/org/broadinstitute/sting/commandline/ArgumentTypeDescriptorUnitTest.java

@@ -25,6 +25,7 @@
 
 package org.broadinstitute.sting.commandline;
 
+import htsjdk.variant.variantcontext.VariantContext;
 import it.unimi.dsi.fastutil.objects.ObjectArrayList;
 import htsjdk.samtools.SAMFileWriter;
 import org.broadinstitute.sting.BaseTest;
@@ -36,6 +37,8 @@ import org.testng.Assert;
 import org.testng.annotations.DataProvider;
 import org.testng.annotations.Test;
 
+import java.io.File;
+import java.io.IOException;
 import java.io.PrintStream;
 import java.util.Arrays;
 import java.util.Collection;
@@ -167,6 +170,54 @@ public class ArgumentTypeDescriptorUnitTest extends BaseTest {
         }
     }
 
+    @Test
+    public void testRodBindingsCollection() {
+
+        final ParsingEngine parser = new ParsingEngine(new ATDTestCommandLineProgram());
+
+        //A list file containing a single VCF
+        final File listFile = new File(privateTestDir+"oneVCF.list");
+
+        try {
+            Object result = ArgumentTypeDescriptor.getRodBindingsCollection(listFile,
+                    parser,
+                    VariantContext.class,
+                    "variant",
+                    new Tags(),
+                    "variantTest");
+            if (!(result instanceof RodBindingCollection))
+                throw new ReviewedStingException("getRodBindingsCollection did not return a RodBindingCollection");
+            RodBindingCollection<?> rbc = (RodBindingCollection) result;
+
+            Assert.assertEquals(rbc.getType(), VariantContext.class);
+            Assert.assertEquals(rbc.getRodBindings().size(), 1);
+
+        } catch (IOException e) {
+            throw new ReviewedStingException(e.getMessage(), e);
+        }
+
+        //The same file, now with an extra blank line
+        final File listFileWithBlank = new File(privateTestDir+"oneVCFwithBlankLine.list");
+
+        try {
+            Object result = ArgumentTypeDescriptor.getRodBindingsCollection(listFileWithBlank,
+                    parser,
+                    VariantContext.class,
+                    "variant",
+                    new Tags(),
+                    "variantTest");
+            if (!(result instanceof RodBindingCollection))
+                throw new ReviewedStingException("getRodBindingsCollection did not return a RodBindingCollection");
+            RodBindingCollection<?> rbc = (RodBindingCollection) result;
+
+            Assert.assertEquals(rbc.getType(), VariantContext.class);
+            Assert.assertEquals(rbc.getRodBindings().size(), 1);
+
+        } catch (IOException e) {
+            throw new ReviewedStingException(e.getMessage(), e);
+        }
+    }
+
     private static boolean outputIsStdout(final Object out) {
         if ( out == null ) {
             return false;