From 29bb3d4dc1bf2f283922c8f480d2b216df2cea9a Mon Sep 17 00:00:00 2001
From: Laura Gauthier <gauthier@broadinstitute.org>
Date: Wed, 12 Feb 2014 10:20:28 -0500
Subject: [PATCH] Check for empty BAM lists in command line input

---
 .../sting/gatk/GenomeAnalysisEngine.java      | 17 +++++++++++++----
 .../gatk/GenomeAnalysisEngineUnitTest.java    | 19 +++++++++++++++++++
 2 files changed, 32 insertions(+), 4 deletions(-)

diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
index 27b030060..0f7333704 100644
--- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
+++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
@@ -497,19 +497,27 @@ public class GenomeAnalysisEngine {
     }
 
     /**
-     * Verifies that the supplied set of reads files mesh with what the walker says it requires,
-     * and also makes sure that there were no duplicate SAM files specified on the command line.
+     * Verifies that the supplied set of reads files mesh with what the walker says it requires;
+     * also makes sure that list of SAM files specified on the command line is not empty and contains
+     * no duplicates.
      */
     protected void validateSuppliedReads() {
         GATKArgumentCollection arguments = this.getArguments();
+        final Boolean samFilesArePresent = (arguments.samFiles != null && !arguments.samFiles.isEmpty());
+
         // Check what the walker says is required against what was provided on the command line.
-        if (WalkerManager.isRequired(walker, DataSource.READS) && (arguments.samFiles == null || arguments.samFiles.size() == 0))
+        if (WalkerManager.isRequired(walker, DataSource.READS) && !samFilesArePresent)
             throw new ArgumentException("Walker requires reads but none were provided.");
 
         // Check what the walker says is allowed against what was provided on the command line.
-        if ((arguments.samFiles != null && arguments.samFiles.size() > 0) && !WalkerManager.isAllowed(walker, DataSource.READS))
+        if (samFilesArePresent && !WalkerManager.isAllowed(walker, DataSource.READS))
             throw new ArgumentException("Walker does not allow reads but reads were provided.");
 
+        //Make sure SAM list specified by the user (if necessary) is not empty
+        if(WalkerManager.isRequired(walker, DataSource.READS) && samFilesArePresent && samReaderIDs.isEmpty() ) {
+            throw new UserException("The list of input files does not contain any BAM files.");
+        }
+
         // Make sure no SAM files were specified multiple times by the user.
         checkForDuplicateSamFiles();
     }
@@ -535,6 +543,7 @@ public class GenomeAnalysisEngine {
             throw new UserException("The following BAM files appear multiple times in the list of input files: " +
                                     duplicateSamFiles + " BAM files may be specified at most once.");
         }
+
     }
 
     /**
diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/GenomeAnalysisEngineUnitTest.java b/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/GenomeAnalysisEngineUnitTest.java
index 84bc6e080..b10043340 100644
--- a/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/GenomeAnalysisEngineUnitTest.java
+++ b/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/GenomeAnalysisEngineUnitTest.java
@@ -28,9 +28,11 @@ package org.broadinstitute.sting.gatk;
 import org.broadinstitute.sting.BaseTest;
 import org.broadinstitute.sting.commandline.ArgumentException;
 import org.broadinstitute.sting.commandline.Tags;
+import org.broadinstitute.sting.gatk.arguments.GATKArgumentCollection;
 import org.broadinstitute.sting.gatk.datasources.reads.SAMReaderID;
 import org.broadinstitute.sting.gatk.iterators.ReadTransformer;
 import org.broadinstitute.sting.gatk.walkers.Walker;
+import org.broadinstitute.sting.gatk.walkers.qc.CountReads;
 import org.broadinstitute.sting.gatk.walkers.readutils.PrintReads;
 import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.GenomeLocSortedSet;
@@ -51,6 +53,23 @@ import java.util.*;
  */
 public class GenomeAnalysisEngineUnitTest extends BaseTest {
 
+    @Test(expectedExceptions=UserException.class)
+    public void testEmptySamFileListHandling() throws Exception {
+        GenomeAnalysisEngine testEngine = new GenomeAnalysisEngine();
+        testEngine.setWalker(new CountReads()); //generalizable to any walker requiring reads
+
+        //supply command line args so validateSuppliedReads() knows whether reads were passed in
+        GATKArgumentCollection testArgs = new GATKArgumentCollection();
+        testArgs.samFiles.add("empty.list");
+        testEngine.setArguments(testArgs);
+
+        //represents the empty list of samFiles read in from empty.list by CommandLineExecutable
+        Collection<SAMReaderID> samFiles = new ArrayList<SAMReaderID>();
+
+        testEngine.setSAMFileIDs(samFiles);
+        testEngine.validateSuppliedReads();
+    }
+
     @Test(expectedExceptions=UserException.class)
     public void testDuplicateSamFileHandlingSingleDuplicate() throws Exception {
         GenomeAnalysisEngine testEngine = new GenomeAnalysisEngine();