Added check in the MalformedReadFilter for reads without stored bases (i.e. that use '*').

* We now throw a User Error for such reads
  * User can override this to filter instead with --filter_bases_not_stored
  * Added appropriate unit test

public/java/src/org/broadinstitute/sting/gatk/filters/MalformedReadFilter.java

@@ -45,6 +45,9 @@ public class MalformedReadFilter extends ReadFilter {
     @Argument(fullName = "filter_mismatching_base_and_quals", shortName = "filterMBQ", doc = "if a read has mismatching number of bases and base qualities, filter out the read instead of blowing up.", required = false)
     boolean filterMismatchingBaseAndQuals = false;
 
+    @Argument(fullName = "filter_bases_not_stored", shortName = "filterNoBases", doc = "if a read has no stored bases (i.e. a '*'), filter out the read instead of blowing up.", required = false)
+    boolean filterBasesNotStored = false;
+
     @Override
     public void initialize(GenomeAnalysisEngine engine) {
         this.header = engine.getSAMFileHeader();
@@ -57,7 +60,8 @@ public class MalformedReadFilter extends ReadFilter {
                 !checkAlignmentDisagreesWithHeader(this.header,read) ||
                 !checkHasReadGroup(read) ||
                 !checkMismatchingBasesAndQuals(read, filterMismatchingBaseAndQuals) ||
-                !checkCigarDisagreesWithAlignment(read);
+                !checkCigarDisagreesWithAlignment(read) ||
+                !checkSeqStored(read, filterBasesNotStored);
     }
 
     private static boolean checkHasReadGroup(final SAMRecord read) {
@@ -146,4 +150,20 @@ public class MalformedReadFilter extends ReadFilter {
 
         return result;
     }
+
+    /**
+     * Check if the read has its base sequence stored
+     * @param read the read to validate
+     * @return true if the sequence is stored and false otherwise ("*" in the SEQ field).
+     */
+    protected static boolean checkSeqStored(final SAMRecord read, final boolean filterBasesNotStored) {
+
+        if ( read.getReadBases() != SAMRecord.NULL_SEQUENCE )
+            return true;
+
+        if ( filterBasesNotStored )
+            return false;
+
+        throw new UserException.MalformedBAM(read, String.format("the BAM file has a read with no stored bases (i.e. it uses '*') which is not supported in the GATK; see the --filter_bases_not_stored argument. Offender: %s", read.getReadName()));
+    }
 }

public/java/test/org/broadinstitute/sting/gatk/filters/MalformedReadFilterUnitTest.java

@@ -0,0 +1,62 @@
+/*
+* Copyright (c) 2012 The Broad Institute
+* 
+* Permission is hereby granted, free of charge, to any person
+* obtaining a copy of this software and associated documentation
+* files (the "Software"), to deal in the Software without
+* restriction, including without limitation the rights to use,
+* copy, modify, merge, publish, distribute, sublicense, and/or sell
+* copies of the Software, and to permit persons to whom the
+* Software is furnished to do so, subject to the following
+* conditions:
+* 
+* The above copyright notice and this permission notice shall be
+* included in all copies or substantial portions of the Software.
+* 
+* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
+* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+*/
+
+package org.broadinstitute.sting.gatk.filters;
+
+import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils;
+import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
+import org.testng.Assert;
+import org.testng.annotations.Test;
+
+
+/**
+ * Tests for the MalformedReadFilter
+ *
+ * @author Eric Banks
+ * @since 3/14/13
+ */
+public class MalformedReadFilterUnitTest {
+
+    //////////////////////////////////////
+    // Test the checkSeqStored() method //
+    //////////////////////////////////////
+
+    @Test(enabled = true)
+    public void testcheckSeqStored () {
+
+        final GATKSAMRecord goodRead = ArtificialSAMUtils.createArtificialRead(new byte[]{(byte)'A'}, new byte[]{(byte)'A'}, "1M");
+        final GATKSAMRecord badRead = ArtificialSAMUtils.createArtificialRead(new byte[]{}, new byte[]{}, "1M");
+        badRead.setReadString("*");
+
+        Assert.assertTrue(MalformedReadFilter.checkSeqStored(goodRead, true));
+        Assert.assertFalse(MalformedReadFilter.checkSeqStored(badRead, true));
+
+        try {
+            MalformedReadFilter.checkSeqStored(badRead, false);
+            Assert.assertTrue(false, "We should have exceptioned out in the previous line");
+        } catch (UserException e) { }
+    }
+}