Added a new filter that can be used to remove reads that are too small and overly clipped.

public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/filters/OverclippedReadFilter.java

@@ -0,0 +1,74 @@
+/*
+* 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.gatk.engine.filters;
+
+import htsjdk.samtools.*;
+import org.broadinstitute.gatk.utils.commandline.Argument;
+import org.broadinstitute.gatk.engine.GenomeAnalysisEngine;
+import org.broadinstitute.gatk.engine.ReadProperties;
+import org.broadinstitute.gatk.utils.ValidationExclusion;
+import org.broadinstitute.gatk.engine.datasources.reads.SAMDataSource;
+import org.broadinstitute.gatk.utils.exceptions.UserException;
+
+/**
+ * Filter out reads that are over-soft-clipped
+ *
+ * <p>
+ *     This filter is intended to filter out reads that are potentially from foreign organisms.
+ *     From experience with sequencing of human DNA we have found cases of contamination by bacterial
+ *     organisms; the symptoms of such contamination are a class of reads with only a small number
+ *     of aligned bases and additionally many soft-clipped bases on both ends.  This filter is intended
+ *     to remove such reads.
+ * </p>
+ *
+ */
+public class OverclippedReadFilter extends ReadFilter {
+
+    @Argument(fullName = "filter_is_too_short_value", shortName = "filterTooShort", doc = "Value for which reads with less than this number of aligned bases is considered too short", required = false)
+    int tooShort = 30;
+
+
+    public boolean filterOut(final SAMRecord read) {
+        boolean sawLeadingSoftclip = false;
+        boolean sawAlignedBase = false;
+        int alignedLength = 0;
+
+        for ( final CigarElement element : read.getCigar().getCigarElements() ) {
+            if ( element.getOperator() == CigarOperator.S ) {
+                if ( sawAlignedBase )  // if this is true then we must also have seen a leading soft-clip
+                    return (alignedLength < tooShort);
+                sawLeadingSoftclip = true;
+            } else if ( element.getOperator().consumesReadBases() ) {   // M, I, X, and EQ (S was already accounted for above)
+                if ( !sawLeadingSoftclip )
+                    return false;
+                sawAlignedBase = true;
+                alignedLength += element.getLength();
+            }
+        }
+
+        return false;
+    }
+}

public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/filters/OverclippedReadFilterUnitTest.java

@@ -0,0 +1,77 @@
+/*
+* 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.gatk.engine.filters;
+
+
+import htsjdk.samtools.Cigar;
+import htsjdk.samtools.SAMRecord;
+import htsjdk.samtools.TextCigarCodec;
+import org.testng.Assert;
+import org.testng.annotations.DataProvider;
+import org.testng.annotations.Test;
+
+import java.util.*;
+
+
+/**
+ * Tests for the OverclippedReadFilter
+ */
+public class OverclippedReadFilterUnitTest extends ReadFilterTest {
+
+    @Test(enabled = true, dataProvider= "OverclippedDataProvider")
+    public void testOverclippedFilter(final String cigarString, final boolean expectedResult) {
+
+       final OverclippedReadFilter filter = new OverclippedReadFilter();
+       final SAMRecord read = buildSAMRecord(cigarString);
+       Assert.assertEquals(filter.filterOut(read), expectedResult, cigarString);
+    }
+
+    private SAMRecord buildSAMRecord(final String cigarString) {
+        final Cigar cigar = TextCigarCodec.decode(cigarString);
+        return this.createRead(cigar, 1, 0, 10);
+    }
+
+    @DataProvider(name= "OverclippedDataProvider")
+    public Iterator<Object[]> overclippedDataProvider() {
+        final List<Object[]> result = new LinkedList<Object[]>();
+
+        result.add(new Object[] { "1S10M1S", true });
+        result.add(new Object[] { "1S10X1S", true });
+        result.add(new Object[] { "1H1S10M1S1H", true });
+        result.add(new Object[] { "1S40M1S", false });
+        result.add(new Object[] { "1S40X1S", false });
+        result.add(new Object[] { "1H10M1S", false });
+        result.add(new Object[] { "1S10M1H", false });
+        result.add(new Object[] { "10M1S", false });
+        result.add(new Object[] { "1S10M", false });
+        result.add(new Object[] { "1S10M10D10M1S", true });
+        result.add(new Object[] { "1S1M40I1S", false });
+        result.add(new Object[] { "1S10I1S", true });
+        result.add(new Object[] { "1S40I1S", false });
+
+        return result.iterator();
+    }
+}