Optimizations:

1. push the ReadBackedPileup filtering up into the ReadFilters for read-based filters
2. stop querying the cigar for its length (just do it once)


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2381 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/gatk/filters/BadMateReadFilter.java

@@ -0,0 +1,46 @@
+/*
+ * Copyright (c) 2009 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 net.sf.picard.filter.SamRecordFilter;
+import net.sf.samtools.SAMRecord;
+import org.broadinstitute.sting.utils.cmdLine.Argument;
+
+/**
+ * Filter out reads with low mapping qualities.
+ *
+ * @author ebanks
+ * @version 0.1
+ */
+
+public class BadMateReadFilter implements SamRecordFilter {
+
+    @Argument(fullName = "use_reads_with_bad_mates", shortName = "bad_mates", doc = "Use reads whose mates are mapped excessively far away for calling", required = false)
+    public boolean USE_BADLY_MATED_READS = false;
+
+    public boolean filterOut(SAMRecord rec) {
+        return (!USE_BADLY_MATED_READS && rec.getReadPairedFlag() && !rec.getMateUnmappedFlag() && rec.getMateReferenceIndex() != rec.getReferenceIndex());
+    }
+}

java/src/org/broadinstitute/sting/gatk/filters/MappingQualityReadFilter.java

@@ -0,0 +1,46 @@
+/*
+ * Copyright (c) 2009 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 net.sf.picard.filter.SamRecordFilter;
+import net.sf.samtools.SAMRecord;
+import org.broadinstitute.sting.utils.cmdLine.Argument;
+
+/**
+ * Filter out reads with low mapping qualities.
+ *
+ * @author ebanks
+ * @version 0.1
+ */
+
+public class MappingQualityReadFilter implements SamRecordFilter {
+
+    @Argument(fullName = "min_mapping_quality_score", shortName = "mmq", doc = "Minimum read mapping quality required to consider a read for calling", required = false)
+    public int MIN_MAPPING_QUALTY_SCORE = 30;
+
+    public boolean filterOut(SAMRecord rec) {
+        return (rec.getMappingQuality() < MIN_MAPPING_QUALTY_SCORE);
+    }
+}

java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageWalker.java

@@ -115,7 +115,7 @@ public class DepthOfCoverageWalker extends LocusWalker<DepthOfCoverageWalker.DoC
 
         // fill in and print all of the per-locus coverage data, then return it to reduce
 
-        ReadBackedPileup pileup = context.getPileup().getBaseAndMappingFilteredPileup(minBaseQ, -1);
+        ReadBackedPileup pileup = context.getPileup().getBaseFilteredPileup(minBaseQ);
 
         DoCInfo info = new DoCInfo();
         info.totalCoverage = pileup.size();

java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java

@@ -91,12 +91,6 @@ public class UnifiedArgumentCollection {
     @Argument(fullName = "min_base_quality_score", shortName = "mbq", doc = "Minimum base quality required to consider a base for calling", required = false)
     public int MIN_BASE_QUALTY_SCORE = 20;
 
-    @Argument(fullName = "min_mapping_quality_score", shortName = "mmq", doc = "Minimum read mapping quality required to consider a read for calling (MQ0 reads are ignored regardless)", required = false)
-    public int MIN_MAPPING_QUALTY_SCORE = 30;
-
     @Argument(fullName = "max_mismatches_in_40bp_window", shortName = "mm40", doc = "Maximum number of mismatches within a 40 bp window (20bp on either side) around the target position for a read to be used for calling", required = false)
     public int MAX_MISMATCHES = 3;
-
-    @Argument(fullName = "use_reads_with_bad_mates", shortName = "bad_mates", doc = "Use reads whose mates are mapped excessively far away for calling", required = false)
-    public boolean USE_BADLY_MATED_READS = false;
 }

java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java

@@ -26,7 +26,7 @@
 package org.broadinstitute.sting.gatk.walkers.genotyper;
 
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
-import org.broadinstitute.sting.gatk.filters.ZeroMappingQualityReadFilter;
+import org.broadinstitute.sting.gatk.filters.*;
 import org.broadinstitute.sting.gatk.contexts.*;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.*;
@@ -38,6 +38,7 @@ import org.broadinstitute.sting.utils.genotype.*;
 import org.broadinstitute.sting.utils.genotype.vcf.*;
 
 import net.sf.samtools.SAMReadGroupRecord;
+import net.sf.picard.filter.SamRecordFilter;
 
 import java.io.File;
 import java.util.*;
@@ -48,7 +49,7 @@ import java.util.*;
  * multi-sample, and pooled data.  The user can choose from several different incorporated calculation models.
  */
 @Reference(window=@Window(start=-20,stop=20))
-@ReadFilters({ZeroMappingQualityReadFilter.class})
+@ReadFilters({ZeroMappingQualityReadFilter.class,MappingQualityReadFilter.class,BadMateReadFilter.class})
 public class UnifiedGenotyper extends LocusWalker<Pair<VariationCall, List<Genotype>>, Integer> {
 
     @ArgumentCollection private UnifiedArgumentCollection UAC = new UnifiedArgumentCollection();
@@ -183,7 +184,10 @@ public class UnifiedGenotyper extends LocusWalker<Pair<VariationCall, List<Genot
             headerInfo.addAll(VCFGenotypeRecord.getSupportedHeaderStrings());
 
         // all of the arguments from the argument collection
-        Map<String,String> commandLineArgs = CommandLineUtils.getApproximateCommandLineArguments(Collections.<Object>singleton(UAC));
+        Set<Object> x = new HashSet<Object>();
+        x.add(UAC);
+        x.addAll(getToolkit().getFilters());
+        Map<String,String> commandLineArgs = CommandLineUtils.getApproximateCommandLineArguments(x);
         for ( Map.Entry<String, String> commandLineArg : commandLineArgs.entrySet() )
             headerInfo.add(new VCFHeaderLine(String.format("UG_%s", commandLineArg.getKey()), commandLineArg.getValue()));            
 
@@ -203,10 +207,10 @@ public class UnifiedGenotyper extends LocusWalker<Pair<VariationCall, List<Genot
             return null;
 
         // filter the context based on min base and mapping qualities
-        ReadBackedPileup pileup = rawContext.getPileup().getBaseAndMappingFilteredPileup(UAC.MIN_BASE_QUALTY_SCORE, UAC.MIN_MAPPING_QUALTY_SCORE);
+        ReadBackedPileup pileup = rawContext.getPileup().getBaseFilteredPileup(UAC.MIN_BASE_QUALTY_SCORE);
 
-        // filter the context based on mismatches and reads with bad mates
+        // filter the context based on mismatches
-        pileup = filterPileup(pileup, refContext, UAC.MAX_MISMATCHES, UAC.USE_BADLY_MATED_READS);
+        pileup = filterPileup(pileup, refContext, UAC.MAX_MISMATCHES);
 
         // an optimization to speed things up when there is no coverage or when overly covered
         if ( pileup.size() == 0 ||
@@ -241,11 +245,10 @@ public class UnifiedGenotyper extends LocusWalker<Pair<VariationCall, List<Genot
     }
 
     // filter based on maximum mismatches and bad mates
-    private static ReadBackedPileup filterPileup(ReadBackedPileup pileup, ReferenceContext refContext, int maxMismatches, boolean useBadMates) {
+    private static ReadBackedPileup filterPileup(ReadBackedPileup pileup, ReferenceContext refContext, int maxMismatches) {
         ArrayList<PileupElement> filteredPileup = new ArrayList<PileupElement>();
         for ( PileupElement p : pileup ) {
-            if ( (useBadMates || !p.getRead().getReadPairedFlag() || p.getRead().getMateUnmappedFlag() || p.getRead().getMateReferenceIndex() == p.getRead().getReferenceIndex()) &&
+            if ( AlignmentUtils.mismatchesInRefWindow(p, refContext, true) <= maxMismatches )
-                 AlignmentUtils.mismatchesInRefWindow(p, refContext, true) <= maxMismatches )
                 filteredPileup.add(p);
         }
         return new ReadBackedPileup(pileup.getLocation(), filteredPileup);

java/src/org/broadinstitute/sting/utils/AlignmentUtils.java

@@ -180,26 +180,28 @@ public class AlignmentUtils {
 
         int mismatches = 0;
 
-        GenomeLoc window = ref.getWindow();
+        int windowStart = (int)ref.getWindow().getStart();
+        int windowStop = (int)ref.getWindow().getStop();
         char[] refBases = ref.getBases();
         byte[] readBases = p.getRead().getReadBases();
         Cigar c = p.getRead().getCigar();
 
         int readIndex = 0;
         int currentPos = p.getRead().getAlignmentStart();
-        int refIndex = Math.max(0, currentPos - (int)window.getStart());
+        int refIndex = Math.max(0, currentPos - windowStart);
 
         for (int i = 0 ; i < c.numCigarElements() ; i++) {
             CigarElement ce = c.getCigarElement(i);
+            int cigarElementLength = ce.getLength();
             switch ( ce.getOperator() ) {
                 case M:
-                    for (int j = 0; j < ce.getLength(); j++, readIndex++, currentPos++) {
+                    for (int j = 0; j < cigarElementLength; j++, readIndex++, currentPos++) {
                         // are we past the ref window?
-                        if ( currentPos > window.getStop() )
+                        if ( currentPos > windowStop )
                             break;
 
                         // are we before the ref window?
-                        if ( currentPos < window.getStart() )
+                        if ( currentPos < windowStart )
                             continue;
 
                         char refChr = refBases[refIndex++];
@@ -214,15 +216,15 @@ public class AlignmentUtils {
                     }
                     break;
                 case I:
-                    readIndex += ce.getLength();
+                    readIndex += cigarElementLength;
                     break;
                 case D:
-                    currentPos += ce.getLength();
+                    currentPos += cigarElementLength;
-                    if ( currentPos > window.getStart() )
+                    if ( currentPos > windowStart )
-                        refIndex += Math.min(ce.getLength(), currentPos - window.getStart());
+                        refIndex += Math.min(cigarElementLength, currentPos - windowStart);
                     break;
                 case S:
-                    readIndex += ce.getLength();
+                    readIndex += cigarElementLength;
                     break;
                 default: throw new StingException("Only M,I,D,S cigar elements are currently supported; there was " + ce.getOperator());
             }

java/src/org/broadinstitute/sting/utils/pileup/ReadBackedPileup.java

@@ -176,6 +176,11 @@ public class ReadBackedPileup implements Iterable<PileupElement> {
 
         return new ReadBackedPileup(loc, filteredPileup);
     }
+
+    public ReadBackedPileup getBaseFilteredPileup( int minBaseQ ) {
+        return getBaseAndMappingFilteredPileup(minBaseQ, -1);
+    }
+        
     /**
      * Returns a pileup randomly downsampled to the desiredCoverage.
      *