Command-line arguments for SamReadFilters.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2014 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/gatk/CommandLineExecutable.java

@@ -11,10 +11,9 @@ import org.broadinstitute.sting.gatk.io.stubs.SAMFileReaderArgumentTypeDescripto
 
 import java.io.File;
 import java.io.FileNotFoundException;
-import java.util.List;
+import java.util.*;
-import java.util.ArrayList;
+
-import java.util.Collection;
+import net.sf.picard.filter.SamRecordFilter;
-import java.util.Arrays;
 
 /*
  * Copyright (c) 2009 The Broad Institute
@@ -77,16 +76,19 @@ public abstract class CommandLineExecutable extends CommandLineProgram {
 
     protected Object executeGATK() {
         Walker<?,?> mWalker = GATKEngine.getWalkerByName(getAnalysisName());
+        Collection<SamRecordFilter> filters = GATKEngine.getFiltersForWalker(getArgumentCollection(),mWalker);
 
-        // load the arguments into the walkers
+        // load the arguments into the walker / filters.
         loadArgumentsIntoObject(mWalker);
+        for(SamRecordFilter filter: filters)
+            loadArgumentsIntoObject(filter);
 
         // process any arguments that need a second pass
         GATKArgumentCollection arguments = getArgumentCollection();
         processArguments(arguments);
 
         // set the analysis name in the argument collection
-        return GATKEngine.execute(arguments, mWalker);
+        return GATKEngine.execute(arguments, mWalker, filters);
     }
 
     /**
@@ -118,7 +120,18 @@ public abstract class CommandLineExecutable extends CommandLineProgram {
     protected Class[] getArgumentSources() {
         // No walker info?  No plugins.
         if (getAnalysisName() == null) return new Class[] {};
-        return new Class[] { GATKEngine.getWalkerByName(getAnalysisName()).getClass() };
+
+        Collection<Class> argumentSources = new ArrayList<Class>();
+
+        Walker walker = GATKEngine.getWalkerByName(getAnalysisName());
+        argumentSources.add(walker.getClass());
+
+        Collection<SamRecordFilter> filters = GATKEngine.getFiltersForWalker(getArgumentCollection(),walker);
+        for(SamRecordFilter filter: filters)
+            argumentSources.add(filter.getClass());
+
+        Class[] argumentSourcesAsArray = new Class[argumentSources.size()];
+        return argumentSources.toArray(argumentSourcesAsArray);
     }
 
     @Override

java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java

@@ -123,7 +123,7 @@ public class GenomeAnalysisEngine {
      * @param my_walker Walker to run over the dataset.  Must not be null.
      * @return the value of this traversal.
      */
-    public Object execute(GATKArgumentCollection args, Walker<?, ?> my_walker) {
+    public Object execute(GATKArgumentCollection args, Walker<?, ?> my_walker, Collection<SamRecordFilter> filters) {
         // validate our parameters
         if (args == null) {
             throw new StingException("The GATKArgumentCollection passed to GenomeAnalysisEngine can not be null.");
@@ -137,7 +137,7 @@ public class GenomeAnalysisEngine {
         this.argCollection = args;
 
         // Prepare the data for traversal.
-        initializeDataSources(my_walker, argCollection);
+        initializeDataSources(my_walker, filters, argCollection);
 
         // our microscheduler, which is in charge of running everything
         MicroScheduler microScheduler = createMicroscheduler(my_walker);
@@ -203,10 +203,26 @@ public class GenomeAnalysisEngine {
         return walkerManager.getName(walkerType);
     }
 
-    private void initializeDataSources(Walker my_walker, GATKArgumentCollection argCollection) {
+    /**
+     * Gets a list of the filters to associate with the given walker.  Will NOT initialize the engine with this filters;
+     * the caller must handle that directly.
+     * @param walker Walker to use when determining which filters to apply.
+     * @return A collection of available filters.
+     */
+    public Collection<SamRecordFilter> getFiltersForWalker(GATKArgumentCollection args, Walker walker) {
+        Set<SamRecordFilter> filters = new HashSet<SamRecordFilter>();        
+        filters.addAll(WalkerManager.getReadFilters(walker,filterManager));
+        if (args.filterZeroMappingQualityReads != null && args.filterZeroMappingQualityReads)
+            filters.add(new ZeroMappingQualityReadFilter());
+        for(String filterName: args.readFilters)
+            filters.add(filterManager.createByName(filterName));
+        return Collections.unmodifiableSet(filters);
+    }
+
+    private void initializeDataSources(Walker my_walker, Collection<SamRecordFilter> filters, GATKArgumentCollection argCollection) {
         validateSuppliedReadsAgainstWalker(my_walker, argCollection);
         logger.info("Strictness is " + argCollection.strictnessLevel);
-        readsDataSource = createReadsDataSource(extractSourceInfo(my_walker, argCollection));
+        readsDataSource = createReadsDataSource(extractSourceInfo(my_walker, filters, argCollection));
 
         validateSuppliedReferenceAgainstWalker(my_walker, argCollection);
         referenceDataSource = openReferenceSequenceFile(argCollection.referenceFile);
@@ -390,15 +406,7 @@ public class GenomeAnalysisEngine {
      * @param argCollection The collection of arguments passed to the engine.
      * @return The reads object providing reads source info.
      */
-    private Reads extractSourceInfo(Walker walker, GATKArgumentCollection argCollection) {
+    private Reads extractSourceInfo(Walker walker, Collection<SamRecordFilter> filters, GATKArgumentCollection argCollection) {
-        List<SamRecordFilter> filters = new ArrayList<SamRecordFilter>();
-
-        filters.addAll(WalkerManager.getReadFilters(walker,filterManager));
-        if (argCollection.filterZeroMappingQualityReads != null && argCollection.filterZeroMappingQualityReads)
-            filters.add(new ZeroMappingQualityReadFilter());
-        for(String filterName: argCollection.readFilters)
-            filters.add(filterManager.createByName(filterName));
-
         return new Reads(argCollection.samFiles,
                 argCollection.strictnessLevel,
                 argCollection.downsampleFraction,

java/src/org/broadinstitute/sting/gatk/Reads.java

@@ -6,6 +6,7 @@ import net.sf.samtools.SAMFileReader;
 import java.io.File;
 import java.util.ArrayList;
 import java.util.List;
+import java.util.Collection;
 /**
  * User: hanna
  * Date: May 14, 2009
@@ -29,7 +30,7 @@ public class Reads {
     private Double downsamplingFraction = null;
     private Integer downsampleToCoverage = null;
     private Boolean beSafe = null;
-    private List<SamRecordFilter> supplementalFilters = null;
+    private Collection<SamRecordFilter> supplementalFilters = null;
     private int maximumReadsAtLocus = Integer.MAX_VALUE; // this should always be set, so we'll default it MAX_INT
     private boolean includeReadsWithDeletionAtLoci = false;
 
@@ -91,7 +92,7 @@ public class Reads {
         return beSafe;
     }
 
-    public List<SamRecordFilter> getSupplementalFilters() {
+    public Collection<SamRecordFilter> getSupplementalFilters() {
         return supplementalFilters;
     }
 
@@ -120,7 +121,7 @@ public class Reads {
            Double downsampleFraction,
            Integer downsampleCoverage,
            Boolean beSafe,
-           List<SamRecordFilter> supplementalFilters,
+           Collection<SamRecordFilter> supplementalFilters,
            int maximumReadsAtLocus,
            boolean includeReadsWithDeletionAtLoci) {
         this.readsFiles = samFiles;

java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SAMDataSource.java

@@ -19,6 +19,7 @@ import org.broadinstitute.sting.utils.sam.SAMReadViolationHistogram;
 
 import java.io.File;
 import java.util.List;
+import java.util.Collection;
 
 /*
  * Copyright (c) 2009 The Broad Institute
@@ -419,7 +420,7 @@ public class SAMDataSource implements SimpleDataSource {
                                                       StingSAMIterator wrappedIterator,
                                                       Double downsamplingFraction,
                                                       Boolean beSafeP,
-                                                      List<SamRecordFilter> supplementalFilters) {
+                                                      Collection<SamRecordFilter> supplementalFilters) {
         // NOTE: this (and other filtering) should be done before on-the-fly sorting
         //  as there is no reason to sort something that we will end of throwing away
         if (downsamplingFraction != null)

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

@@ -0,0 +1,22 @@
+package org.broadinstitute.sting.gatk.filters;
+
+import net.sf.picard.filter.SamRecordFilter;
+import net.sf.samtools.SAMRecord;
+import org.broadinstitute.sting.utils.cmdLine.Argument;
+
+/**
+ * Filters out reads whose length is >= some value.
+ *
+ * @author mhanna
+ * @version 0.1
+ */
+public class MaxReadLengthFilter implements SamRecordFilter {
+    @Argument(fullName = "maxReadLength", shortName = "maxRead", doc="Discard reads with length greater than the specified value", required=true)
+    private int maxReadLength;
+    
+    public boolean filterOut(SAMRecord read) {
+        // check the length
+        return read.getReadLength() > maxReadLength;
+    }
+
+}

java/src/org/broadinstitute/sting/gatk/walkers/PrintReadsWalker.java

@@ -42,8 +42,6 @@ public class PrintReadsWalker extends ReadWalker<SAMRecord, SAMFileWriter> {
     /** an optional argument to dump the reads out to a BAM file */
     @Argument(fullName = "outputBamFile", shortName = "of", doc = "Write output to this BAM filename instead of STDOUT", required = false)
     SAMFileWriter outputBamFile = null;
-    @Argument(fullName = "maxReadLength", shortName = "maxRead", doc="Discard reads with length greater than the specified value", required = false)
-    Integer maxLength = null;
     @Argument(fullName = "readGroup", shortName = "readGroup", doc="Discard reads not belonging to the specified read group", required = false)
     String readGroup = null;
     @Argument(fullName = "platform", shortName = "platform", doc="Discard reads not generated by the specified platform", required = false)
@@ -65,10 +63,6 @@ public class PrintReadsWalker extends ReadWalker<SAMRecord, SAMFileWriter> {
      * @return true if the read passes the filter, false if it doesn't
      */
     public boolean filter(char[] ref, SAMRecord read) {
-        // check the length
-        if ( maxLength != null && read.getReadLength() > maxLength )
-            return false;
-
         // check the read group
         if  ( readGroup != null ) {
             SAMReadGroupRecord myReadGroup = read.getReadGroup();