Added some documentation to the helper classes. Fixed an error case in TableRecalibrationWalker.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2046 348d0f76-0448-11de-a6fe-93d51630548a
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rpoplin
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@ -390,6 +390,7 @@ public class CovariateCounterWalker extends LocusWalker<Integer, PrintStream> {
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// For each Covariate in the key
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for( Comparable comp : entry.getKey() ) {
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// Output the Covariate's value
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if( NO_PRINT_HEADER && comp instanceof String ) { continue; } // BUGBUG
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recalTableStream.print( comp + "," );
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}
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// Output the RecalDatum entry
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@ -63,7 +63,7 @@ public class CycleCovariate implements Covariate {
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}
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return cycle;
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} else if( platform.equalsIgnoreCase( "454" ) ) {
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int cycle = 1;
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int cycle = 0;
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char prevBase = bases[0];
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for( int iii = 1; iii <= offset; iii++ ) {
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if(bases[iii] != prevBase) { // this base doesn't match the previous one so it is a new cycle
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@ -74,7 +74,7 @@ public class CycleCovariate implements Covariate {
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return cycle;
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} else if( platform.equalsIgnoreCase( "SOLID" ) ) {
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// the ligation cycle according to http://www3.appliedbiosystems.com/cms/groups/mcb_marketing/documents/generaldocuments/cms_057511.pdf
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return (offset / 5) + 1; // integer division
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return offset / 5; // integer division
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} else {
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throw new StingException( "Requested platform (" + platform + ") not supported in CycleCovariate." );
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}
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@ -1,7 +1,6 @@
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package org.broadinstitute.sting.playground.gatk.walkers.Recalibration;
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import net.sf.samtools.SAMRecord;
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import org.broadinstitute.sting.utils.QualityUtils;
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/*
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* Copyright (c) 2009 The Broad Institute
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@ -34,6 +34,9 @@ import java.util.*;
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* Created by IntelliJ IDEA.
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* User: rpoplin
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* Date: Oct 30, 2009
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*
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* A HashMap that maps a list of comparables to any object <T>.
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* There is functionality for the mappings to be given back to you in sorted order.
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*/
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public class NHashMap<T> extends HashMap<List<? extends Comparable>, T> {
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@ -113,9 +116,7 @@ public class NHashMap<T> extends HashMap<List<? extends Comparable>, T> {
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return theSet;
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}
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public List<T> makeList(T... args) {
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public static <T> List<T> makeList(T... args) {
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List<T> list = new ArrayList<T>();
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for (T arg : args)
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{
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@ -1,7 +1,6 @@
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package org.broadinstitute.sting.playground.gatk.walkers.Recalibration;
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import net.sf.samtools.SAMRecord;
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import org.broadinstitute.sting.utils.QualityUtils;
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/*
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* Copyright (c) 2009 The Broad Institute
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@ -34,6 +34,8 @@ import java.util.*;
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* Created by IntelliJ IDEA.
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* User: rpoplin
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* Date: Nov 6, 2009
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*
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* This helper class holds the data HashMap as well as submaps that represent the marginal distributions collapsed over all needed dimensions.
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*/
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public class RecalDataManager {
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@ -42,9 +44,9 @@ public class RecalDataManager {
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private NHashMap<RecalDatum> dataCollapsedQualityScore; // table where everything except read group and quality score has been collapsed
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private ArrayList<NHashMap<RecalDatum>> dataCollapsedByCovariate; // tables where everything except read group, quality score, and given covariate has been collapsed
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private boolean collapsedTablesCreated;
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public NHashMap<Double> dataSumExpectedErrors;
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public NHashMap<Double> dataSumExpectedErrors; // table used to calculate the overall aggregate quality score in which everything except read group is collapsed
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public final static String ORIGINAL_QUAL_ATTRIBUTE_TAG = "OQ";
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public final static String ORIGINAL_QUAL_ATTRIBUTE_TAG = "OQ"; // the tag in a BAM file that holds the original quality scores
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RecalDataManager() {
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data = new NHashMap<RecalDatum>();
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@ -58,6 +60,10 @@ public class RecalDataManager {
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}
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// BUGBUG: A lot going on in this method, doing a lot of pre-calculations for use in the sequential mode calculation later in TableRecalibrationWalker
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/**
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* Create all the collapsed tables that will be used in the sequential calculation in TableRecalibrationWalker
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* @param numCovariates The number of covariates you have determines the number of tables to create
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*/
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public final void createCollapsedTables( final int numCovariates ) {
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dataCollapsedReadGroup = new NHashMap<RecalDatum>();
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dataCollapsedQualityScore = new NHashMap<RecalDatum>();
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@ -88,7 +94,8 @@ public class RecalDataManager {
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} else {
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collapsedDatum.increment( thisDatum );
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}
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// create dataSumExpectedErrors, the table used to calculate the overall aggregate quality score in which everything except read group is collapsed
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newKey = new ArrayList<Comparable>();
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newKey.add( key.get(0) ); // make a new key with just the read group
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sumExpectedErrors = dataSumExpectedErrors.get( newKey );
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@ -129,6 +136,11 @@ public class RecalDataManager {
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collapsedTablesCreated = true;
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}
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/**
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* Get the appropriate collapsed table out of the set of all the tables held by this Object
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* @param covariate Which covariate indexes the desired collapsed HashMap
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* @return The desired collapsed HashMap
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*/
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public final NHashMap<RecalDatum> getCollapsedTable( final int covariate ) {
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if( !collapsedTablesCreated ) {
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throw new StingException("Trying to get collapsed tables before they have been populated. Null pointers abound.");
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@ -34,6 +34,8 @@ import java.util.*;
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* Created by IntelliJ IDEA.
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* User: rpoplin
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* Date: Nov 3, 2009
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*
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* An individual piece of recalibration data. Each bin counts up the number of observations and the number of reference mismatches seen for that combination of covariates.
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*/
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public class RecalDatum {
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@ -230,6 +230,9 @@ public class TableRecalibrationWalker extends ReadWalker<SAMRecord, SAMFileWrite
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// These calls are expensive so only do them once for each read
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String readGroup = read.getReadGroup().getReadGroupId();
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char[] bases = read.getReadString().toCharArray();
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if( refBases.length != bases.length ) {
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return read; // something is wrong with the mapping of the read so leave it alone
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}
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String myRefBases = new String(refBases);
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if( read.getReadNegativeStrandFlag() ) {
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bases = BaseUtils.simpleComplement( read.getReadString() ).toCharArray();
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