A walker that generates a table of secondary base counts in a bam file.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2031 348d0f76-0448-11de-a6fe-93d51630548a
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mmelgar
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package org.broadinstitute.sting.playground.gatk.walkers.secondaryBases;
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import net.sf.picard.reference.ReferenceSequence;
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import net.sf.samtools.SAMRecord;
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import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
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import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
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import org.broadinstitute.sting.gatk.refdata.IntervalRod;
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import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
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import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
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import org.broadinstitute.sting.gatk.refdata.RodGenotypeChipAsGFF;
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import org.broadinstitute.sting.gatk.walkers.*;
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import org.broadinstitute.sting.utils.Pair;
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import org.broadinstitute.sting.utils.ReadBackedPileup;
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import org.broadinstitute.sting.utils.fasta.IndexedFastaSequenceFile;
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import javax.xml.transform.Result;
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import java.io.File;
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import java.io.IOException;
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import java.util.HashMap;
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import java.util.List;
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/**
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* Created by IntelliJ IDEA.
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* User: michael
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* Date: Nov 2, 2009
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* Time: 8:45:32 PM
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* To change this template use File | Settings | File Templates.
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*/
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@Reference(window=@Window(start=-1,stop=1))
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public class SecondaryBaseTransitionTableWalker extends LocusWalker<Integer, Integer> {
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HashMap<String,Long> counts = new HashMap<String,Long>();
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public IndexedFastaSequenceFile refSeq;
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/*public void initialize() {
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File refFile = this.getToolkit().getArguments().referenceFile;
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try {
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refSeq = new IndexedFastaSequenceFile(refFile);
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} catch (IOException e) {
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refSeq = null;
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}
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}*/
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public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
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String refBase = Character.toString(ref.getBase());
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ReadBackedPileup pileup = new ReadBackedPileup(ref.getBase(),context);
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String primaryBases = pileup.getBasesWithStrand();
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String secondaryBases = pileup.getSecondaryBasePileup();
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String contextBases = new String(ref.getBases());
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/*if (refSeq != null) {
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long startPos = context.getPosition() - 1;
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long stopPos = context.getPosition() + 1;
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ReferenceSequence prevRefSequence = refSeq.getSubsequenceAt(context.getContig(), startPos, context.getPosition() - 1);
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ReferenceSequence nextRefSequence = refSeq.getSubsequenceAt(context.getContig(), context.getPosition() + 1, stopPos);
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String prev = new String(prevRefSequence.getBases());
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String next = new String(nextRefSequence.getBases());
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String total = new String(refSeq.getSubsequenceAt(context.getContig(),startPos,stopPos).getBases());
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out.println(total + " " + prev + " " + refBase + " " + next);
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}*/
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String precedingBase = contextBases.substring(0,1);
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String nextBase = contextBases.substring(2);
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/*out.println(contextBases + " " + precedingBase + " " + refBase + " " + nextBase);*/
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/*out.println(" ");*/
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boolean rods = false;
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for ( ReferenceOrderedDatum datum : tracker.getAllRods() ) {
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if (datum != null && !(datum instanceof IntervalRod)) {
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rods = true;}
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}
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if (!rods && precedingBase != null && secondaryBases != null) {
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for (int i = 0; i < primaryBases.length(); i ++) {
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if (secondaryBases.charAt(i) != 'N' && secondaryBases.charAt(i) != '.' && Character.toUpperCase(primaryBases.charAt(i)) != 'N') {
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String quenchingBase;
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if (primaryBases.charAt(i) == Character.toUpperCase(primaryBases.charAt(i))) {
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quenchingBase = precedingBase;
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}
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else {
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quenchingBase = nextBase;
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}
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String reference = Character.toString(Character.toUpperCase(refBase.charAt(0)));
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String primary = Character.toString(Character.toUpperCase(primaryBases.charAt(i)));
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String quencher = Character.toString(Character.toUpperCase(quenchingBase.charAt(0)));
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String secondary = Character.toString(Character.toUpperCase(secondaryBases.charAt(i)));
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String key = reference + primary + quencher + secondary;
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if (counts.containsKey(key)) {
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counts.put(key, counts.get(key) + Long.valueOf(1));
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}
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else {
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counts.put(key, Long.valueOf(1));
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}
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}
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}
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}
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return 1;
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}
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public Integer reduceInit() {return 0;}
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public Integer reduce(Integer value, Integer sum) {return sum + value;}
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public void onTraversalDone(Integer result) {
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out.println("ReferenceBase \tPrimaryBase \tPreviousBase \tSecondaryBase \tCount");
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for (String key : counts.keySet()) {
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out.println(key.charAt(0)+"\t"+key.charAt(1)+"\t"+key.charAt(2)+"\t"+key.charAt(3)+"\t"+counts.get(key));
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}
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}
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}
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