Rename to distinguish this transition table calculator from the scala version.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1838 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
chartl
parent
1d055011bd
commit
0a09fa4d5c
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@ -0,0 +1,468 @@
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package org.broadinstitute.sting.playground.gatk.walkers;
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import org.broadinstitute.sting.gatk.walkers.LocusWalker;
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import org.broadinstitute.sting.gatk.walkers.By;
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import org.broadinstitute.sting.gatk.walkers.DataSource;
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import org.broadinstitute.sting.gatk.walkers.genotyper.*;
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import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
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import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
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import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
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import org.broadinstitute.sting.utils.cmdLine.Argument;
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import org.broadinstitute.sting.utils.*;
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import java.util.List;
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import java.util.LinkedList;
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import java.util.ListIterator;
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import java.io.PrintStream;
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import net.sf.samtools.SAMRecord;
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/**
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* Created by IntelliJ IDEA.
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* User: chartl
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* Date: Oct 12, 2009
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* Time: 2:43:06 PM
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* To change this template use File | Settings | File Templates.
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*/
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@By(DataSource.REFERENCE)
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public class BaseTransitionTableCalculatorJavaWalker extends LocusWalker<ReferenceContextWindow,BaseTransitionTable>{
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@Argument(fullName="usePreviousBases", doc="Use previous bases as part of the calculation, uses the specified number, defaults to 0", required=false)
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int nPreviousBases = 0;
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@Argument(fullName="useSecondaryBase",doc="Use the secondary base of a read as part of the calculation", required=false)
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boolean useSecondaryBase = false;
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@Argument(fullName="confidentRefThreshold",doc="Set the lod score that defines confidence in ref, defaults to 4", required=false)
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int confidentRefThreshold = 4;
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@Argument(fullName="pileupMismatchThreshold",doc="Set the maximum number of mismatches at a locus before choosing not to use it in calculation. Defaults to 1.", required=false)
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int pileupMismatchThreshold = 1;
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private UnifiedGenotyper ug;
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private ReferenceContextWindow refWindow;
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public void initialize() {
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ug = new UnifiedGenotyper();
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ug.initialize();
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refWindow = new ReferenceContextWindow(nPreviousBases);
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}
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public BaseTransitionTable reduceInit() {
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return new BaseTransitionTable(nPreviousBases,useSecondaryBase);
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}
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public ReferenceContextWindow map( RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context ) {
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ReadBackedPileup pileup = new ReadBackedPileup(ref.getBase(),context);
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refWindow.update(ref,pileup,baseIsUsable(tracker,ref,pileup,context));
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return refWindow;
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}
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public BaseTransitionTable reduce( ReferenceContextWindow map, BaseTransitionTable confusionCounts ) {
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// todo -- refactor
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if ( map.isValidWindow() ) {
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List<SAMRecord> reads = map.getPileup().getReads();
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List<Integer> offsets = map.getPileup().getOffsets();
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ReferenceContext ref = map.getMiddleReferenceContext();
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String forwardContext = map.getForwardRefString();
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String reverseContext = map.getReverseRefString();
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for ( int r = 0; r < reads.size(); r ++ ) {
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if ( includeRead(reads.get(r) ,offsets.get(r)) ) {
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confusionCounts.update(createConfusionContext(reads.get(r),offsets.get(r),ref,forwardContext,reverseContext));
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}
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}
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}
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return confusionCounts;
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}
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public void onTraversalDone( BaseTransitionTable table ) {
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out.printf("%s%n", makeHeader() );
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table.print(out);
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}
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public boolean baseIsConfidentRef( RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context ) {
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List<GenotypeCall> calls = ug.map(tracker,ref,context);
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return ( ! calls.get(0).isVariant(ref.getBase()) && calls.get(0).getNegLog10PError() >= confidentRefThreshold );
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}
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public boolean baseIsUsable ( RefMetaDataTracker tracker, ReferenceContext ref, ReadBackedPileup pileup, AlignmentContext context ) {
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return pileupBelowMismatchThreshold(ref,pileup) && baseIsConfidentRef(tracker,ref,context) && refIsNotN(ref);
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}
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public boolean pileupBelowMismatchThreshold( ReferenceContext ref, ReadBackedPileup pileup ) {
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char[] bases = pileup.getBases().toCharArray();
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int mismatches = 0;
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for ( char b : bases ) {
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if ( Character.toUpperCase(b) == ref.getBase() ) {
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mismatches++;
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}
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}
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return mismatches > pileupMismatchThreshold;
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}
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public boolean refIsNotN(ReferenceContext ref) {
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return ref.getBase() != 'N';
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}
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public boolean includeRead ( SAMRecord read, int offset) {
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// todo -- do we want to filter out individual reads?
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return true;
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}
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public boolean readWindowContainsNonBaseCharacters( SAMRecord read, int offset, int posNeg ) {
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byte[] bases = read.getReadBases();
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if ( posNeg > 0 ) {
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for ( int i = offset; i < offset + nPreviousBases; i ++ ) {
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char base = Character.toUpperCase(convertIUPACByteToChar(bases[i]));
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if ( ! ( base == 'A' || base == 'G' || base == 'C' || base == 'T') ) {
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return true;
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}
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}
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return false;
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} else {
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for ( int i = offset; i > offset - nPreviousBases; i -- ) {
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char base = Character.toUpperCase(convertIUPACByteToChar(bases[i]));
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if ( ! ( base == 'A' || base == 'G' || base == 'C' || base == 'T') ) {
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return true;
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}
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}
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return false;
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}
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}
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public Pair<String,char[]> createConfusionContext(SAMRecord read, int offset, ReferenceContext ref, String refFor, String refRev) {
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char[] baseChars;
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if ( useSecondaryBase ) {
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baseChars = new char[3];
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} else {
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baseChars = new char[2];
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}
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baseChars[0] = Character.toUpperCase(ref.getBase());
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baseChars[1] = Character.toUpperCase(convertIUPACByteToChar(read.getReadBases()[offset]));
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if ( useSecondaryBase ) {
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baseChars[2] = Character.toUpperCase(BaseUtils.baseIndexToSimpleBase(QualityUtils.compressedQualityToBaseIndex(((byte[]) read.getAttribute("SQ"))[offset])));
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}
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Pair<String,char[]> confusionContext;
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if ( read.getReadNegativeStrandFlag() ) {
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confusionContext = new Pair<String,char[]>(refRev, baseChars);
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} else {
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confusionContext = new Pair<String,char[]>(refFor, baseChars);
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}
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return confusionContext;
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}
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private char convertIUPACByteToChar(byte iupacBase) {
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char compBase;
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switch (iupacBase) {
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case 'A':
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case 'a': compBase = 'A'; break;
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case 'C':
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case 'c': compBase = 'C'; break;
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case 'G':
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case 'g': compBase = 'G'; break;
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case 'T':
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case 't': compBase = 'T'; break;
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default: compBase = '.'; break;
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}
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return compBase;
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}
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public String makeHeader() {
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String output = "Reference_Base\tObserved_Base";
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if ( useSecondaryBase ) {
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output = output + "\tSecondary_Base";
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}
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for ( int i = 0; i < nPreviousBases; i ++ ) {
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output = String.format("%s\t%s", output, "Previous_Base_"+Integer.toString(i));
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}
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output = String.format("%s\t%s\t%s\t%s", output, "Hash", "N_Observations", "As_Proportion");
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return output;
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}
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}
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class BaseTransitionTable {
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final int N_BASES = 4;
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final int A_OFFSET = 0;
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final int C_OFFSET = 1;
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final int G_OFFSET = 2;
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final int T_OFFSET = 3;
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private BaseStringHash strHash;
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protected int[][] confusionTable;
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protected boolean useSecondaryBase;
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public BaseTransitionTable( int prevBaseStringLength, boolean useSecondaryBase ) {
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this.useSecondaryBase = useSecondaryBase;
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if ( useSecondaryBase ) {
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strHash = new BaseStringHash(prevBaseStringLength+2);
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} else {
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strHash = new BaseStringHash(prevBaseStringLength+1);
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}
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confusionTable = new int[strHash.hashSize()][N_BASES];
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for ( int i = 0; i < strHash.hashSize(); i ++ ) {
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for ( int j = 0; j < N_BASES; j ++ ) {
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confusionTable[i][j] = 0;
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}
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}
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}
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public void update( Pair<String, char[]> confusionContext ) {
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//TODO -- THIS [done]
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String context = confusionContext.getFirst();
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char[] bases = confusionContext.getSecond();
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// secondary base is a part of the hash
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if ( useSecondaryBase ) {
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context = context + bases[2] + bases[1];
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} else {
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context = context + bases[1];
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}
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confusionTable[strHash.hash(context)][strHash.hash(bases[0])] ++;
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}
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public void print( PrintStream out ) {
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long totalCounts = countOverTable();
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for ( int hash = 0; hash < strHash.maxHash(); hash ++ ) {
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for ( int ref = 0; ref < N_BASES; ref ++ ) {
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char[] contextBases = strHash.inverse(hash).toCharArray();
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String output = Character.toString(strHash.invert(ref));
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for ( int b = contextBases.length-1; b > 0; b ++ ) {
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output = output + "\t" + Character.toString(contextBases[b]);
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}
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output = String.format("%s\t%f\t%d\t%f",output,hash+(double)ref/4,confusionTable[hash][ref], ((double)confusionTable[hash][ref])/totalCounts);
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out.printf("%s%n",output);
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}
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}
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}
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public long countOverTable() {
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long count = 0l;
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for (int hash = 0; hash < strHash.maxHash(); hash++ ) {
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for ( int ref = 0; ref < N_BASES; ref ++ ) {
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count += confusionTable[hash][ref];
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}
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}
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return count;
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}
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}
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class BaseStringHash {
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// character-level mappings and inverses for
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// recursive hash
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final int A_HASH = 0;
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final int C_HASH = 1;
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final int G_HASH = 2;
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final int T_HASH = 3;
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final char INV_0 = 'A';
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final char INV_1 = 'C';
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final char INV_2 = 'G';
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final char INV_3 = 'T';
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int stringLength;
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public BaseStringHash( int stringLength ) {
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this.stringLength = stringLength;
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}
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public int maxHash() {
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return (int) Math.round(Math.pow(4,stringLength));
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}
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public int hashSize() {
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return (int) Math.round(Math.pow(4,stringLength+1));
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}
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public int hash( char b ) {
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switch(b) {
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case 'A':
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return A_HASH;
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case 'C':
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return C_HASH;
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case 'G':
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return G_HASH;
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case 'T':
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return T_HASH;
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default:
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throw new StingException("Incorrect base type sent to base hashing function, was: "+b);
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}
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}
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public int hash ( String s ) {
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return recursiveHash(s,0);
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}
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public int recursiveHash( String s, int offset ) {
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if ( offset == s.length() ) {
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return 0;
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} else {
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return (int) Math.round(hash(s.charAt(offset))*Math.pow(4,s.length()-offset)) + recursiveHash(s, offset+1);
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}
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}
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public String inverse( int h ) {
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return recursiveInverse(h, 0);
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}
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public char invert( int h ) {
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switch(h) {
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case 0:
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return INV_0;
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case 1:
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return INV_1;
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case 2:
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return INV_2;
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case 3:
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return INV_3;
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default:
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throw new StingException("Non-primitive base-string hash code sent to invert. Expected [0,1,2,3]; received "+ Integer.toString(h));
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}
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}
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public String recursiveInverse(int h, int k ) {
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if ( h == 0 ) {
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return "";
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} else {
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double quaternary = Math.pow(4,stringLength-k);
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int coef = (int) Math.floor( h/quaternary );
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return Character.toString(invert(coef)) + recursiveInverse(h - (int) Math.floor(quaternary), k+1);
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}
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}
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}
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class ReferenceContextWindow {
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protected int windowSize;
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protected int nPrevBases;
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protected LinkedList<ReadBackedPileup> prevAlignments;
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protected LinkedList<ReferenceContext> prevRefs;
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protected LinkedList<Boolean> usePrevious;
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protected boolean initialized;
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public ReferenceContextWindow( int nPrevBases ) {
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windowSize = 2*nPrevBases + 1;
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this.nPrevBases = nPrevBases;
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prevAlignments = new LinkedList<ReadBackedPileup>();
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prevRefs = new LinkedList<ReferenceContext>();
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usePrevious = new LinkedList<Boolean>();
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initialized = false;
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}
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public void update( ReferenceContext ref, ReadBackedPileup pileup, boolean useLocus ) {
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if ( ! initialized ) {
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prevAlignments.add(pileup);
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prevRefs.add(ref);
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usePrevious.add(useLocus);
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if ( prevAlignments.size() == windowSize ) {
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initialized = true;
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}
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} else {
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prevAlignments.removeFirst();
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prevRefs.removeFirst();
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usePrevious.removeFirst();
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prevAlignments.add(pileup);
|
||||||
|
prevRefs.add(ref);
|
||||||
|
usePrevious.add(useLocus);
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
public String getReferenceString() {
|
||||||
|
String ref = "";
|
||||||
|
for ( ReferenceContext c : prevRefs ) {
|
||||||
|
ref = ref + c.getBase();
|
||||||
|
}
|
||||||
|
|
||||||
|
return ref;
|
||||||
|
}
|
||||||
|
|
||||||
|
public String getForwardRefString() {
|
||||||
|
String ref = "";
|
||||||
|
for ( ReferenceContext c : prevRefs.subList(0,nPrevBases+1) ) {
|
||||||
|
ref = ref + c.getBase();
|
||||||
|
}
|
||||||
|
|
||||||
|
return ref;
|
||||||
|
}
|
||||||
|
|
||||||
|
public String getReverseRefString() { // todo -- make sure we want to flip this done (yes we do)
|
||||||
|
String ref = "";
|
||||||
|
for ( int base = prevRefs.size()-1; base >= nPrevBases; base -- ) {
|
||||||
|
ref = ref + prevRefs.get(base).getBase();
|
||||||
|
}
|
||||||
|
|
||||||
|
return ref;
|
||||||
|
}
|
||||||
|
|
||||||
|
public ReadBackedPileup getPileup() {
|
||||||
|
// because lists are 0-indexed, this returns the alignments
|
||||||
|
// to the middle base in the window.
|
||||||
|
return prevAlignments.get(nPrevBases);
|
||||||
|
}
|
||||||
|
|
||||||
|
public ReferenceContext getMiddleReferenceContext() {
|
||||||
|
return prevRefs.get(nPrevBases);
|
||||||
|
}
|
||||||
|
|
||||||
|
public boolean isValidWindow() {
|
||||||
|
boolean valid;
|
||||||
|
if ( ! initialized ) {
|
||||||
|
valid = false;
|
||||||
|
} else {
|
||||||
|
valid = true;
|
||||||
|
// check if everything is confident ref
|
||||||
|
for ( Boolean b : usePrevious ) {
|
||||||
|
if ( !b ) {
|
||||||
|
valid = false;
|
||||||
|
break;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
// if still valid, check distances
|
||||||
|
if ( valid ) {
|
||||||
|
ListIterator<ReferenceContext> iter = prevRefs.listIterator();
|
||||||
|
ReferenceContext prev = iter.next();
|
||||||
|
while ( iter.hasNext() ) {
|
||||||
|
ReferenceContext cur = iter.next();
|
||||||
|
|
||||||
|
if ( cur.getLocus().distance(prev.getLocus()) > 1 ) {
|
||||||
|
valid = false;
|
||||||
|
break;
|
||||||
|
}
|
||||||
|
|
||||||
|
prev = cur;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
return valid;
|
||||||
|
}
|
||||||
|
|
||||||
|
public int getWindowSize() {
|
||||||
|
return windowSize;
|
||||||
|
}
|
||||||
|
|
||||||
|
}
|
||||||
|
|
@ -1,139 +0,0 @@
|
||||||
package org.broadinstitute.sting.playground.gatk.walkers;
|
|
||||||
|
|
||||||
import org.broadinstitute.sting.gatk.walkers.LocusWalker;
|
|
||||||
import org.broadinstitute.sting.gatk.walkers.By;
|
|
||||||
import org.broadinstitute.sting.gatk.walkers.DataSource;
|
|
||||||
import org.broadinstitute.sting.gatk.walkers.genotyper.*;
|
|
||||||
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
|
|
||||||
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
|
|
||||||
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
|
|
||||||
import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
|
|
||||||
import org.broadinstitute.sting.utils.cmdLine.Argument;
|
|
||||||
import org.broadinstitute.sting.utils.genotype.GenotypeWriterFactory;
|
|
||||||
import org.broadinstitute.sting.utils.genotype.GenotypeWriter;
|
|
||||||
import org.broadinstitute.sting.utils.StingException;
|
|
||||||
import org.broadinstitute.sting.utils.Pair;
|
|
||||||
import org.broadinstitute.sting.utils.QualityUtils;
|
|
||||||
import org.broadinstitute.sting.utils.BaseUtils;
|
|
||||||
|
|
||||||
import java.util.HashSet;
|
|
||||||
import java.util.List;
|
|
||||||
import java.util.LinkedList;
|
|
||||||
import java.util.ListIterator;
|
|
||||||
import java.io.PrintStream;
|
|
||||||
|
|
||||||
import net.sf.samtools.SAMReadGroupRecord;
|
|
||||||
import net.sf.samtools.SAMRecord;
|
|
||||||
|
|
||||||
|
|
||||||
class ReferenceContextWindow {
|
|
||||||
|
|
||||||
protected int windowSize;
|
|
||||||
protected int nPrevBases;
|
|
||||||
protected LinkedList<AlignmentContext> prevAlignments;
|
|
||||||
protected LinkedList<ReferenceContext> prevRefs;
|
|
||||||
protected LinkedList<Boolean> usePrevious;
|
|
||||||
protected boolean initialized;
|
|
||||||
|
|
||||||
public ReferenceContextWindow( int nPrevBases ) {
|
|
||||||
windowSize = 2*nPrevBases + 1;
|
|
||||||
this.nPrevBases = nPrevBases;
|
|
||||||
prevAlignments = new LinkedList<AlignmentContext>();
|
|
||||||
prevRefs = new LinkedList<ReferenceContext>();
|
|
||||||
usePrevious = new LinkedList<Boolean>();
|
|
||||||
initialized = false;
|
|
||||||
}
|
|
||||||
|
|
||||||
public void update( ReferenceContext ref, AlignmentContext context, boolean useLocus ) {
|
|
||||||
if ( ! initialized ) {
|
|
||||||
prevAlignments.add(context);
|
|
||||||
prevRefs.add(ref);
|
|
||||||
usePrevious.add(useLocus);
|
|
||||||
if ( prevAlignments.size() == windowSize ) {
|
|
||||||
initialized = true;
|
|
||||||
}
|
|
||||||
} else {
|
|
||||||
prevAlignments.removeFirst();
|
|
||||||
prevRefs.removeFirst();
|
|
||||||
usePrevious.removeFirst();
|
|
||||||
prevAlignments.add(context);
|
|
||||||
prevRefs.add(ref);
|
|
||||||
usePrevious.add(useLocus);
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
||||||
public String getReferenceString() {
|
|
||||||
String ref = "";
|
|
||||||
for ( ReferenceContext c : prevRefs ) {
|
|
||||||
ref = ref + c.getBase();
|
|
||||||
}
|
|
||||||
|
|
||||||
return ref;
|
|
||||||
}
|
|
||||||
|
|
||||||
public String getForwardRefString() {
|
|
||||||
String ref = "";
|
|
||||||
for ( ReferenceContext c : prevRefs.subList(0,nPrevBases+1) ) {
|
|
||||||
ref = ref + c.getBase();
|
|
||||||
}
|
|
||||||
|
|
||||||
return ref;
|
|
||||||
}
|
|
||||||
|
|
||||||
public String getReverseRefString() { // todo -- make sure we want to flip this done (yes we do)
|
|
||||||
String ref = "";
|
|
||||||
for ( int base = prevRefs.size()-1; base >= nPrevBases; base -- ) {
|
|
||||||
ref = ref + prevRefs.get(base).getBase();
|
|
||||||
}
|
|
||||||
|
|
||||||
return ref;
|
|
||||||
}
|
|
||||||
|
|
||||||
public AlignmentContext getContext() {
|
|
||||||
// because lists are 0-indexed, this returns the alignments
|
|
||||||
// to the middle base in the window.
|
|
||||||
return prevAlignments.get(nPrevBases);
|
|
||||||
}
|
|
||||||
|
|
||||||
public ReferenceContext getMiddleReferenceContext() {
|
|
||||||
return prevRefs.get(nPrevBases);
|
|
||||||
}
|
|
||||||
|
|
||||||
public boolean isValidWindow() {
|
|
||||||
boolean valid;
|
|
||||||
if ( ! initialized ) {
|
|
||||||
valid = false;
|
|
||||||
} else {
|
|
||||||
valid = true;
|
|
||||||
// check if everything is confident ref
|
|
||||||
for ( Boolean b : usePrevious ) {
|
|
||||||
if ( !b ) {
|
|
||||||
valid = false;
|
|
||||||
break;
|
|
||||||
}
|
|
||||||
}
|
|
||||||
// if still valid, check distances
|
|
||||||
if ( valid ) {
|
|
||||||
ListIterator<ReferenceContext> iter = prevRefs.listIterator();
|
|
||||||
ReferenceContext prev = iter.next();
|
|
||||||
while ( iter.hasNext() ) {
|
|
||||||
ReferenceContext cur = iter.next();
|
|
||||||
|
|
||||||
if ( cur.getLocus().distance(prev.getLocus()) > 1 ) {
|
|
||||||
valid = false;
|
|
||||||
break;
|
|
||||||
}
|
|
||||||
|
|
||||||
prev = cur;
|
|
||||||
}
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
||||||
return valid;
|
|
||||||
}
|
|
||||||
|
|
||||||
public int getWindowSize() {
|
|
||||||
return windowSize;
|
|
||||||
}
|
|
||||||
|
|
||||||
}
|
|
||||||
Loading…
Reference in New Issue