Oops! Restore changes that were clobbered during the move.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@37 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna
parent
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@ -0,0 +1,78 @@
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package org.broadinstitute.sting.atk;
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/**
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* Created by IntelliJ IDEA.
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* User: andrewk
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* Date: Mar 9, 2009
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* Time: 3:34:08 PM
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* To change this template use File | Settings | File Templates.
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*/
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public class GenotypeEvidence {
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int[] nuc2num = new int[128];
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int[] nucs = new int[4];
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int a = nucs[0];
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int c = nucs[1];
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int t = nucs[2];
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int g = nucs[3];
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float[] nuc_pcnt = new float[4];
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char ref;
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public float q; // % non-reference alleles
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public int refbases;
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public int allbases;
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public GenotypeEvidence(String bases, char ref){
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this.ref = ref;
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nuc2num['A'] = 0;
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nuc2num['C'] = 1;
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nuc2num['T'] = 2;
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nuc2num['G'] = 3;
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nuc2num['a'] = 0;
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nuc2num['c'] = 1;
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nuc2num['t'] = 2;
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nuc2num['g'] = 3;
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for (char b : bases.toCharArray()) {
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nucs[nuc2num[b]] += 1;
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/*switch (b) {
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case 'A': nucs[0] += 1; break;
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case 'C': nucs[1] += 1; break;
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case 'T': nucs[2] += 1; break;
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case 'G': nucs[3] += 1; break;
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} */
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}
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// Calculate q = ref. bases / nonref. bases
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refbases = nucs[nuc2num[ref]];
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allbases = bases.length();
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q = 1 - ((float)refbases / allbases);
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/*for (int i=0; i<4; i++) {
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nuc_pcnt[i] = (float)nucs[i] / len;
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//if
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}*/
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}
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public boolean SigNonref(float cutoff_fraction) {
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/* for (char nuc : nucs) {
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}*/
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return true;
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}
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public void print() {
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System.out.format("A %2d | ", nucs[0]);
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System.out.format("C %2d | ", nucs[1]);
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System.out.format("T %2d | ", nucs[2]);
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System.out.format("G %2d | ", nucs[3]);
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System.out.format("Ref %s | ", ref);
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}
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}
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@ -33,6 +33,7 @@ public class LocusIterator implements Iterable<LocusIterator>, CloseableIterator
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public List<SAMRecord> getReads() { return reads; }
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public List<Integer> getOffsets() { return offsets; }
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public int numReads() { return reads.size(); }
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// -----------------------------------------------------------------------------------------------------------------
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//
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@ -0,0 +1,88 @@
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package org.broadinstitute.sting.atk.modules;
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import org.broadinstitute.sting.atk.LocusIterator;
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import org.broadinstitute.sting.atk.GenotypeEvidence;
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import org.broadinstitute.sting.utils.ReferenceOrderedDatum;
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import net.sf.samtools.SAMRecord;
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import java.util.List;
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import static java.lang.System.currentTimeMillis;
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public class GenotypeWalker extends BasicLociWalker<Integer, Integer> {
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public Integer map(List<ReferenceOrderedDatum> rodData, char ref, LocusIterator context) {
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//char[] = new char(26);
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long start_tm = currentTimeMillis();
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List<SAMRecord> reads = context.getReads();
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List<Integer> offsets = context.getOffsets();
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String bases = "";
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String quals = "";
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//String offsetString = "";
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for ( int i = 0; i < reads.size(); i++ ) {
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SAMRecord read = reads.get(i);
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int offset = offsets.get(i);
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//if ( offset >= read.getReadString().length() )
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// System.out.printf(" [%2d] [%s] %s%n", offset, read.format(), read.getReadString());
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bases += read.getReadString().charAt(offset);
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//quals += read.getBaseQualityString().charAt(offset);
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//offsetString += i;
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//System.out.printf(" [%2d] [%s] %s%n", offset, read.getReadString().charAt(offset), read.getReadString());
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}
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GenotypeEvidence all = new GenotypeEvidence(bases, ref);
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// P(q|G) - prob of nonref mixture given the genotype
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float qobs = all.q; // observed percent of non-ref bases
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double G; // % non-ref bases in observed
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if (qobs >= 0.1) {
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all.print();
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System.out.format("q %.2f | ", all.q);
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System.out.format("%s | ", context.getLocation());
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System.out.format("Total %4d | ", context.numReads());
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System.out.println();
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for (int q = 0; q < all.allbases; q ++) {
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for (G = 0.01; G <= 1.0; G += 0.49) { // iterate over: ref (0%), het (50%) and hom (100%) nonref bases observed
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//double pqG = binomialProb(all.allbases - all.refbases, all.allbases, G);
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double pqG = binomialProb(q, all.allbases, G);
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//all.print();
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System.out.format("P(q|G) %.3f | ", pqG);
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}
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System.out.println();
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}
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long stop_tm = currentTimeMillis();
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System.out.format("%.3fs\n", (float)(stop_tm - start_tm) / 1000);
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}
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return 1;
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}
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static double binomialProb(int k, int n, double p) {
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// k - numebr of successes
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// n - number of Bernoulli trials
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// p - probability of success
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return (double)nchoosek(n, k) * Math.pow(p, k) * Math.pow(1-p, n-k);
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}
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static int nchoosek(int n, int k) {
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int t = 1;
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int m = n - k;
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if (k < m) {
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k = m;
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}
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for (int i = n, j = 1; i > k; i--, j++) {
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t = t * i / j;
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}
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return t;
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}
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public Integer reduceInit() { return 0; }
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public Integer reduce(Integer value, Integer sum) {
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return value + sum;
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}
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}
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@ -0,0 +1,44 @@
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package org.broadinstitute.sting.atk.modules;
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import org.broadinstitute.sting.atk.LocusWalker;
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import org.broadinstitute.sting.atk.LocusIterator;
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import org.broadinstitute.sting.utils.ReferenceOrderedDatum;
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import org.broadinstitute.sting.utils.rodDbSNP;
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import org.broadinstitute.sting.utils.Utils;
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import net.sf.samtools.SAMRecord;
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import java.util.List;
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// Null traversal. For ATK performance measuring.
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// j.maguire 3-7-2009
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public class NullWalker implements LocusWalker<Integer, Integer> {
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public void initialize() {
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}
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public String walkerType() { return "ByLocus"; }
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// Do we actually want to operate on the context?
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public boolean filter(List<ReferenceOrderedDatum> rodData, char ref, LocusIterator context) {
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return true; // We are keeping all the reads
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}
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// Map over the org.broadinstitute.sting.atk.LocusContext
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public Integer map(List<ReferenceOrderedDatum> rodData, char ref, LocusIterator context)
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{
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return 1;
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}
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// Given result of map function
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public Integer reduceInit()
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{
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return 0;
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}
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public Integer reduce(Integer value, Integer sum)
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{
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return 0;
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}
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public void onTraveralDone() {
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}
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}
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@ -0,0 +1,149 @@
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package org.broadinstitute.sting.atk.modules;
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import org.broadinstitute.sting.atk.LocusWalker;
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import org.broadinstitute.sting.atk.LocusIterator;
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import org.broadinstitute.sting.utils.ReferenceOrderedDatum;
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import org.broadinstitute.sting.utils.rodDbSNP;
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import org.broadinstitute.sting.utils.Utils;
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import net.sf.samtools.SAMRecord;
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import java.util.List;
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// Draft single sample genotyper
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// j.maguire 3-7-2009
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public class SingleSampleGenotyper implements LocusWalker<Integer, Integer> {
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public void initialize() {
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}
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public String walkerType() { return "ByLocus"; }
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// Do we actually want to operate on the context?
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public boolean filter(List<ReferenceOrderedDatum> rodData, char ref, LocusIterator context) {
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return true; // We are keeping all the reads
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}
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protected class GenotypeLikelihoods
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{
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public double[] likelihoods;
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public String[] genotypes;
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GenotypeLikelihoods()
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{
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likelihoods = new double[10];
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genotypes = new String[10];
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genotypes[0] = "AA";
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genotypes[1] = "AC";
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genotypes[2] = "AG";
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genotypes[3] = "AT";
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genotypes[4] = "CC";
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genotypes[5] = "CG";
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genotypes[6] = "CT";
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genotypes[7] = "GG";
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genotypes[8] = "GT";
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genotypes[9] = "TT";
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}
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void add(char ref, char read, byte qual)
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{
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double p_error = Math.pow(10.0, (double)qual / -10);
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for (int i = 0; i < genotypes.length; i++)
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{
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likelihoods[i] += AlleleLikelihood(ref, read, genotypes[i], p_error);
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}
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}
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double AlleleLikelihood(char ref, char read, String genotype, double p_error)
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{
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char h1 = genotype.charAt(0);
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char h2 = genotype.charAt(1);
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double p_base;
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if ((h1 == h2) && (h1 == read)) { p_base = Math.log10(1-p_error); }
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else if ((h1 != h2) && (h1 == read) || (h2 == read)) { p_base = Math.log10(0.5 - (p_error/2.0)); }
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else { p_base = Math.log10(p_error); }
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return p_base;
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}
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public String toString()
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{
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Integer[] permutation = Utils.SortPermutation(likelihoods);
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String[] sorted_genotypes = Utils.PermuteArray(genotypes, permutation);
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double[] sorted_likelihoods = Utils.PermuteArray(likelihoods, permutation);
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String s = "";
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for (int i = sorted_genotypes.length-1; i >= 0; i--)
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{
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if (i != sorted_genotypes.length-1) { s = s + " "; }
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s = s + sorted_genotypes[i] + ":" + sorted_likelihoods[i];
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}
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return s;
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}
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}
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// Map over the org.broadinstitute.sting.atk.LocusContext
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public Integer map(List<ReferenceOrderedDatum> rodData, char ref, LocusIterator context) {
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//System.out.printf("Reads %s:%d %d%n", context.getContig(), context.getPosition(), context.getReads().size());
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//for ( SAMRecord read : context.getReads() ) {
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// System.out.println(" -> " + read.getReadName());
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//}
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List<SAMRecord> reads = context.getReads();
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List<Integer> offsets = context.getOffsets();
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String bases = "";
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String quals = "";
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//String offsetString = "";
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// Look up hapmap and dbsnp priors
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String rodString = "";
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for ( ReferenceOrderedDatum datum : rodData )
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{
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if ( datum != null )
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{
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if ( datum instanceof rodDbSNP)
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{
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rodDbSNP dbsnp = (rodDbSNP)datum;
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rodString += dbsnp.toMediumString();
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}
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else
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{
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rodString += datum.toSimpleString();
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}
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}
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}
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if ( rodString != "" )
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rodString = "[ROD: " + rodString + "]";
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// Accumulate genotype likelihoods
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GenotypeLikelihoods G = new GenotypeLikelihoods();
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for ( int i = 0; i < reads.size(); i++ )
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{
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SAMRecord read = reads.get(i);
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int offset = offsets.get(i);
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bases += read.getReadString().charAt(offset);
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quals += read.getBaseQualityString().charAt(offset);
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G.add(ref, read.getReadString().charAt(offset), read.getBaseQualities()[offset]);
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}
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if ( context.getLocation().getStart() % 1 == 0 ) {
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//System.out.printf("%s: %s %s %s %s%n", context.getLocation(), ref, bases, quals, rodString);
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System.out.printf("%s %s %s %s\n", ref, bases, G.toString(), rodString);
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}
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return 1;
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}
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// Given result of map function
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public Integer reduceInit() { return 0; }
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public Integer reduce(Integer value, Integer sum) {
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return value + sum;
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}
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public void onTraveralDone() {
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}
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}
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@ -108,4 +108,93 @@ public class Utils {
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GenomeLoc.setContigOrdering(refContigOrdering);
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}
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// Java Generics can't do primitive types, so I had to do this the simplistic way
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public static Integer[] SortPermutation(final int[] A)
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{
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class comparator implements Comparator
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{
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public int compare(Object a, Object b)
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{
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if (A[(Integer)a] < A[(Integer)b]) { return -1; }
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if (A[(Integer)a] == A[(Integer)b]) { return 0; }
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if (A[(Integer)a] > A[(Integer)b]) { return 1; }
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return 0;
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}
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}
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Integer[] permutation = new Integer[A.length];
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for (int i = 0; i < A.length; i++)
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{
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permutation[i] = i;
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}
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Arrays.sort(permutation, new comparator());
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return permutation;
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}
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public static Integer[] SortPermutation(final double[] A)
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{
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class comparator implements Comparator
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{
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public int compare(Object a, Object b)
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{
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if (A[(Integer)a] < A[(Integer)b]) { return -1; }
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if (A[(Integer)a] == A[(Integer)b]) { return 0; }
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if (A[(Integer)a] > A[(Integer)b]) { return 1; }
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return 0;
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}
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}
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Integer[] permutation = new Integer[A.length];
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for (int i = 0; i < A.length; i++)
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{
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permutation[i] = i;
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}
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Arrays.sort(permutation, new comparator());
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return permutation;
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}
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public static int[] PermuteArray(int[] array, Integer[] permutation)
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{
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int[] output = new int[array.length];
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for (int i = 0; i < output.length; i++)
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{
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output[i] = array[permutation[i]];
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}
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return output;
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}
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public static double[] PermuteArray(double[] array, Integer[] permutation)
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{
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double[] output = new double[array.length];
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for (int i = 0; i < output.length; i++)
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{
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output[i] = array[permutation[i]];
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}
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return output;
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}
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public static Object[] PermuteArray(Object[] array, Integer[] permutation)
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{
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Object[] output = new Object[array.length];
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for (int i = 0; i < output.length; i++)
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{
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output[i] = array[permutation[i]];
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}
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return output;
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}
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public static String[] PermuteArray(String[] array, Integer[] permutation)
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{
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String[] output = new String[array.length];
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for (int i = 0; i < output.length; i++)
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{
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output[i] = array[permutation[i]];
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}
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return output;
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}
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}
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