First inklings of a unified allele caller!
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@32 348d0f76-0448-11de-a6fe-93d51630548a
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andrewk
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150610d63d
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@ -37,6 +37,7 @@ public class AnalysisTK extends CommandLineProgram {
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addModule("CountReads", new CountReadsWalker());
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addModule("PrintReads", new PrintReadsWalker());
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addModule("Base_Quality_Histogram", new BaseQualityHistoWalker());
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addModule("Genotype", new GenotypeWalker());
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addModule("SingleSampleGenotyper", new SingleSampleGenotyper());
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addModule("Null", new NullWalker());
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}
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@ -0,0 +1,78 @@
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package edu.mit.broad.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 edu.mit.broad.sting.atk.modules;
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import edu.mit.broad.sting.atk.LocusIterator;
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import edu.mit.broad.sting.atk.GenotypeEvidence;
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import edu.mit.broad.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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