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Partial implementation of single sample allele calling 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@64 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
andrewk 2009-03-16 19:30:42 +00:00
parent 4808dff110
commit 685fc8bd61
1 changed files with 66 additions and 32 deletions
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98
playground/java/src/org/broadinstitute/sting/gatk/walkers/AlleleFrequencyWalker.java
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@ -1,5 +1,6 @@
package org.broadinstitute.sting.gatk.walkers;
//import org.broadinstitute.sting.gatk.iterators.LocusIterator;
import org.broadinstitute.sting.gatk.LocusContext;
import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
import net.sf.samtools.SAMRecord;
@ -9,6 +10,7 @@ import java.util.List;
public class AlleleFrequencyWalker extends BasicLociWalker<Integer, Integer> {
public Integer map(List<ReferenceOrderedDatum> rodData, char ref, LocusContext context) {
@ -16,6 +18,7 @@ public class AlleleFrequencyWalker extends BasicLociWalker<Integer, Integer> {
// Set number of chromosomes, N, to 2 for now
int N = 2;
boolean debug = false;
// Convert bases to CharArray
int numReads = context.getReads().size(); //numReads();
@ -40,16 +43,6 @@ public class AlleleFrequencyWalker extends BasicLociWalker<Integer, Integer> {
quals[i][b] = nonref_quals;
}
// Print quals for debugging
System.out.println("Base quality matrix");
for (int b=0; b<4; b++) {
System.out.print(num2nuc[b]);
for (int i=0; i < numReads; i++){
System.out.format(" %.4f", quals[i][b]);
}
System.out.println();
}
// Count bases
int[] base_counts = new int[4];
for (byte b : bases)
@ -67,23 +60,21 @@ public class AlleleFrequencyWalker extends BasicLociWalker<Integer, Integer> {
}
assert(altnum > 0);
if (true) { //altcount > 2) {
System.out.format("Pos: %s | ref: %c | alt: %c | %2dA | %2dC | %2dT | %2dG | %2d total\n", context.getLocation(), num2nuc[refnum], num2nuc[altnum],
base_counts[0], base_counts[1], base_counts[2], base_counts[3], bases.length);
if (bases.length > 0) { //altcount > 2) {
System.out.format("Pos: %s | ref: %c | alt: %c | %2dA | %2dC | %2dT | %2dG | %2d total | ", context.getLocation(), num2nuc[refnum],
num2nuc[altnum], base_counts[0], base_counts[1], base_counts[2], base_counts[3], bases.length);
if (debug) print_base_qual_matrix(quals, numReads);
// Check if we really want to do this one
if (bases.length == 0) {
System.out.println("No reads at position; no call being made");
}else{
AlleleFrequencyEstimator(N, bases, quals, refnum, altnum);
}
AlleleFrequencyEstimator(N, bases, quals, refnum, altnum, debug);
}
System.out.println();
if (debug) System.out.println();
return 1;
}
static void AlleleFrequencyEstimator(int N, byte[] bases, double[][] quals, int refnum, int altnum) {
static void AlleleFrequencyEstimator(int N, byte[] bases, double[][] quals, int refnum, int altnum, boolean debug) {
// q = hypothetical %nonref
// qstar = true %nonref
@ -94,10 +85,12 @@ public class AlleleFrequencyWalker extends BasicLociWalker<Integer, Integer> {
double epsilon = 0; // 1e-2;
double qstar;
System.out.format("%4s | ", "q ");
for (qstar = epsilon; qstar <= 1.0; qstar += (1.0 - 2*epsilon)/N)
System.out.format("%5s%12s %12s %12s | ", "qstar", "p(D|q) ", "p(q|G) ", "posterior ");
System.out.println();
if (debug) {
System.out.format("%4s | ", "q ");
for (qstar = epsilon; qstar <= 1.0; qstar += (1.0 - 2*epsilon)/N)
System.out.format("%5s%12s %12s %12s | ", "qstar", "p(D|q) ", "p(q|G) ", "posterior ");
if (debug) System.out.println();
}
double highest_posterior = -1.0;
double highest_qstar = -1.0;
@ -106,30 +99,31 @@ public class AlleleFrequencyWalker extends BasicLociWalker<Integer, Integer> {
double qstep = 0.01;
double qend = 1.0 + qstep / 10; // makes sure we get to 1.0 even with rounding error of qsteps accumulating
for (double q=0.0; q <= qend; q += qstep) {
System.out.format("%.2f | ", q);
if (debug) System.out.format("%.2f | ", q);
for (qstar = epsilon; qstar <= 1.0; qstar += (1.0 - 2*epsilon)/N) {
double pDq = P_D_q(bases, quals, q, refnum, altnum);
double pqG = P_q_G(bases, N, q, qstar);
double pG = P_G(N, qstar, altnum);
double posterior = pDq * pqG * pG;
System.out.format("%.2f %.10f %.10f %.10f | ", qstar, pDq, pqG, posterior);
if (debug) System.out.format("%.2f %.10f %.10f %.10f | ", qstar, pDq, pqG, posterior);
if (posterior > highest_posterior) {
highest_posterior = posterior;
highest_qstar = qstar;
highest_q = q;
}
}
System.out.println();
if (debug) System.out.println();
}
System.out.printf("Maximal likelihood posterior: %.6f\n", highest_posterior);
/*System.out.printf("Maximal likelihood posterior: %.6f\n", highest_posterior);
System.out.printf("q that maximimizes posterior: %.6f\n", highest_q);
System.out.printf("qstar used when calculating max q: %.6f\n", highest_qstar);
System.out.printf("qstar used when calculating max q: %.6f\n", highest_qstar);*/
System.out.printf("qhat %.2f | qstar %.2f | ", highest_q, highest_qstar);
// Print out the called bases
long numNonrefBases = Math.round(highest_q * N);
long numRefBases = N - numNonrefBases;
String genotype = repeat(num2nuc[refnum], numRefBases) + repeat(num2nuc[altnum], numNonrefBases);
System.out.printf("Maximal likelihood genotype: %s\n", genotype);
System.out.printf("gen: %s\n", genotype);
}
static double P_D_q(byte[] bases, double[][]quals, double q, int refnum, int altnum) {
@ -147,7 +141,11 @@ public class AlleleFrequencyWalker extends BasicLociWalker<Integer, Integer> {
}
static double P_G(int N, double qstar, int altnum) {
return 1.0;
if (N==2) {
return p_G_N_2[ Math.round((float)(qstar * N)) ];
}else{
return 1.0;
}
}
static double binomialProb(long k, long n, double p) {
@ -187,6 +185,7 @@ public class AlleleFrequencyWalker extends BasicLociWalker<Integer, Integer> {
static int nuc2num[];
static char num2nuc[];
static double p_G_N_2[]; // pop. gen. priors for N=2
public AlleleFrequencyWalker() {
nuc2num = new int[128];
nuc2num['A'] = 0;
@ -197,10 +196,45 @@ public class AlleleFrequencyWalker extends BasicLociWalker<Integer, Integer> {
nuc2num['c'] = 1;
nuc2num['t'] = 2;
nuc2num['g'] = 3;
num2nuc = new char[4];
num2nuc[0] = 'A';
num2nuc[1] = 'C';
num2nuc[2] = 'T';
num2nuc[3] = 'G';
p_G_N_2 = new double[3];
p_G_N_2[0] = 0.999;
p_G_N_2[1] = 1e-3;
p_G_N_2[2] = 1e-5;
}
}
void print_base_qual_matrix(double [][]quals, int numReads) {
// Print quals for debugging
System.out.println("Base quality matrix");
for (int b=0; b<4; b++) {
System.out.print(num2nuc[b]);
for (int i=0; i < numReads; i++){
System.out.format(" %.4f", quals[i][b]);
}
System.out.println();
}
}
}