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A bunch of refactoring, and more on the way. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@122 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
jmaguire 2009-03-20 21:31:07 +00:00
parent b806a9cf68
commit 5dca560c3c
2 changed files with 97 additions and 88 deletions
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4
playground/java/src/org/broadinstitute/sting/gatk/walkers/AlleleFrequencyMetricsWalker.java
View File

@ -41,7 +41,7 @@ public class AlleleFrequencyMetricsWalker extends BasicLociWalker<Integer, Integ
}
}
if (alleleFreq.getQstar() > 0.0 && alleleFreq.getLogOddsVarRef() >= LOD_cutoff) { // we confidently called it a SNP!
if (alleleFreq.getQstar() > 0.0 && alleleFreq.getLOD() >= LOD_cutoff) { // we confidently called it a SNP!
if (is_dbSNP_SNP) {
dbsnp_tp += 1;
}else{
@ -49,7 +49,7 @@ public class AlleleFrequencyMetricsWalker extends BasicLociWalker<Integer, Integ
}
}
if (alleleFreq.getQstar() > 0.0 && alleleFreq.getLogOddsVarRef() >= LOD_cutoff) {
if (alleleFreq.getQstar() > 0.0 && alleleFreq.getLOD() >= LOD_cutoff) {
//System.out.println(alleleFreq.getLogOddsVarRef());
num_snps++;
}

181
playground/java/src/org/broadinstitute/sting/gatk/walkers/AlleleFrequencyWalker.java
View File

@ -18,7 +18,6 @@ public class AlleleFrequencyWalker extends BasicLociWalker<AlleleFrequencyEstima
// Set number of chromosomes, N, to 2 for now
int N = 2;
int debug = 0;
// Convert bases to CharArray
int numReads = context.getReads().size(); //numReads();
@ -61,17 +60,12 @@ public class AlleleFrequencyWalker extends BasicLociWalker<AlleleFrequencyEstima
altnum = b; altcount = base_counts[b];
}
}
assert(altnum > 0);
assert(altnum != -1);
if (debug >= 1) System.out.format("Pos: %s ref: %c alt: %c ", context.getLocation(), num2nuc[refnum], num2nuc[altnum]);
//System.out.format("%2dA %2dC %2dT %2dG %2d total", base_counts[0], base_counts[1], base_counts[2], base_counts[3], bases.length);
if (debug >= 2) print_base_qual_matrix(quals, numReads);
AlleleFrequencyEstimate alleleFreq = AlleleFrequencyEstimator(N, bases, quals, refnum, altnum, debug);
AlleleFrequencyEstimate alleleFreq = AlleleFrequencyEstimator(N, bases, quals, refnum, altnum);
// Print dbSNP data if its there
if (debug >= 1) {
if (false) {
for ( ReferenceOrderedDatum datum : rodData ) {
if ( datum != null && datum instanceof rodDbSNP) {
rodDbSNP dbsnp = (rodDbSNP)datum;
@ -80,13 +74,21 @@ public class AlleleFrequencyWalker extends BasicLociWalker<AlleleFrequencyEstima
}
}
}
if (debug >= 1) System.out.format(" %s\n", base_string);
if (debug >= 2) System.out.println();
System.out.print(String.format("RESULT %s %c %c %f %f %f %d\n",
context.getLocation(),
alleleFreq.ref,
alleleFreq.alt,
alleleFreq.qhat,
alleleFreq.qstar,
alleleFreq.LOD,
base_string.length()));
return alleleFreq;
}
AlleleFrequencyEstimate AlleleFrequencyEstimator(int N, byte[] bases, double[][] quals, int refnum, int altnum, int debug) {
public AlleleFrequencyEstimate AlleleFrequencyEstimator(int N, byte[] bases, double[][] quals, int refnum, int altnum)
{
// q = hypothetical %nonref
// qstar = true %nonref
@ -101,61 +103,43 @@ public class AlleleFrequencyWalker extends BasicLociWalker<AlleleFrequencyEstima
double epsilon = 0; // 1e-2;
double qstar;
int qstar_N;
if (debug >= 2) {
System.out.format("%4s ", "q ");
for (qstar = epsilon; qstar <= 1.0; qstar += (1.0 - 2*epsilon)/N)
System.out.format("%5s%10s %10s %10s ", "qstar", "p(D|q) ", "p(q|G) ", "posterior ");
System.out.println();
}
MixtureLikelihood[] bestMixtures = { new MixtureLikelihood(-1,-1,-1), new MixtureLikelihood(-1,-1,-1), new MixtureLikelihood(-1,-1,-1) };
/*double[] highest_posterior = new double[] {-1.0, -1.0, -1.0};
double[] highest_qstar = new double[] {-1.0, -1.0, -1.0};
double[] highest_q = new double[] {-1.0, -1.0, -1.0};*/
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) { // hypothetic allele balance that we sample over
if (debug >= 2) System.out.format("%.2f ", q);
double best_qstar = Math.log10(0);
double best_qhat = Math.log10(0);
double best_posterior = Math.log10(0);
for (double q=0.0; q <= qend; q += qstep) // hypothetic allele balance that we sample over
{
long q_R = Math.round(q*bases.length);
for (qstar = epsilon, qstar_N = 0; qstar <= 1.0; qstar += (1.0 - 2*epsilon)/N, qstar_N++) { // qstar - true allele balances
for (qstar = epsilon, qstar_N = 0; qstar <= 1.0; qstar += (1.0 - 2*epsilon)/N, qstar_N++) // qstar - true allele balances
{
// for N=2: these are 0.0 + epsilon, 0.5, 1.0 - epsilon corresponding to reference, het-SNP, homo-SNP
//int qstar_N = Math.round((float)qstar*N);
double pDq = P_D_q(bases, quals, q, refnum, altnum);
double pqG = P_q_G(bases, N, q, qstar, q_R);
double pG = P_G(N, qstar_N); //= P_G(N, qstar);
double posterior = pDq * pqG * pG;
if (debug >= 2) System.out.format("%.2f %10.7f %10.7f %10.7f ", qstar, Math.log10(pDq), Math.log10(pqG), Math.log10(posterior));
if (posterior > bestMixtures[qstar_N].posterior)
bestMixtures[qstar_N] = new MixtureLikelihood(posterior, qstar, q);
double pG = P_G(N, qstar_N); //= P_G(N, qstar);
double posterior = pDq + pqG; // + pG;
if (posterior > best_posterior)
{
best_qstar = qstar;
best_qhat = q;
best_posterior = posterior;
}
}
if (debug >= 2) System.out.println();
}
// Calculate log-odds difference - must happen before mixtures are sorted by posterior prob.
double logOddsVarRef = logOddsNonrefRef(bestMixtures);
if (debug >= 1) System.out.printf("LOD(Var,Ref): %6.2f ", logOddsVarRef);
double posterior_null_hyp = P_D_q(bases, quals, 0.0, refnum, altnum) + P_q_G(bases, N, 0.0, 0.0, 0) + P_G(N, 0);
double LOD = best_posterior - posterior_null_hyp;
// Print all mixture likelihoods in order of qstar
for (MixtureLikelihood mix : bestMixtures) // outputs: "het 3.26 "
if (debug >= 1) System.out.printf("%3s: %6.2f ", genotypeTypeString(mix.qstar, N), Math.log10(mix.posterior / (1-mix.posterior)));
// Sort by posterior probability
Arrays.sort(bestMixtures); // We only used best entry, so this could be a generic max function (optimization)
if (debug >= 1) System.out.printf("qhat: %.2f qstar: %.2f ", bestMixtures[0].qhat, bestMixtures[0].qstar); //highest_q, highest_qstar);
if (debug >= 1) System.out.printf("prob: %.2e ", bestMixtures[0].posterior);
if (debug >= 1) System.out.printf("type: %3s ", genotypeTypeString(bestMixtures[0].qstar, N));
double posterior_null_hyp = P_D_q(bases, quals, 0.0, refnum, altnum) * P_q_G(bases, N, 0.0, 0.0, 0) * P_G(N, 0);
if (debug >= 1) System.out.printf("P(null): %.2e ", posterior_null_hyp);
//double LOD = Math.log10(bestMixtures[0].posterior) - Math.log10(posterior_null_hyp);
double LOD = logOdds(bestMixtures[0].posterior, posterior_null_hyp);
if (debug >= 1) System.out.printf("LOD: %6.2f ", LOD);
AlleleFrequencyEstimate alleleFreq = new AlleleFrequencyEstimate(num2nuc[refnum], num2nuc[refnum],
N, bestMixtures[0].qhat, bestMixtures[0].qstar, logOddsVarRef);
if (debug >= 1) System.out.printf("gen: %s", genotypeTypeString(bestMixtures[0].qstar, N));
AlleleFrequencyEstimate alleleFreq = new AlleleFrequencyEstimate(num2nuc[refnum],
num2nuc[altnum],
N,
best_qhat,
best_qstar,
LOD);
return alleleFreq;
}
@ -179,41 +163,32 @@ public class AlleleFrequencyWalker extends BasicLociWalker<AlleleFrequencyEstima
}
}
static double logOdds(double prob1, double prob2) {
return Math.log10(prob1 / (1-prob1)) - Math.log10(prob2 / (1-prob2));
}
static double P_D_q(byte[] bases, double[][]quals, double q, int refnum, int altnum)
{
double p = 0.0;
static double logOddsNonrefRef(MixtureLikelihood[] mixtures) {
// takes list of mixtureLikelihoods SORTED BY QSTAR (default ordering)
// Works for N == 2 right now!
assert (mixtures.length == 2);
MixtureLikelihood bestNonref = ((mixtures[1].posterior > mixtures[2].posterior) ? mixtures[1] : mixtures[2]);
return logOdds(bestNonref.posterior, mixtures[0].posterior);
// Code to calculate LOD using qstar=0 qhat=0
//double posterior_null_hyp = P_D_q(bases, quals, 0.0, refnum, altnum) * P_q_G(bases, N, 0.0, 0.0) * P_G(N, 0.0);
//double LOD = Math.log10(highest_posterior) - Math.log10(posterior_null_hyp);
}
static double P_D_q(byte[] bases, double[][]quals, double q, int refnum, int altnum) {
double p = 1.0;
for (int i=0; i<bases.length; i++) {
p *= (1-q) * quals[i][refnum] + q * quals[i][altnum];
for (int i=0; i<bases.length; i++)
{
p += Math.log10((1-q) * quals[i][refnum] + q * quals[i][altnum]);
}
return p;
}
static double P_q_G(byte [] bases, int N, double q, double qstar, long q_R) {
return binomialProb(q_R, bases.length, qstar);
static double P_q_G(byte [] bases, int N, double q, double qstar, long q_R)
{
return Math.log10(binomialProb(q_R, bases.length, qstar));
}
static double P_G(int N, int qstar_N) {
if (N==2) {
return p_G_N_2[ qstar_N ];
}else{
return 1.0;
static double P_G(int N, int qstar_N)
{
if (N==2)
{
return Math.log10(p_G_N_2[ qstar_N ]);
}
else
{
return Math.log10(1.0);
}
}
@ -260,10 +235,9 @@ public class AlleleFrequencyWalker extends BasicLociWalker<AlleleFrequencyEstima
public Integer reduceInit() { return 0; }
public Integer reduce(AlleleFrequencyEstimate alleleFreq, Integer sum) {
//System.out.printf("%s %.2f\n", alleleFreq.asString(), alleleFreq.logOddsVarRef);
return 0;//value + sum;
public Integer reduce(AlleleFrequencyEstimate alleleFreq, Integer sum)
{
return 0;
}
@ -307,6 +281,41 @@ public class AlleleFrequencyWalker extends BasicLociWalker<AlleleFrequencyEstima
}
}
public static void main(String[] args)
{
int N = 2;
byte[] het_bases = {0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1};
double[][] het_quals = {{0.999, 0.001/3.0, 0.001/3.0, 0.001/3.0},
{0.999, 0.001/3.0, 0.001/3.0, 0.001/3.0},
{0.999, 0.001/3.0, 0.001/3.0, 0.001/3.0},
{0.999, 0.001/3.0, 0.001/3.0, 0.001/3.0},
{0.999, 0.001/3.0, 0.001/3.0, 0.001/3.0},
{0.999, 0.001/3.0, 0.001/3.0, 0.001/3.0},
{0.999, 0.001/3.0, 0.001/3.0, 0.001/3.0},
{0.999, 0.001/3.0, 0.001/3.0, 0.001/3.0},
{0.999, 0.001/3.0, 0.001/3.0, 0.001/3.0},
{0.999, 0.001/3.0, 0.001/3.0, 0.001/3.0},
{0.001/3.0, 0.999, 0.001/3.0, 0.001/3.0},
{0.001/3.0, 0.999, 0.001/3.0, 0.001/3.0},
{0.001/3.0, 0.999, 0.001/3.0, 0.001/3.0},
{0.001/3.0, 0.999, 0.001/3.0, 0.001/3.0},
{0.001/3.0, 0.999, 0.001/3.0, 0.001/3.0},
{0.001/3.0, 0.999, 0.001/3.0, 0.001/3.0},
{0.001/3.0, 0.999, 0.001/3.0, 0.001/3.0},
{0.001/3.0, 0.999, 0.001/3.0, 0.001/3.0},
{0.001/3.0, 0.999, 0.001/3.0, 0.001/3.0},
{0.001/3.0, 0.999, 0.001/3.0, 0.001/3.0}};
AlleleFrequencyWalker w = new AlleleFrequencyWalker();
AlleleFrequencyEstimate estimate = w.AlleleFrequencyEstimator(N, het_bases, het_quals, 0, 1);
System.out.print(String.format("50/50 Het : %s %c %c %f %f %f %d %s\n",
"null", estimate.ref, estimate.alt, estimate.qhat, estimate.qstar, estimate.LOD, 20, "null"));
}
}