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All bases are now indexed as A:0, C:1, G:2, T:3. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@401 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
kiran 2009-04-14 14:49:43 +00:00
parent 40ea22eb17
commit dafdff1974
1 changed files with 31 additions and 23 deletions
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54
java/src/org/broadinstitute/sting/playground/gatk/walkers/AlleleFrequencyWalker.java
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@ -241,25 +241,27 @@ public class AlleleFrequencyWalker extends LocusWalker<AlleleFrequencyEstimate,
//System.out.printf("SAM record: %s\n", read.format());
byte hex_qual = hex_quals[offset];
int baseIndex = QualityUtils.compressedQualityToBaseIndex(hex_qual);
// Todo: Andrew indexes his nucleotides as 0:A, 1:C, 2:T, 3:G. Kiran indexes his nucleotides as 0:A, 1:C, 2:G, 3:T. This must be reconciled. Here, I just translate appropriately.
int called2num = 0;
switch (baseIndex) {
case 0: called2num = 0; break;
case 1: called2num = 1; break;
case 2: called2num = 3; break;
case 3: called2num = 2; break;
default: assert(baseIndex >= 0 && baseIndex < 4); break;
}
int called2num = QualityUtils.compressedQualityToBaseIndex(hex_qual);
double qual2 = QualityUtils.compressedQualityToProb(hex_qual);
//System.out.printf("2ND %x %d %f\n", hex_qual, called2num, qual2);
quals[i][called2num] = qual2;
/*
int crossTalkPartnerIndex = BaseUtils.crossTalkPartnerIndex(callednum);
if (called2num == crossTalkPartnerIndex) {
double nonref_quals = (1.0 - quals[i][callednum]) / 3.0;
for (int b=0; b<4; b++)
if (b != callednum)
quals[i][b] = nonref_quals;
} else {
*/
double qual2 = QualityUtils.compressedQualityToProb(hex_qual);
//System.out.printf("2ND %x %d %f\n", hex_qual, called2num, qual2);
quals[i][called2num] = qual2;
double nonref_quals = (1.0 - quals[i][callednum] - quals[i][called2num]) / 2;
for (int b=0; b<4; b++)
if (b != callednum && b != called2num)
quals[i][b] = nonref_quals;
double nonref_quals = (1.0 - quals[i][callednum] - quals[i][called2num]) / 2.0;
for (int b=0; b<4; b++)
if (b != callednum && b != called2num)
quals[i][b] = nonref_quals;
//}
}
}
@ -569,18 +571,24 @@ public class AlleleFrequencyWalker extends LocusWalker<AlleleFrequencyEstimate,
nuc2num = new int[128];
nuc2num['A'] = 0;
nuc2num['C'] = 1;
nuc2num['T'] = 2;
nuc2num['G'] = 3;
//nuc2num['T'] = 2;
nuc2num['G'] = 2;
//nuc2num['G'] = 3;
nuc2num['T'] = 3;
nuc2num['a'] = 0;
nuc2num['c'] = 1;
nuc2num['t'] = 2;
nuc2num['g'] = 3;
//nuc2num['t'] = 2;
nuc2num['g'] = 2;
//nuc2num['g'] = 3;
nuc2num['t'] = 3;
num2nuc = new char[4];
num2nuc[0] = 'A';
num2nuc[1] = 'C';
num2nuc[2] = 'T';
num2nuc[3] = 'G';
//num2nuc[2] = 'T';
num2nuc[2] = 'G';
//num2nuc[3] = 'G';
num2nuc[3] = 'T';
//if (System.getenv("N") != null) { this.N = (new Integer(System.getenv("N"))).intValue(); }
//else { this.N = 2; }