* change the order of PL/GL according to the latest VCF spec

[samtools.git] / bcftools / prob1.c

diff --git a/bcftools/prob1.c b/bcftools/prob1.c
index 9d418c55acdb5d0b276bda0d718a23708bf24f6a..193c4a0c535126496b254869a6aee193ac4ebbf6 100644 (file)
--- a/bcftools/prob1.c
+++ b/bcftools/prob1.c
@@ -168,18 +168,16 @@ void bcf_p1_destroy(bcf_p1aux_t *ma)
 
 static int cal_pdg(const bcf1_t *b, bcf_p1aux_t *ma)
 {
-       int i, j, k;
+       int i, j;
        long *p, tmp;
        p = alloca(b->n_alleles * sizeof(long));
        memset(p, 0, sizeof(long) * b->n_alleles);
        for (j = 0; j < ma->n; ++j) {
                const uint8_t *pi = ma->PL + j * ma->PL_len;
                double *pdg = ma->pdg + j * 3;
-               pdg[0] = ma->q2p[pi[b->n_alleles]]; pdg[1] = ma->q2p[pi[1]]; pdg[2] = ma->q2p[pi[0]];
-               for (i = k = 0; i < b->n_alleles; ++i) {
-                       p[i] += (int)pi[k];
-                       k += b->n_alleles - i;
-               }
+               pdg[0] = ma->q2p[pi[2]]; pdg[1] = ma->q2p[pi[1]]; pdg[2] = ma->q2p[pi[0]];
+               for (i = 0; i < b->n_alleles; ++i)
+                       p[i] += (int)pi[(i+1)*(i+2)/2-1];
        }
        for (i = 0; i < b->n_alleles; ++i) p[i] = p[i]<<4 | i;
        for (i = 1; i < b->n_alleles; ++i) // insertion sort