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Uploaded samtools_0.1.16-1_amd64.changes.
[samtools.git]
/
bam_maqcns.c
diff --git
a/bam_maqcns.c
b/bam_maqcns.c
index 2f3fc082be79aa0fa3feae9c1d9a03ad44592877..99310362afa0dfa216b7b678b04f2d69d2103150 100644
(file)
--- a/
bam_maqcns.c
+++ b/
bam_maqcns.c
@@
-22,8
+22,6
@@
typedef struct {
uint32_t c[4];
} glf_call_aux_t;
uint32_t c[4];
} glf_call_aux_t;
-char bam_nt16_nt4_table[] = { 4, 0, 1, 4, 2, 4, 4, 4, 3, 4, 4, 4, 4, 4, 4, 4 };
-
/*
P(<b1,b2>) = \theta \sum_{i=1}^{N-1} 1/i
P(D|<b1,b2>) = \sum_{k=1}^{N-1} p_k 1/2 [(k/N)^n_2(1-k/N)^n_1 + (k/N)^n1(1-k/N)^n_2]
/*
P(<b1,b2>) = \theta \sum_{i=1}^{N-1} 1/i
P(D|<b1,b2>) = \sum_{k=1}^{N-1} p_k 1/2 [(k/N)^n_2(1-k/N)^n_1 + (k/N)^n1(1-k/N)^n_2]
@@
-154,7
+152,7
@@
glf1_t *bam_maqcns_glfgen(int _n, const bam_pileup1_t *pl, uint8_t ref_base, bam
const bam_pileup1_t *p = pl + i;
uint32_t q, x = 0, qq;
uint16_t y = 0;
const bam_pileup1_t *p = pl + i;
uint32_t q, x = 0, qq;
uint16_t y = 0;
- if (p->is_del || (p->b->core.flag&BAM_FUNMAP)) continue;
+ if (p->is_del ||
p->is_refskip ||
(p->b->core.flag&BAM_FUNMAP)) continue;
q = (uint32_t)bam1_qual(p->b)[p->qpos];
if (q < bm->min_baseQ) continue;
x |= (uint32_t)bam1_strand(p->b) << 18 | q << 8 | p->b->core.qual;
q = (uint32_t)bam1_qual(p->b)[p->qpos];
if (q < bm->min_baseQ) continue;
x |= (uint32_t)bam1_strand(p->b) << 18 | q << 8 | p->b->core.qual;
@@
-166,7
+164,7
@@
glf1_t *bam_maqcns_glfgen(int _n, const bam_pileup1_t *pl, uint8_t ref_base, bam
y |= q << 5;
qq = bam1_seqi(bam1_seq(p->b), p->qpos);
q = bam_nt16_nt4_table[qq? qq : ref_base];
y |= q << 5;
qq = bam1_seqi(bam1_seq(p->b), p->qpos);
q = bam_nt16_nt4_table[qq? qq : ref_base];
- if (!p->is_del && q < 4) x |= 1 << 21 | q << 16, y |= q;
+ if (!p->is_del &&
!p->is_refskip &&
q < 4) x |= 1 << 21 | q << 16, y |= q;
bm->aux->info16[n] = y;
bm->aux->info[n++] = x;
}
bm->aux->info16[n] = y;
bm->aux->info[n++] = x;
}