allow to set seed in view-subsampling

[samtools.git] / bam2bcf.c

diff --git a/bam2bcf.c b/bam2bcf.c
index 45a0ccc36592edbcd8647e731a6476900c4b2c31..f263fad55a5d1f1438fd50d127fb2362309f100b 100644 (file)
--- a/bam2bcf.c
+++ b/bam2bcf.c
@@ -11,6 +11,7 @@ extern        void ks_introsort_uint32_t(size_t n, uint32_t a[]);
 #define CALL_ETA 0.03f
 #define CALL_MAX 256
 #define CALL_DEFTHETA 0.83f
+#define DEF_MAPQ 20
 
 #define CAP_DIST 25
 
@@ -22,8 +23,9 @@ bcf_callaux_t *bcf_call_init(double theta, int min_baseQ)
        bca->capQ = 60;
        bca->openQ = 40; bca->extQ = 20; bca->tandemQ = 100;
        bca->min_baseQ = min_baseQ;
-       bca->last_mnp_pos = -100;
        bca->e = errmod_init(1. - theta);
+       bca->min_frac = 0.002;
+       bca->min_support = 1;
        return bca;
 }
 
@@ -33,10 +35,8 @@ void bcf_call_destroy(bcf_callaux_t *bca)
        errmod_destroy(bca->e);
        free(bca->bases); free(bca->inscns); free(bca);
 }
-/* Compute genotype likelihood by combining likelihood of each
- * read. ref_base is the 4-bit representation of the reference base. It
- * is negative if we are looking at an indel or an MNP. Indel and MNP
- * are indistinguishable in this function. */
+/* ref_base is the 4-bit representation of the reference base. It is
+ * negative if we are looking at an indel. */
 int bcf_call_glfgen(int _n, const bam_pileup1_t *pl, int ref_base, bcf_callaux_t *bca, bcf_callret1_t *r)
 {
        int i, n, ref4, is_indel, ori_depth = 0;
@@ -64,7 +64,8 @@ int bcf_call_glfgen(int _n, const bam_pileup1_t *pl, int ref_base, bcf_callaux_t
                seqQ = is_indel? (p->aux>>8&0xff) : 99;
                if (q < bca->min_baseQ) continue;
                if (q > seqQ) q = seqQ;
-               mapQ = p->b->core.qual < bca->capQ? p->b->core.qual : bca->capQ;
+               mapQ = p->b->core.qual < 255? p->b->core.qual : DEF_MAPQ; // special case for mapQ==255
+               mapQ = mapQ < bca->capQ? mapQ : bca->capQ;
                if (q > mapQ) q = mapQ;
                if (q > 63) q = 63;
                if (q < 4) q = 4;
@@ -78,7 +79,7 @@ int bcf_call_glfgen(int _n, const bam_pileup1_t *pl, int ref_base, bcf_callaux_t
                }
                bca->bases[n++] = q<<5 | (int)bam1_strand(p->b)<<4 | b;
                // collect annotations
-               r->qsum[b] += q;
+               if (b < 4) r->qsum[b] += q;
                ++r->anno[0<<2|is_diff<<1|bam1_strand(p->b)];
                min_dist = p->b->core.l_qseq - 1 - p->qpos;
                if (min_dist > p->qpos) min_dist = p->qpos;
@@ -95,9 +96,7 @@ int bcf_call_glfgen(int _n, const bam_pileup1_t *pl, int ref_base, bcf_callaux_t
        errmod_cal(bca->e, n, 5, bca->bases, r->p);
        return r->depth;
 }
-/* Combine individual calls. ref_base is a 4-bit A/C/G/T for a SNP, or
- * B2B_REF_MNP, or B2B_REF_INDEL. Indel and MNP are indistinguishable in
- * this function. */
+
 int bcf_call_combine(int n, const bcf_callret1_t *calls, int ref_base /*4-bit*/, bcf_call_t *call)
 {
        int ref4, i, j, qsum[4];
@@ -105,7 +104,7 @@ int bcf_call_combine(int n, const bcf_callret1_t *calls, int ref_base /*4-bit*/,
        if (ref_base >= 0) {
                call->ori_ref = ref4 = bam_nt16_nt4_table[ref_base];
                if (ref4 > 4) ref4 = 4;
-       } else call->ori_ref = ref_base, ref4 = 0; // ref_base < 0
+       } else call->ori_ref = -1, ref4 = 0;
        // calculate qsum
        memset(qsum, 0, 4 * sizeof(int));
        for (i = 0; i < n; ++i)
@@ -130,7 +129,7 @@ int bcf_call_combine(int n, const bcf_callret1_t *calls, int ref_base /*4-bit*/,
                if (((ref4 < 4 && j < 4) || (ref4 == 4 && j < 5)) && i >= 0)
                        call->unseen = j, call->a[j++] = qsum[i]&3;
                call->n_alleles = j;
-       } else { // for indels and MNPs
+       } else {
                call->n_alleles = j;
                if (call->n_alleles == 1) return -1; // no reliable supporting read. stop doing anything
        }
@@ -145,8 +144,8 @@ int bcf_call_combine(int n, const bcf_callret1_t *calls, int ref_base /*4-bit*/,
                x = call->n_alleles * (call->n_alleles + 1) / 2;
                // get the possible genotypes
                for (i = z = 0; i < call->n_alleles; ++i)
-                       for (j = i; j < call->n_alleles; ++j)
-                               g[z++] = call->a[i] * 5 + call->a[j];
+                       for (j = 0; j <= i; ++j)
+                               g[z++] = call->a[j] * 5 + call->a[i];
                for (i = 0; i < n; ++i) {
                        uint8_t *PL = call->PL + x * i;
                        const bcf_callret1_t *r = calls + i;
@@ -173,8 +172,7 @@ int bcf_call_combine(int n, const bcf_callret1_t *calls, int ref_base /*4-bit*/,
        }
        return 0;
 }
-/* Fill a bcf1_t record. The type of the record (SNP, MNP or INDEL) is
- * determined by bca->ori_ref. */
+
 int bcf_call2bcf(int tid, int pos, bcf_call_t *bc, bcf1_t *b, bcf_callret1_t *bcr, int is_SP,
                                 const bcf_callaux_t *bca, const char *ref)
 {
@@ -185,7 +183,7 @@ int bcf_call2bcf(int tid, int pos, bcf_call_t *bc, bcf1_t *b, bcf_callret1_t *bc
        b->tid = tid; b->pos = pos; b->qual = 0;
        s.s = b->str; s.m = b->m_str; s.l = 0;
        kputc('\0', &s);
-       if (bc->ori_ref == B2B_REF_INDEL) { // an indel
+       if (bc->ori_ref < 0) { // an indel
                // write REF
                kputc(ref[pos], &s);
                for (j = 0; j < bca->indelreg; ++j) kputc(ref[pos+1+j], &s);
@@ -208,16 +206,6 @@ int bcf_call2bcf(int tid, int pos, bcf_call_t *bc, bcf1_t *b, bcf_callret1_t *bc
                        }
                }
                kputc('\0', &s);
-       } else if (bc->ori_ref == B2B_REF_MNP) {
-               for (j = 0; j < bca->indelreg; ++j) kputc(ref[pos+j], &s);
-               kputc('\0', &s);
-               for (i = 1; i < 4; ++i) {
-                       if (bc->a[i] < 0) break;
-                       if (i > 1) kputc(',', &s);
-                       for (j = 0; j < bca->indelreg; ++j)
-                               kputc("ACGT"[bca->indel_types[i]>>2*j&3], &s);
-               }
-               kputc('\0', &s);
        } else { // a SNP
                kputc("ACGTN"[bc->ori_ref], &s); kputc('\0', &s);
                for (i = 1; i < 5; ++i) {
@@ -229,8 +217,7 @@ int bcf_call2bcf(int tid, int pos, bcf_call_t *bc, bcf1_t *b, bcf_callret1_t *bc
        }
        kputc('\0', &s);
        // INFO
-       if (bc->ori_ref == B2B_REF_INDEL) kputs("INDEL;", &s);
-       else if (bc->ori_ref == B2B_REF_MNP) kputs("MNP;", &s);
+       if (bc->ori_ref < 0) kputs("INDEL;", &s);
        kputs("DP=", &s); kputw(bc->ori_depth, &s); kputs(";I16=", &s);
        for (i = 0; i < 16; ++i) {
                if (i) kputc(',', &s);
@@ -249,7 +236,7 @@ int bcf_call2bcf(int tid, int pos, bcf_call_t *bc, bcf1_t *b, bcf_callret1_t *bc
        memcpy(b->gi[0].data, bc->PL, b->gi[0].len * bc->n);
        if (bcr) {
                uint16_t *dp = (uint16_t*)b->gi[1].data;
-               uint8_t *sp = is_SP? b->gi[2].data : 0;
+               int32_t *sp = is_SP? b->gi[2].data : 0;
                for (i = 0; i < bc->n; ++i) {
                        bcf_callret1_t *p = bcr + i;
                        dp[i] = p->depth < 0xffff? p->depth : 0xffff;