* samtools-0.1.12-2 (r877)

[samtools.git] / bam2bcf.c

diff --git a/bam2bcf.c b/bam2bcf.c
index de6a3ed367b90bea3a4fc7430c9f4b4fa5bf26e4..08120fc46c2a3902e01582b45de0659d4b333eb6 100644 (file)
--- a/bam2bcf.c
+++ b/bam2bcf.c
@@ -20,9 +20,11 @@ bcf_callaux_t *bcf_call_init(double theta, int min_baseQ)
        if (theta <= 0.) theta = CALL_DEFTHETA;
        bca = calloc(1, sizeof(bcf_callaux_t));
        bca->capQ = 60;
-       bca->openQ = 40; bca->extQ = 20; bca->tandemQ = 80;
+       bca->openQ = 40; bca->extQ = 20; bca->tandemQ = 100;
        bca->min_baseQ = min_baseQ;
        bca->e = errmod_init(1. - theta);
+       bca->min_frac = 0.002;
+       bca->min_support = 1;
        return bca;
 }
 
@@ -30,13 +32,13 @@ void bcf_call_destroy(bcf_callaux_t *bca)
 {
        if (bca == 0) return;
        errmod_destroy(bca->e);
-       free(bca->bases); free(bca);
+       free(bca->bases); free(bca->inscns); free(bca);
 }
 /* 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;
+       int i, n, ref4, is_indel, ori_depth = 0;
        memset(r, 0, sizeof(bcf_callret1_t));
        if (ref_base >= 0) {
                ref4 = bam_nt16_nt4_table[ref_base];
@@ -53,11 +55,14 @@ int bcf_call_glfgen(int _n, const bam_pileup1_t *pl, int ref_base, bcf_callaux_t
        memset(r, 0, sizeof(bcf_callret1_t));
        for (i = n = 0; i < _n; ++i) {
                const bam_pileup1_t *p = pl + i;
-               int q, b, mapQ, baseQ, is_diff, min_dist;
+               int q, b, mapQ, baseQ, is_diff, min_dist, seqQ;
                // set base
                if (p->is_del || p->is_refskip || (p->b->core.flag&BAM_FUNMAP)) continue;
+               ++ori_depth;
                baseQ = q = is_indel? p->aux&0xff : (int)bam1_qual(p->b)[p->qpos]; // base/indel quality
+               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;
                if (q > mapQ) q = mapQ;
                if (q > 63) q = 63;
@@ -67,7 +72,7 @@ int bcf_call_glfgen(int _n, const bam_pileup1_t *pl, int ref_base, bcf_callaux_t
                        b = bam_nt16_nt4_table[b? b : ref_base]; // b is the 2-bit base
                        is_diff = (ref4 < 4 && b == ref4)? 0 : 1;
                } else {
-                       b = p->aux>>8&0x3f;
+                       b = p->aux>>16&0x3f;
                        is_diff = (b != 0);
                }
                bca->bases[n++] = q<<5 | (int)bam1_strand(p->b)<<4 | b;
@@ -84,7 +89,7 @@ int bcf_call_glfgen(int _n, const bam_pileup1_t *pl, int ref_base, bcf_callaux_t
                r->anno[3<<2|is_diff<<1|0] += min_dist;
                r->anno[3<<2|is_diff<<1|1] += min_dist * min_dist;
        }
-       r->depth = n;
+       r->depth = n; r->ori_depth = ori_depth;
        // glfgen
        errmod_cal(bca->e, n, 5, bca->bases, r->p);
        return r->depth;
@@ -122,7 +127,10 @@ 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 call->n_alleles = j;
+       } else {
+               call->n_alleles = j;
+               if (call->n_alleles == 1) return -1; // no reliable supporting read. stop doing anything
+       }
        // set the PL array
        if (call->n < n) {
                call->n = n;
@@ -155,26 +163,48 @@ int bcf_call_combine(int n, const bcf_callret1_t *calls, int ref_base /*4-bit*/,
        }
        // combine annotations
        memset(call->anno, 0, 16 * sizeof(int));
-       for (i = call->depth = 0, tmp = 0; i < n; ++i) {
+       for (i = call->depth = call->ori_depth = 0, tmp = 0; i < n; ++i) {
                call->depth += calls[i].depth;
+               call->ori_depth += calls[i].ori_depth;
                for (j = 0; j < 16; ++j) call->anno[j] += calls[i].anno[j];
        }
        return 0;
 }
 
-int bcf_call2bcf(int tid, int pos, bcf_call_t *bc, bcf1_t *b, bcf_callret1_t *bcr, int is_SP)
+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)
 {
        extern double kt_fisher_exact(int n11, int n12, int n21, int n22, double *_left, double *_right, double *two);
        kstring_t s;
-       int i;
+       int i, j;
        b->n_smpl = bc->n;
        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 < 0) {
-               kputc('N', &s); kputc('\0', &s);
-               kputs("<INDEL>", &s); kputc('\0', &s);
-       } else {
+       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);
+               kputc('\0', &s);
+               // write ALT
+               kputc(ref[pos], &s);
+               for (i = 1; i < 4; ++i) {
+                       if (bc->a[i] < 0) break;
+                       if (i > 1) {
+                               kputc(',', &s); kputc(ref[pos], &s);
+                       }
+                       if (bca->indel_types[bc->a[i]] < 0) { // deletion
+                               for (j = -bca->indel_types[bc->a[i]]; j < bca->indelreg; ++j)
+                                       kputc(ref[pos+1+j], &s);
+                       } else { // insertion; cannot be a reference unless a bug
+                               char *inscns = &bca->inscns[bc->a[i] * bca->maxins];
+                               for (j = 0; j < bca->indel_types[bc->a[i]]; ++j)
+                                       kputc("ACGTN"[(int)inscns[j]], &s);
+                               for (j = 0; j < bca->indelreg; ++j) kputc(ref[pos+1+j], &s);
+                       }
+               }
+               kputc('\0', &s);
+       } else { // a SNP
                kputc("ACGTN"[bc->ori_ref], &s); kputc('\0', &s);
                for (i = 1; i < 5; ++i) {
                        if (bc->a[i] < 0) break;
@@ -185,7 +215,8 @@ int bcf_call2bcf(int tid, int pos, bcf_call_t *bc, bcf1_t *b, bcf_callret1_t *bc
        }
        kputc('\0', &s);
        // INFO
-       kputs("I16=", &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);
                kputw(bc->anno[i], &s);