* samtools-0.1.10 (r831)

[samtools.git] / bam2bcf.c

diff --git a/bam2bcf.c b/bam2bcf.c
index 088635c0b04a549b762d1a3b28efad82f4bb5c80..fe447e6aafb610fb984d3e07c9c507a5572630ca 100644 (file)
--- a/bam2bcf.c
+++ b/bam2bcf.c
@@ -22,6 +22,7 @@ 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);
        return bca;
 }
@@ -32,8 +33,10 @@ void bcf_call_destroy(bcf_callaux_t *bca)
        errmod_destroy(bca->e);
        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. */
+/* 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. */
 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;
@@ -92,7 +95,9 @@ 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];
@@ -100,7 +105,7 @@ 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 = -1, ref4 = 0;
+       } else call->ori_ref = ref_base, ref4 = 0; // ref_base < 0
        // calculate qsum
        memset(qsum, 0, 4 * sizeof(int));
        for (i = 0; i < n; ++i)
@@ -125,7 +130,7 @@ 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 {
+       } else { // for indels and MNPs
                call->n_alleles = j;
                if (call->n_alleles == 1) return -1; // no reliable supporting read. stop doing anything
        }
@@ -168,7 +173,8 @@ 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)
 {
@@ -179,7 +185,7 @@ 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 < 0) { // an indel
+       if (bc->ori_ref == B2B_REF_INDEL) { // an indel
                // write REF
                kputc(ref[pos], &s);
                for (j = 0; j < bca->indelreg; ++j) kputc(ref[pos+1+j], &s);
@@ -202,6 +208,16 @@ 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+1+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*i&3], &s);
+               }
+               kputc('\0', &s);
        } else { // a SNP
                kputc("ACGTN"[bc->ori_ref], &s); kputc('\0', &s);
                for (i = 1; i < 5; ++i) {
@@ -213,7 +229,8 @@ 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 < 0) kputs("INDEL;", &s);
+       if (bc->ori_ref == B2B_REF_INDEL) kputs("INDEL;", &s);
+       else if (bc->ori_ref == B2B_REF_MNP) kputs("MNP;", &s);
        kputs("DP=", &s); kputw(bc->ori_depth, &s); kputs(";I16=", &s);
        for (i = 0; i < 16; ++i) {
                if (i) kputc(',', &s);