X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=samtools.git;a=blobdiff_plain;f=bam2bcf.c;fp=bam2bcf.c;h=e55212ca98cbb28041fb6a6dfc46619ff595ee09;hp=0000000000000000000000000000000000000000;hb=8d2494d1fb7cd0fa7c63be5ffba8dd1a11457522;hpb=cb12a866906ec4ac644de0e658679261c82ab098

diff --git a/bam2bcf.c b/bam2bcf.c
new file mode 100644
index 0000000..e55212c
--- /dev/null
+++ b/bam2bcf.c
@@ -0,0 +1,186 @@
+#include <math.h>
+#include <stdint.h>
+#include "bam.h"
+#include "kstring.h"
+#include "bam2bcf.h"
+#include "errmod.h"
+#include "bcftools/bcf.h"
+
+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 CAP_DIST 25
+
+struct __bcf_callaux_t {
+	int max_bases, capQ, min_baseQ;
+	uint16_t *bases;
+	errmod_t *e;
+};
+
+bcf_callaux_t *bcf_call_init(double theta, int min_baseQ)
+{
+	bcf_callaux_t *bca;
+	if (theta <= 0.) theta = CALL_DEFTHETA;
+	bca = calloc(1, sizeof(bcf_callaux_t));
+	bca->capQ = 60;
+	bca->min_baseQ = min_baseQ;
+	bca->e = errmod_init(1. - theta);
+	return bca;
+}
+
+void bcf_call_destroy(bcf_callaux_t *bca)
+{
+	if (bca == 0) return;
+	errmod_destroy(bca->e);
+	free(bca->bases); free(bca);
+}
+
+int bcf_call_glfgen(int _n, const bam_pileup1_t *pl, int ref_base /*4-bit*/, bcf_callaux_t *bca, bcf_callret1_t *r)
+{
+	int i, n, ref4;
+	memset(r, 0, sizeof(bcf_callret1_t));
+	ref4 = bam_nt16_nt4_table[ref_base];
+	if (_n == 0) return -1;
+
+	// enlarge the bases array if necessary
+	if (bca->max_bases < _n) {
+		bca->max_bases = _n;
+		kroundup32(bca->max_bases);
+		bca->bases = (uint16_t*)realloc(bca->bases, 2 * bca->max_bases);
+	}
+	// fill the bases array
+	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;
+		// set base
+		if (p->is_del || (p->b->core.flag&BAM_FUNMAP)) continue; // skip unmapped reads and deleted bases
+		baseQ = q = (int)bam1_qual(p->b)[p->qpos]; // base quality
+		if (q < bca->min_baseQ) continue;
+		mapQ = p->b->core.qual < bca->capQ? p->b->core.qual : bca->capQ;
+		if (q > mapQ) q = mapQ;
+		if (q > 63) q = 63;
+		if (q < 4) q = 4;
+		b = bam1_seqi(bam1_seq(p->b), p->qpos); // base
+		b = bam_nt16_nt4_table[b? b : ref_base]; // b is the 2-bit base
+		bca->bases[n++] = q<<5 | (int)bam1_strand(p->b)<<4 | b;
+		// collect annotations
+		r->qsum[b] += q;
+		is_diff = (ref4 < 4 && b == ref4)? 0 : 1;
+		++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;
+		if (min_dist > CAP_DIST) min_dist = CAP_DIST;
+		r->anno[1<<2|is_diff<<1|0] += baseQ;
+		r->anno[1<<2|is_diff<<1|1] += baseQ * baseQ;
+		r->anno[2<<2|is_diff<<1|0] += mapQ;
+		r->anno[2<<2|is_diff<<1|1] += mapQ * mapQ;
+		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;
+	// glfgen
+	errmod_cal(bca->e, n, 5, bca->bases, r->p);
+	return r->depth;
+}
+
+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];
+	int64_t tmp;
+	call->ori_ref = ref4 = bam_nt16_nt4_table[ref_base];
+	if (ref4 > 4) ref4 = 4;
+	// calculate qsum
+	memset(qsum, 0, 4 * sizeof(int));
+	for (i = 0; i < n; ++i)
+		for (j = 0; j < 4; ++j)
+			qsum[j] += calls[i].qsum[j];
+	for (j = 0; j < 4; ++j) qsum[j] = qsum[j] << 2 | j;
+	// find the top 2 alleles
+	for (i = 1; i < 4; ++i) // insertion sort
+		for (j = i; j > 0 && qsum[j] < qsum[j-1]; --j)
+			tmp = qsum[j], qsum[j] = qsum[j-1], qsum[j-1] = tmp;
+	// set the reference allele and alternative allele(s)
+	for (i = 0; i < 5; ++i) call->a[i] = -1;
+	call->unseen = -1;
+	call->a[0] = ref4;
+	for (i = 3, j = 1; i >= 0; --i) {
+		if ((qsum[i]&3) != ref4) {
+			if (qsum[i]>>2 != 0) call->a[j++] = qsum[i]&3;
+			else break;
+		}
+	}
+	if (((ref4 < 4 && j < 4) || (ref4 == 4 && j < 5)) && i >= 0)
+		call->unseen = j, call->a[j++] = qsum[i]&3;
+	call->n_alleles = j;
+	// set the PL array
+	if (call->n < n) {
+		call->n = n;
+		call->PL = realloc(call->PL, 15 * n);
+	}
+	{
+		int x, g[15], z;
+		double sum_min = 0.;
+		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 (i = 0; i < n; ++i) {
+			uint8_t *PL = call->PL + x * i;
+			const bcf_callret1_t *r = calls + i;
+			float min = 1e37;
+			for (j = 0; j < x; ++j)
+				if (min > r->p[g[j]]) min = r->p[g[j]];
+			sum_min += min;
+			for (j = 0; j < x; ++j) {
+				int y;
+				y = (int)(r->p[g[j]] - min + .499);
+				if (y > 255) y = 255;
+				PL[j] = y;
+			}
+		}
+		call->shift = (int)(sum_min + .499);
+	}
+	// combine annotations
+	memset(call->anno, 0, 16 * sizeof(int));
+	for (i = call->depth = 0, tmp = 0; i < n; ++i) {
+		call->depth += calls[i].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)
+{
+	kstring_t s;
+	int i;
+	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);
+	kputc("ACGTN"[bc->ori_ref], &s); kputc('\0', &s);
+	for (i = 1; i < 5; ++i) {
+		if (bc->a[i] < 0) break;
+		if (i > 1) kputc(',', &s);
+		kputc(bc->unseen == i? 'X' : "ACGT"[bc->a[i]], &s);
+	}
+	kputc('\0', &s);
+	kputc('\0', &s);
+	// INFO
+	kputs("I16=", &s);
+	for (i = 0; i < 16; ++i) {
+		if (i) kputc(',', &s);
+		kputw(bc->anno[i], &s);
+	}
+	kputc('\0', &s);
+	// FMT
+	kputs("PL", &s); kputc('\0', &s);
+	b->m_str = s.m; b->str = s.s; b->l_str = s.l;
+	bcf_sync(b);
+	memcpy(b->gi[0].data, bc->PL, b->gi[0].len * bc->n);
+	return 0;
+}