X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=pysam.git;a=blobdiff_plain;f=samtools%2Fbam2bcf.c.pysam.c;fp=samtools%2Fbam2bcf.c.pysam.c;h=06f85998d432012ac9baa56fa2f8ded3ae68ec5e;hp=0000000000000000000000000000000000000000;hb=d02fe5283ed7a93a2f76a5d6dc6e37b40c11b9b1;hpb=d828f9c9aa78e3d1687265b52de841f3f3852089

diff --git a/samtools/bam2bcf.c.pysam.c b/samtools/bam2bcf.c.pysam.c
new file mode 100644
index 0000000..06f8599
--- /dev/null
+++ b/samtools/bam2bcf.c.pysam.c
@@ -0,0 +1,262 @@
+#include "pysam.h"
+
+#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 DEF_MAPQ 20
+
+#define CAP_DIST 25
+
+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->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;
+}
+
+void bcf_call_destroy(bcf_callaux_t *bca)
+{
+	if (bca == 0) return;
+	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. */
+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;
+	memset(r, 0, sizeof(bcf_callret1_t));
+	if (ref_base >= 0) {
+		ref4 = bam_nt16_nt4_table[ref_base];
+		is_indel = 0;
+	} else ref4 = 4, is_indel = 1;
+	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, 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 < 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;
+		if (!is_indel) {
+			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
+			is_diff = (ref4 < 4 && b == ref4)? 0 : 1;
+		} else {
+			b = p->aux>>16&0x3f;
+			is_diff = (b != 0);
+		}
+		bca->bases[n++] = q<<5 | (int)bam1_strand(p->b)<<4 | b;
+		// collect annotations
+		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;
+		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; r->ori_depth = ori_depth;
+	// 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;
+	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;
+	// 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 (ref_base >= 0) { // for SNPs, find the "unseen" base
+		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;
+		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;
+		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 = 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;
+			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;
+			}
+		}
+//		if (ref_base < 0) fprintf(pysamerr, "%d,%d,%f,%d\n", call->n_alleles, x, sum_min, call->unseen);
+		call->shift = (int)(sum_min + .499);
+	}
+	// combine annotations
+	memset(call->anno, 0, 16 * sizeof(int));
+	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,
+				 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, 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) { // 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;
+			if (i > 1) kputc(',', &s);
+			kputc(bc->unseen == i? 'X' : "ACGT"[bc->a[i]], &s);
+		}
+		kputc('\0', &s);
+	}
+	kputc('\0', &s);
+	// INFO
+	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);
+	}
+	kputc('\0', &s);
+	// FMT
+	kputs("PL", &s);
+	if (bcr) {
+		kputs(":DP", &s);
+		if (is_SP) kputs(":SP", &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);
+	if (bcr) {
+		uint16_t *dp = (uint16_t*)b->gi[1].data;
+		uint8_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;
+			if (is_SP) {
+				if (p->anno[0] + p->anno[1] < 2 || p->anno[2] + p->anno[3] < 2
+					|| p->anno[0] + p->anno[2] < 2 || p->anno[1] + p->anno[3] < 2)
+				{
+					sp[i] = 0;
+				} else {
+					double left, right, two;
+					int x;
+					kt_fisher_exact(p->anno[0], p->anno[1], p->anno[2], p->anno[3], &left, &right, &two);
+					x = (int)(-4.343 * log(two) + .499);
+					if (x > 255) x = 255;
+					sp[i] = x;
+				}
+			}
+		}
+	}
+	return 0;
+}