X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bam2bcf.c;h=89d6f9001bfd6dfaed29fa49430e3a23289f58da;hb=53afc90ef53f3c5cd3060377f16828363f55ed00;hp=95532254a084caf3fbd6e05840819225848e952b;hpb=f69357a6a9e701f12d1f01c52cc0d2893bb2ac7a;p=samtools.git

diff --git a/bam2bcf.c b/bam2bcf.c
index 9553225..89d6f90 100644
--- a/bam2bcf.c
+++ b/bam2bcf.c
@@ -14,18 +14,13 @@ extern	void ks_introsort_uint32_t(size_t n, uint32_t a[]);
 
 #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->openQ = 40; bca->extQ = 20; bca->tandemQ = 100;
 	bca->min_baseQ = min_baseQ;
 	bca->e = errmod_init(1. - theta);
 	return bca;
@@ -154,10 +149,12 @@ int bcf_call_combine(int n, const bcf_callret1_t *calls, int ref_base /*4-bit*/,
 	return 0;
 }
 
-int bcf_call2bcf(int tid, int pos, bcf_call_t *bc, bcf1_t *b)
+int bcf_call2bcf(int tid, int pos, bcf_call_t *bc, bcf1_t *b, bcf_callret1_t *bcr, int is_SP)
 {
+	extern double kt_fisher_exact(int n11, int n12, int n21, int n22, double *_left, double *_right, double *two);
 	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);
@@ -177,9 +174,36 @@ int bcf_call2bcf(int tid, int pos, bcf_call_t *bc, bcf1_t *b)
 	}
 	kputc('\0', &s);
 	// FMT
-	kputs("PL", &s); kputc('\0', &s);
+	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(bc->n, b);
+	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;
 }