From 7943d9b7b1c159da840cbcfeb9cb277bb58474f2 Mon Sep 17 00:00:00 2001
From: Heng Li <lh3@live.co.uk>
Date: Sat, 20 Nov 2010 04:16:08 +0000
Subject: [PATCH]  * samtools-0.1.10-9 (r844)  * added the "folded" or
 reference-free mode for variant calling

---
 bamtk.c          |  2 +-
 bcftools/call1.c |  8 ++++++--
 bcftools/prob1.c | 21 +++++++++++++++++++--
 bcftools/prob1.h |  1 +
 4 files changed, 27 insertions(+), 5 deletions(-)

diff --git a/bamtk.c b/bamtk.c
index 6d4eb76..cb17906 100644
--- a/bamtk.c
+++ b/bamtk.c
@@ -9,7 +9,7 @@
 #endif
 
 #ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.1.10-8 (r841)"
+#define PACKAGE_VERSION "0.1.10-9 (r844)"
 #endif
 
 int bam_taf2baf(int argc, char *argv[]);
diff --git a/bcftools/call1.c b/bcftools/call1.c
index b0b14fc..5e4fc9f 100644
--- a/bcftools/call1.c
+++ b/bcftools/call1.c
@@ -26,6 +26,7 @@ KSTREAM_INIT(gzFile, gzread, 16384)
 #define VC_CALL_GT 2048
 #define VC_ADJLD   4096
 #define VC_NO_INDEL 8192
+#define VC_FOLDED 16384
 
 typedef struct {
 	int flag, prior_type, n1;
@@ -216,8 +217,9 @@ int bcfview(int argc, char *argv[])
 	tid = begin = end = -1;
 	memset(&vc, 0, sizeof(viewconf_t));
 	vc.prior_type = vc.n1 = -1; vc.theta = 1e-3; vc.pref = 0.5; vc.indel_frac = -1.;
-	while ((c = getopt(argc, argv, "N1:l:cHAGvbSuP:t:p:QgLi:I")) >= 0) {
+	while ((c = getopt(argc, argv, "fN1:l:cHAGvbSuP:t:p:QgLi:I")) >= 0) {
 		switch (c) {
+		case 'f': vc.flag |= VC_FOLDED; break;
 		case '1': vc.n1 = atoi(optarg); break;
 		case 'l': vc.fn_list = strdup(optarg); break;
 		case 'N': vc.flag |= VC_ACGT_ONLY; break;
@@ -260,6 +262,7 @@ int bcfview(int argc, char *argv[])
 		fprintf(stderr, "         -Q        output the QCALL likelihood format\n");
 		fprintf(stderr, "         -L        calculate LD for adjacent sites\n");
 		fprintf(stderr, "         -I        skip indels\n");
+		fprintf(stderr, "         -f        reference-free variant calling\n");
 		fprintf(stderr, "         -1 INT    number of group-1 samples [0]\n");
 		fprintf(stderr, "         -l FILE   list of sites to output [all sites]\n");
 		fprintf(stderr, "         -t FLOAT  scaled substitution mutation rate [%.4lg]\n", vc.theta);
@@ -293,7 +296,8 @@ int bcfview(int argc, char *argv[])
 			bcf_p1_set_n1(p1, vc.n1);
 			bcf_p1_init_subprior(p1, vc.prior_type, vc.theta);
 		}
-		if (vc.indel_frac > 0.) bcf_p1_indel_prior(p1, vc.indel_frac);
+		if (vc.indel_frac > 0.) bcf_p1_indel_prior(p1, vc.indel_frac); // otherwise use the default indel_frac
+		if (vc.flag & VC_FOLDED) bcf_p1_set_folded(p1);
 	}
 	if (vc.fn_list) hash = bcf_load_pos(vc.fn_list, h);
 	if (optind + 1 < argc && !(vc.flag&VC_VCFIN)) {
diff --git a/bcftools/prob1.c b/bcftools/prob1.c
index 176a0fc..8bf968f 100644
--- a/bcftools/prob1.c
+++ b/bcftools/prob1.c
@@ -32,7 +32,7 @@ unsigned char seq_nt4_table[256] = {
 };
 
 struct __bcf_p1aux_t {
-	int n, M, n1, is_indel;
+	int n, M, n1, is_indel, is_folded;
 	double *q2p, *pdg; // pdg -> P(D|g)
 	double *phi, *phi_indel;
 	double *z, *zswap; // aux for afs
@@ -43,6 +43,13 @@ struct __bcf_p1aux_t {
 	int PL_len;
 };
 
+static void fold_array(int M, double *x)
+{
+	int k;
+	for (k = 0; k < M/2; ++k)
+		x[k] = x[M-k] = (x[k] + x[M-k]) / 2.;
+}
+
 void bcf_p1_indel_prior(bcf_p1aux_t *ma, double x)
 {
 	int i;
@@ -155,6 +162,15 @@ int bcf_p1_set_n1(bcf_p1aux_t *b, int n1)
 	return 0;
 }
 
+void bcf_p1_set_folded(bcf_p1aux_t *p1a)
+{
+	if (p1a->n1 < 0) {
+		p1a->is_folded = 1;
+		fold_array(p1a->M, p1a->phi);
+		fold_array(p1a->M, p1a->phi_indel);
+	}
+}
+
 void bcf_p1_destroy(bcf_p1aux_t *ma)
 {
 	if (ma) {
@@ -373,7 +389,7 @@ int bcf_p1_cal(bcf1_t *b, bcf_p1aux_t *ma, bcf_p1rst_t *rst)
 	// 
 	rst->rank0 = cal_pdg(b, ma);
 	rst->f_exp = mc_cal_afs(ma);
-	rst->p_ref = ma->afs1[ma->M];
+	rst->p_ref = ma->is_folded? ma->afs1[ma->M] + ma->afs1[0] : ma->afs1[ma->M];
 	// calculate f_flat and f_em
 	for (k = 0, sum = 0.; k <= ma->M; ++k)
 		sum += (long double)ma->z[k];
@@ -412,6 +428,7 @@ int bcf_p1_cal(bcf1_t *b, bcf_p1aux_t *ma, bcf_p1rst_t *rst)
 void bcf_p1_dump_afs(bcf_p1aux_t *ma)
 {
 	int k;
+	if (ma->is_folded) fold_array(ma->M, ma->afs);
 	fprintf(stderr, "[afs]");
 	for (k = 0; k <= ma->M; ++k)
 		fprintf(stderr, " %d:%.3lf", k, ma->afs[ma->M - k]);
diff --git a/bcftools/prob1.h b/bcftools/prob1.h
index 6d9d28e..3827534 100644
--- a/bcftools/prob1.h
+++ b/bcftools/prob1.h
@@ -32,6 +32,7 @@ extern "C" {
 	int bcf_p1_read_prior(bcf_p1aux_t *ma, const char *fn);
 	long double bcf_p1_cal_g3(bcf_p1aux_t *p1a, double g[3]);
 	int bcf_p1_set_n1(bcf_p1aux_t *b, int n1);
+	void bcf_p1_set_folded(bcf_p1aux_t *p1a); // only effective when set_n1() is not called
 
 #ifdef __cplusplus
 }
-- 
2.39.2