From 082c52f3cb5517db50987bf1dc43aef845c45fd8 Mon Sep 17 00:00:00 2001
From: Heng Li <lh3@live.co.uk>
Date: Tue, 31 Aug 2010 14:20:57 +0000
Subject: [PATCH]  * rename vcfout.c as call1.c  * prepare to add two-sample
 comparison

---
 bcftools/Makefile              |  2 +-
 bcftools/{vcfout.c => call1.c} |  0
 bcftools/prob1.c               | 10 +++++++++-
 3 files changed, 10 insertions(+), 2 deletions(-)
 rename bcftools/{vcfout.c => call1.c} (100%)

diff --git a/bcftools/Makefile b/bcftools/Makefile
index 6a6bdb8..5a3dc76 100644
--- a/bcftools/Makefile
+++ b/bcftools/Makefile
@@ -3,7 +3,7 @@ CFLAGS=		-g -Wall -O2 #-m64 #-arch ppc
 DFLAGS=		-D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE
 LOBJS=		bcf.o vcf.o bcfutils.o prob1.o kfunc.o index.o fet.o
 OMISC=		..
-AOBJS=		vcfout.o main.o $(OMISC)/kstring.o $(OMISC)/bgzf.o $(OMISC)/knetfile.o
+AOBJS=		call1.o main.o $(OMISC)/kstring.o $(OMISC)/bgzf.o $(OMISC)/knetfile.o
 PROG=		bcftools
 INCLUDES=	
 SUBDIRS=	.
diff --git a/bcftools/vcfout.c b/bcftools/call1.c
similarity index 100%
rename from bcftools/vcfout.c
rename to bcftools/call1.c
diff --git a/bcftools/prob1.c b/bcftools/prob1.c
index 4611af1..e124b0f 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;
+	int n, M, n1;
 	double *q2p, *pdg; // pdg -> P(D|g)
 	double *phi;
 	double *z, *zswap; // aux for afs
@@ -100,6 +100,7 @@ bcf_p1aux_t *bcf_p1_init(int n) // FIXME: assuming diploid
 	bcf_p1aux_t *ma;
 	int i;
 	ma = calloc(1, sizeof(bcf_p1aux_t));
+	ma->n1 = -1;
 	ma->n = n; ma->M = 2 * n;
 	ma->q2p = calloc(256, sizeof(double));
 	ma->pdg = calloc(3 * ma->n, sizeof(double));
@@ -114,6 +115,13 @@ bcf_p1aux_t *bcf_p1_init(int n) // FIXME: assuming diploid
 	return ma;
 }
 
+int bcf_p1_set_n1(bcf_p1aux_t *b, int n1)
+{
+	if (n1 == 0 || n1 >= b->n) return -1;
+	b->n1 = n1;
+	return 0;
+}
+
 void bcf_p1_destroy(bcf_p1aux_t *ma)
 {
 	if (ma) {
-- 
2.39.2