Merge remote branch 'remotes/master/master' into fb-annots

[samtools.git] / bcftools / prob1.c

diff --git a/bcftools/prob1.c b/bcftools/prob1.c
index d6557223e729eddbf0b2f70bd561c2d3d326143c..f04cf085f0a499e29bf4470356acf5de90a6b396 100644 (file)
--- a/bcftools/prob1.c
+++ b/bcftools/prob1.c
@@ -5,6 +5,7 @@
 #include <errno.h>
 #include <assert.h>
 #include <limits.h>
+#include <zlib.h>
 #include "prob1.h"
 #include "kstring.h"
 
@@ -15,6 +16,8 @@ KSTREAM_INIT(gzFile, gzread, 16384)
 #define MC_EM_EPS 1e-5
 #define MC_DEF_INDEL 0.15
 
+gzFile bcf_p1_fp_lk;
+
 unsigned char seq_nt4_table[256] = {
        4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4, 
        4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4, 
@@ -165,6 +168,8 @@ bcf_p1aux_t *bcf_p1_init(int n, uint8_t *ploidy)
        return ma;
 }
 
+int bcf_p1_get_M(bcf_p1aux_t *b) { return b->M; }
+
 int bcf_p1_set_n1(bcf_p1aux_t *b, int n1)
 {
        if (n1 == 0 || n1 >= b->n) return -1;
@@ -751,6 +756,8 @@ static void mc_cal_y_core(bcf_p1aux_t *ma, int beg)
                }
        }
        if (z[0] != ma->z) memcpy(ma->z, z[0], sizeof(double) * (ma->M + 1));
+       if (bcf_p1_fp_lk)
+               gzwrite(bcf_p1_fp_lk, ma->z, sizeof(double) * (ma->M + 1));
 }
 
 static void mc_cal_y(bcf_p1aux_t *ma)