Imported Upstream version 0.5

[pysam.git] / samtools / bcftools / prob1.h

diff --git a/samtools/bcftools/prob1.h b/samtools/bcftools/prob1.h
new file mode 100644 (file)
index 0000000..571f42f
--- /dev/null
+++ b/samtools/bcftools/prob1.h
@@ -0,0 +1,41 @@
+#ifndef BCF_PROB1_H
+#define BCF_PROB1_H
+
+#include "bcf.h"
+
+struct __bcf_p1aux_t;
+typedef struct __bcf_p1aux_t bcf_p1aux_t;
+
+typedef struct {
+       int rank0, perm_rank; // NB: perm_rank is always set to -1 by bcf_p1_cal()
+       double f_exp, f_flat, p_ref_folded, p_ref, p_var_folded, p_var;
+       double cil, cih;
+       double cmp[3], p_chi2; // used by contrast2()
+} bcf_p1rst_t;
+
+#define MC_PTYPE_FULL  1
+#define MC_PTYPE_COND2 2
+#define MC_PTYPE_FLAT  3
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+       bcf_p1aux_t *bcf_p1_init(int n, uint8_t *ploidy);
+       void bcf_p1_init_prior(bcf_p1aux_t *ma, int type, double theta);
+       void bcf_p1_init_subprior(bcf_p1aux_t *ma, int type, double theta);
+       void bcf_p1_destroy(bcf_p1aux_t *ma);
+       int bcf_p1_cal(const bcf1_t *b, int do_contrast, bcf_p1aux_t *ma, bcf_p1rst_t *rst);
+       int bcf_p1_call_gt(const bcf_p1aux_t *ma, double f0, int k);
+       void bcf_p1_dump_afs(bcf_p1aux_t *ma);
+       int bcf_p1_read_prior(bcf_p1aux_t *ma, const char *fn);
+       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
+
+       int bcf_em1(const bcf1_t *b, int n1, int flag, double x[9]);
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif