Imported Upstream version 0.5

[pysam.git] / samtools / bam2bcf.h

diff --git a/samtools/bam2bcf.h b/samtools/bam2bcf.h
new file mode 100644 (file)
index 0000000..9585672
--- /dev/null
+++ b/samtools/bam2bcf.h
@@ -0,0 +1,55 @@
+#ifndef BAM2BCF_H
+#define BAM2BCF_H
+
+#include <stdint.h>
+#include "errmod.h"
+#include "bcftools/bcf.h"
+
+#define B2B_INDEL_NULL 10000
+
+typedef struct __bcf_callaux_t {
+       int capQ, min_baseQ;
+       int openQ, extQ, tandemQ; // for indels
+       int min_support; // for collecting indel candidates
+       double min_frac; // for collecting indel candidates
+       // for internal uses
+       int max_bases;
+       int indel_types[4];
+       int maxins, indelreg;
+       char *inscns;
+       uint16_t *bases;
+       errmod_t *e;
+       void *rghash;
+} bcf_callaux_t;
+
+typedef struct {
+       int depth, ori_depth, qsum[4];
+       int anno[16];
+       float p[25];
+} bcf_callret1_t;
+
+typedef struct {
+       int a[5]; // alleles: ref, alt, alt2, alt3
+       int n, n_alleles, shift, ori_ref, unseen;
+       int anno[16], depth, ori_depth;
+       uint8_t *PL;
+} bcf_call_t;
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+       bcf_callaux_t *bcf_call_init(double theta, int min_baseQ);
+       void bcf_call_destroy(bcf_callaux_t *bca);
+       int bcf_call_glfgen(int _n, const bam_pileup1_t *pl, int ref_base, bcf_callaux_t *bca, bcf_callret1_t *r);
+       int bcf_call_combine(int n, const bcf_callret1_t *calls, int ref_base /*4-bit*/, bcf_call_t *call);
+       int bcf_call2bcf(int tid, int pos, bcf_call_t *bc, bcf1_t *b, bcf_callret1_t *bcr, int is_SP,
+                                        const bcf_callaux_t *bca, const char *ref);
+       int bcf_call_gap_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_callaux_t *bca, const char *ref,
+                                                 const void *rghash);
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif