X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bam2bcf.h;h=0de76f99afa54461fe3a74416098182d2471bdfa;hb=4c8c9dfc1e3b3b066a62a703fd3ba04db6ad5a45;hp=b6514c05c2b5633a93104524bcd4fa8533c3ba80;hpb=df7cadac556f302bdd0bc48c235c2b61b699dfe1;p=samtools.git

diff --git a/bam2bcf.h b/bam2bcf.h
index b6514c0..0de76f9 100644
--- a/bam2bcf.h
+++ b/bam2bcf.h
@@ -5,30 +5,35 @@
 #include "errmod.h"
 #include "bcftools/bcf.h"
 
-#define BAM2BCF_INDELREG_THRES 13
+#define B2B_INDEL_NULL 10000
+#define B2B_MAX_MNP    4 // cannot be larger than 4!!!
+#define B2B_MNP_WIN    10
+#define B2B_REF_INDEL  (-1)
+#define B2B_REF_MNP    (-2)
 
 typedef struct __bcf_callaux_t {
-	int max_bases, capQ, min_baseQ;
+	int capQ, min_baseQ;
 	int openQ, extQ, tandemQ;
 	// for internal uses
+	int max_bases;
+	int indel_types[4];
+	int maxins, indelreg, last_mnp_pos;
+	char *inscns;
 	uint16_t *bases;
 	errmod_t *e;
+	void *rghash;
 } bcf_callaux_t;
 
 typedef struct {
-	int depth, indelreg;
-	float ins_len, del_len;
-	int qsum[4];
+	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 indelreg;
-	float ins_len, del_len;
-	int depth, anno[16];
+	int n, n_alleles, shift, ori_ref, unseen; // ori_ref can be B2B_REF_INDEL/B2B_REF_MNP
+	int anno[16], depth, ori_depth;
 	uint8_t *PL;
 } bcf_call_t;
 
@@ -38,11 +43,13 @@ extern "C" {
 
 	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 /*4-bit*/, bcf_callaux_t *bca, bcf_callret1_t *r);
+	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_call_combine_gap(int n, const bcf_callret1_t *calls, 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);
-	int bcf_call_glfgen_gap(int pos, int _n, const bam_pileup1_t *pl, bcf_callaux_t *bca, bcf_callret1_t *r);
+	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);
+	int bcf_call_mnp_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_callaux_t *bca, const char *ref);
 
 #ifdef __cplusplus
 }