Merge pull request #44 from peterjc/check_bins

[samtools.git] / bam2bcf.h

diff --git a/bam2bcf.h b/bam2bcf.h
index 4af080c4753b2070192bec5e04e16174ca5bb5f8..b2b1825cd59a17a1973b040f722f1efb13ef24f0 100644 (file)
--- a/bam2bcf.h
+++ b/bam2bcf.h
@@ -7,15 +7,22 @@
 
 #define B2B_INDEL_NULL 10000
 
+#define B2B_FMT_DP 0x1
+#define B2B_FMT_SP 0x2
+#define B2B_FMT_DV 0x4
+
 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
+       int min_support, max_support; // for collecting indel candidates
+       double min_frac, max_frac; // for collecting indel candidates
+    int per_sample_flt; // indel filtering strategy
+    int *ref_pos, *alt_pos, npos; // for ReadPosBias
        // for internal uses
        int max_bases;
        int indel_types[4];
        int maxins, indelreg;
+    int read_len;
        char *inscns;
        uint16_t *bases;
        errmod_t *e;
@@ -23,18 +30,21 @@ typedef struct __bcf_callaux_t {
 } bcf_callaux_t;
 
 typedef struct {
-       int depth, ori_depth, qsum[4];
-       int anno[16];
+       int depth, n_supp, ori_depth, qsum[4];
+       unsigned int anno[16];
        float p[25];
-    int mvd[3]; // mean variant distance, number of variant reads, average read length
 } bcf_callret1_t;
 
 typedef struct {
        int a[5]; // alleles: ref, alt, alt2, alt3
+    float qsum[4];
        int n, n_alleles, shift, ori_ref, unseen;
-       int anno[16], depth, ori_depth;
+       int n_supp; // number of supporting non-reference reads
+       unsigned int anno[16], depth, ori_depth;
        uint8_t *PL;
     float vdb; // variant distance bias
+    float read_pos_bias;
+    struct { float avg, var; int dp; } read_pos;
 } bcf_call_t;
 
 #ifdef __cplusplus
@@ -44,8 +54,8 @@ 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, 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,
+       int bcf_call_combine(int n, const bcf_callret1_t *calls, bcf_callaux_t *bca, 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 fmt_flag,
                                         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);