samtools/bam2bcf.h at develop · mcshane/samtools · GitHub

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#ifndef BAM2BCF_H
#define BAM2BCF_H

#include <stdint.h>
#include <htslib/vcf.h>
#include "errmod.h"

/**
 *  A simplified version of Mann-Whitney U-test is calculated
 *  by default (no CDF) because it is faster and seems to work
 *  better in machine learning filtering. When enabled by setting
 *  CDF_MWU_TESTS, additional annotations will appear on mpileup's
 *  output (RPB2 in addition to RPB, etc.).
 */
#ifndef CDF_MWU_TESTS
#define CDF_MWU_TESTS 0
#endif

#define B2B_INDEL_NULL 10000

#define B2B_FMT_DP      (1<<0)
#define B2B_FMT_SP      (1<<1)
#define B2B_FMT_DV      (1<<2)
#define B2B_FMT_DP4     (1<<3)
#define B2B_FMT_DPR     (1<<4)
#define B2B_INFO_DPR    (1<<5)

typedef struct __bcf_callaux_t {
	int capQ, min_baseQ;
	int openQ, extQ, tandemQ; // for indels
	uint32_t min_support, max_support; // for collecting indel candidates
	float min_frac, max_frac; // for collecting indel candidates
    int per_sample_flt; // indel filtering strategy
    int *ref_pos, *alt_pos, npos, *ref_mq, *alt_mq, *ref_bq, *alt_bq, *fwd_mqs, *rev_mqs, nqual; // for bias tests
	// for internal uses
	int max_bases;
	int indel_types[4];     // indel lengths
	int maxins, indelreg;
    int read_len;
	char *inscns;
	uint16_t *bases;        // 5bit: unused, 6:quality, 1:is_rev, 4:2-bit base or indel allele (index to bcf_callaux_t.indel_types)
	errmod_t *e;
	void *rghash;
} bcf_callaux_t;

typedef struct {
    uint32_t ori_depth;
	unsigned int mq0;
    int32_t *DPR;
    float qsum[4];
    // The fields are:
    //      depth fwd   .. ref (0) and non-ref (2)
    //      depth rev   .. ref (1) and non-ref (3)
    //      baseQ       .. ref (4) and non-ref (6)
    //      baseQ^2     .. ref (5) and non-ref (7)
    //      mapQ        .. ref (8) and non-ref (10)
    //      mapQ^2      .. ref (9) and non-ref (11)
    //      minDist     .. ref (12) and non-ref (14)
    //      minDist^2   .. ref (13) and non-ref (15)
    // Note that this probably needs a more thorough fix: int types in
    // bcf_call_t do overflow with high-coverage data, such as exomes, and
    // BCFv2 supports only floats which may not suffice.
	double anno[16];
	float p[25];        // phred-scaled likelihood of each genotype
} bcf_callret1_t;

typedef struct {
    int tid, pos;
    bcf_hdr_t *bcf_hdr;
	int a[5]; // alleles: ref, alt, alt2, alt3
    float qsum[5];  // for the QS tag
	int n, n_alleles, shift, ori_ref, unseen;
	int n_supp; // number of supporting non-reference reads
	double anno[16];
    unsigned int depth, ori_depth, mq0;
	int32_t *PL, *DP4, *DPR;
    uint8_t *fmt_arr;
    float vdb; // variant distance bias
    float mwu_pos, mwu_mq, mwu_bq, mwu_mqs;
#if CDF_MWU_TESTS
    float mwu_pos_cdf, mwu_mq_cdf, mwu_bq_cdf, mwu_mqs_cdf;
#endif
    float seg_bias;
    kstring_t tmp;
} 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, bcf_callaux_t *bca, int ref_base /*4-bit*/, bcf_call_t *call);
	int bcf_call2bcf(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);
    void bcf_callaux_clean(bcf_callaux_t *bca, bcf_call_t *call);

#ifdef __cplusplus
}
#endif

#endif