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1 #ifndef BAM2BCF_H
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2 #define BAM2BCF_H
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3
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4 #include <stdint.h>
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5 #include "errmod.h"
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6 #include "bcftools/bcf.h"
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7
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8 #define B2B_INDEL_NULL 10000
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9
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10 #define B2B_FMT_DP 0x1
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11 #define B2B_FMT_SP 0x2
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12 #define B2B_FMT_DV 0x4
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13
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14 typedef struct __bcf_callaux_t {
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15 int capQ, min_baseQ;
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16 int openQ, extQ, tandemQ; // for indels
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17 int min_support, max_support; // for collecting indel candidates
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18 double min_frac, max_frac; // for collecting indel candidates
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19 int per_sample_flt; // indel filtering strategy
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20 int *ref_pos, *alt_pos, npos; // for ReadPosBias
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21 // for internal uses
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22 int max_bases;
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23 int indel_types[4];
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24 int maxins, indelreg;
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25 int read_len;
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26 char *inscns;
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27 uint16_t *bases;
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28 errmod_t *e;
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29 void *rghash;
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30 } bcf_callaux_t;
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31
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32 typedef struct {
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33 int depth, n_supp, ori_depth, qsum[4];
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34 unsigned int anno[16];
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35 float p[25];
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36 } bcf_callret1_t;
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37
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38 typedef struct {
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39 int a[5]; // alleles: ref, alt, alt2, alt3
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40 float qsum[4];
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41 int n, n_alleles, shift, ori_ref, unseen;
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42 int n_supp; // number of supporting non-reference reads
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43 unsigned int anno[16], depth, ori_depth;
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44 uint8_t *PL;
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45 float vdb; // variant distance bias
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46 float read_pos_bias;
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47 struct { float avg, var; int dp; } read_pos;
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48 } bcf_call_t;
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49
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50 #ifdef __cplusplus
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51 extern "C" {
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52 #endif
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53
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54 bcf_callaux_t *bcf_call_init(double theta, int min_baseQ);
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55 void bcf_call_destroy(bcf_callaux_t *bca);
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56 int bcf_call_glfgen(int _n, const bam_pileup1_t *pl, int ref_base, bcf_callaux_t *bca, bcf_callret1_t *r);
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57 int bcf_call_combine(int n, const bcf_callret1_t *calls, bcf_callaux_t *bca, int ref_base /*4-bit*/, bcf_call_t *call);
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58 int bcf_call2bcf(int tid, int pos, bcf_call_t *bc, bcf1_t *b, bcf_callret1_t *bcr, int fmt_flag,
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59 const bcf_callaux_t *bca, const char *ref);
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60 int bcf_call_gap_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_callaux_t *bca, const char *ref,
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61 const void *rghash);
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62
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63 #ifdef __cplusplus
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64 }
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65 #endif
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66
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67 #endif
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