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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 typedef struct __bcf_callaux_t {
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11 int capQ, min_baseQ;
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12 int openQ, extQ, tandemQ; // for indels
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13 int min_support; // for collecting indel candidates
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14 double min_frac; // for collecting indel candidates
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15 // for internal uses
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16 int max_bases;
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17 int indel_types[4];
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18 int maxins, indelreg;
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19 char *inscns;
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20 uint16_t *bases;
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21 errmod_t *e;
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22 void *rghash;
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23 } bcf_callaux_t;
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24
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25 typedef struct {
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26 int depth, ori_depth, qsum[4];
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27 int anno[16];
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28 float p[25];
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29 } bcf_callret1_t;
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30
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31 typedef struct {
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32 int a[5]; // alleles: ref, alt, alt2, alt3
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33 int n, n_alleles, shift, ori_ref, unseen;
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34 int anno[16], depth, ori_depth;
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35 uint8_t *PL;
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36 } bcf_call_t;
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37
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38 #ifdef __cplusplus
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39 extern "C" {
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40 #endif
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41
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42 bcf_callaux_t *bcf_call_init(double theta, int min_baseQ);
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43 void bcf_call_destroy(bcf_callaux_t *bca);
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44 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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45 int bcf_call_combine(int n, const bcf_callret1_t *calls, int ref_base /*4-bit*/, bcf_call_t *call);
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46 int bcf_call2bcf(int tid, int pos, bcf_call_t *bc, bcf1_t *b, bcf_callret1_t *bcr, int is_SP,
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47 const bcf_callaux_t *bca, const char *ref);
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48 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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49 const void *rghash);
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50
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51 #ifdef __cplusplus
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52 }
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53 #endif
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54
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55 #endif
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