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1 #ifndef BAM_MAQCNS_H
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2 #define BAM_MAQCNS_H
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3
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4 #include "glf.h"
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5
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6 #define BAM_ERRMOD_MAQ2 0
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7 #define BAM_ERRMOD_MAQ 1
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8 #define BAM_ERRMOD_SOAP 2
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9
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10 struct __bmc_aux_t;
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11
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12 typedef struct {
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13 float het_rate, theta;
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14 int n_hap, cap_mapQ, errmod, min_baseQ;
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15
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16 float eta, q_r;
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17 double *fk, *coef;
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18 double *lhet;
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19 struct __bmc_aux_t *aux;
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20 } bam_maqcns_t;
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21
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22 typedef struct {
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23 int q_indel; // indel sequencing error, phred scaled
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24 float r_indel; // indel prior
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25 float r_snp; // snp prior
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26 // hidden parameters, unchangeable from command line
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27 int mm_penalty, indel_err, ambi_thres;
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28 } bam_maqindel_opt_t;
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29
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30 typedef struct {
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31 int indel1, indel2;
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32 int cnt1, cnt2, cnt_anti;
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33 int cnt_ref, cnt_ambi;
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34 char *s[2];
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35 //
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36 int gt, gl[2];
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37 int q_cns, q_ref;
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38 } bam_maqindel_ret_t;
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39
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40 #ifdef __cplusplus
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41 extern "C" {
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42 #endif
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43
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44 bam_maqcns_t *bam_maqcns_init();
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45 void bam_maqcns_prepare(bam_maqcns_t *bm);
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46 void bam_maqcns_destroy(bam_maqcns_t *bm);
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47 glf1_t *bam_maqcns_glfgen(int n, const bam_pileup1_t *pl, uint8_t ref_base, bam_maqcns_t *bm);
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48 uint32_t bam_maqcns_call(int n, const bam_pileup1_t *pl, bam_maqcns_t *bm);
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49 // return: cns<<28 | cns2<<24 | mapQ<<16 | cnsQ<<8 | cnsQ2
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50 uint32_t glf2cns(const glf1_t *g, int q_r);
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51
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52 bam_maqindel_opt_t *bam_maqindel_opt_init();
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53 bam_maqindel_ret_t *bam_maqindel(int n, int pos, const bam_maqindel_opt_t *mi, const bam_pileup1_t *pl, const char *ref,
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54 int _n_types, int *_types);
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55 void bam_maqindel_ret_destroy(bam_maqindel_ret_t*);
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56
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57 #ifdef __cplusplus
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58 }
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59 #endif
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60
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61 #endif
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