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