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1 #ifndef BCF_PROB1_H
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2 #define BCF_PROB1_H
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3
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4 #include "bcf.h"
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5
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6 struct __bcf_p1aux_t;
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7 typedef struct __bcf_p1aux_t bcf_p1aux_t;
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8
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9 typedef struct {
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10 int rank0, perm_rank; // NB: perm_rank is always set to -1 by bcf_p1_cal()
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11 int ac; // ML alternative allele count
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12 double f_exp, f_flat, p_ref_folded, p_ref, p_var_folded, p_var;
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13 double cil, cih;
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14 double cmp[3], p_chi2, lrt; // used by contrast2()
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15 } bcf_p1rst_t;
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16
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17 typedef struct {
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18 double p[4];
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19 int mq, depth, is_tested, d[4];
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20 } anno16_t;
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21
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22 #define MC_PTYPE_FULL 1
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23 #define MC_PTYPE_COND2 2
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24 #define MC_PTYPE_FLAT 3
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25
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26 #ifdef __cplusplus
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27 extern "C" {
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28 #endif
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29
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30 bcf_p1aux_t *bcf_p1_init(int n, uint8_t *ploidy);
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31 void bcf_p1_init_prior(bcf_p1aux_t *ma, int type, double theta);
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32 void bcf_p1_init_subprior(bcf_p1aux_t *ma, int type, double theta);
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33 void bcf_p1_destroy(bcf_p1aux_t *ma);
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34 void bcf_p1_set_ploidy(bcf1_t *b, bcf_p1aux_t *ma);
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35 int bcf_p1_cal(const bcf1_t *b, int do_contrast, bcf_p1aux_t *ma, bcf_p1rst_t *rst);
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36 int call_multiallelic_gt(bcf1_t *b, bcf_p1aux_t *ma, double threshold, int var_only);
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37 int bcf_p1_call_gt(const bcf_p1aux_t *ma, double f0, int k);
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38 void bcf_p1_dump_afs(bcf_p1aux_t *ma);
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39 int bcf_p1_read_prior(bcf_p1aux_t *ma, const char *fn);
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40 int bcf_p1_set_n1(bcf_p1aux_t *b, int n1);
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41 void bcf_p1_set_folded(bcf_p1aux_t *p1a); // only effective when set_n1() is not called
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42
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43 int bcf_em1(const bcf1_t *b, int n1, int flag, double x[10]);
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44
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45 #ifdef __cplusplus
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46 }
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47 #endif
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48
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49 #endif
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