4 #include "primer_bed.h"     5 #include "htslib/sam.h"     7 #ifndef trim_primer_quality     8 #define trim_primer_quality    16 int trim_bam_qual_primer(std::string bam, std::string bed, std::string bam_out, std::string region_, uint8_t min_qual, uint8_t sliding_window, 
int min_length);
    17 int32_t get_pos_on_query(uint32_t *cigar, uint32_t ncigar, int32_t pos, int32_t ref_start);
    18 int32_t get_pos_on_reference(uint32_t *cigar, uint32_t ncigar, uint32_t pos, uint32_t ref_start);
    19 void reverse_qual(uint8_t *q, 
int l);
    20 void reverse_cigar(uint32_t *cigar, 
int l);
    21 double mean_quality(uint8_t *a, 
int s, 
int e);
    22 cigar_ quality_trim(bam1_t* r, 
int qual_threshold, 
int sliding_window);
    23 void print_cigar(uint32_t *cigar, 
int nlength);
    24 cigar_ primer_trim(bam1_t *r, int32_t new_pos);
    25 void replace_cigar(bam1_t *b, 
int n, uint32_t *cigar);
    26 int16_t get_overlapping_primer_indice(bam1_t* r, std::vector<primer> primers);
    27 cigar_ remove_trailing_query_ref_consumption(uint32_t* cigar, uint32_t n);
    28 cigar_ condense_cigar(uint32_t* cigar, uint32_t n);
 Definition: trim_primer_quality.h:10