static int fetch_disc_read_callback(const bam1_t* alignment, void* data) {
// MEI_data* mei_data = static_cast<MEI_data*>(data);
std::pair<MEI_data*, UserDefinedSettings*>* env = static_cast<std::pair<MEI_data*, UserDefinedSettings*>*>(data);
MEI_data* mei_data = env->first;
UserDefinedSettings* userSettings = env->second;
if (!(alignment->core.flag & BAM_FUNMAP || alignment->core.flag & BAM_FMUNMAP) && // Both ends are mapped.
!is_concordant(alignment, mei_data->current_insert_size) && // Ends map discordantly.
// Extra check for (very) large mapping distance. This is done beside the check for read
// discordance to speed up computation by ignoring signals from small structural variants.
(alignment->core.tid != alignment->core.mtid ||
abs(alignment->core.pos - alignment->core.mpos) > userSettings->MIN_DD_MAP_DISTANCE)) {
// Save alignment as simple_read object.
std::string read_name = enrich_read_name(bam1_qname(alignment), alignment->core.flag & BAM_FREAD1);
char strand = bam1_strand(alignment)? Minus : Plus;
char mate_strand = bam1_mstrand(alignment)? Minus : Plus;
std::string read_group;
get_read_group(alignment, read_group);
std::string sample_name;
get_sample_name(read_group, mei_data->sample_names, sample_name);
simple_read* read = new simple_read(read_name, alignment->core.tid, alignment->core.pos, strand, sample_name,
get_sequence(bam1_seq(alignment), alignment->core.l_qseq),
alignment->core.mtid, alignment->core.mpos, mate_strand);
mei_data->discordant_reads.push_back(read);
}
return 0;
}
// Returns true for a given read whether it is concordantly mapped together with its mate.
bool is_concordant(const bam1_t* read, unsigned int insert_size) {
if (read->core.flag & BAM_FUNMAP || read->core.flag & BAM_FMUNMAP) {
// At least one of the pair is unmapped.
return false;
}
if (read->core.tid != read->core.mtid) {
// Reads mapping to different chromosomes.
return false;
}
if (bam1_strand(read) == bam1_mstrand(read)) {
// Reads mapping to the same strand.
return false;
}
// Return true if insert size is as expected. This definition of concordance is
// equivalent to read-pair construction elsewhere in Pindel.
return (unsigned int) abs(read->core.isize) < read->core.l_qseq + 2 * insert_size;
}
int bam1_mstrand_(bam1_t *b) { return bam1_mstrand(b); }
