Alignment bam_to_alignment(const bam1_t *b, map<string, string>& rg_sample) {
Alignment alignment;
// get the sequence and qual
int32_t lqseq = b->core.l_qseq;
string sequence; sequence.resize(lqseq);
uint8_t* qualptr = bam_get_qual(b);
string quality;//(lqseq, 0);
quality.assign((char*)qualptr, lqseq);
// process the sequence into chars
uint8_t* seqptr = bam_get_seq(b);
for (int i = 0; i < lqseq; ++i) {
sequence[i] = "=ACMGRSVTWYHKDBN"[bam_seqi(seqptr, i)];
}
// get the read group and sample name
uint8_t *rgptr = bam_aux_get(b, "RG");
char* rg = (char*) (rgptr+1);
//if (!rg_sample
string sname;
if (!rg_sample.empty()) {
sname = rg_sample[string(rg)];
}
// Now name the read after the scaffold
string read_name = bam_get_qname(b);
// Decide if we are a first read (/1) or second (last) read (/2)
if(b->core.flag & BAM_FREAD1) {
read_name += "/1";
}
if(b->core.flag & BAM_FREAD2) {
read_name += "/2";
}
// If we are marked as both first and last we get /1/2, and if we are marked
// as neither the scaffold name comes through unchanged as the read name.
// TODO: produce correct names for intermediate reads on >2 read scaffolds.
// add features to the alignment
alignment.set_name(read_name);
alignment.set_sequence(sequence);
alignment.set_quality(quality);
// TODO: htslib doesn't wrap this flag for some reason.
alignment.set_is_secondary(b->core.flag & BAM_FSECONDARY);
if (sname.size()) {
alignment.set_sample_name(sname);
alignment.set_read_group(rg);
}
return alignment;
}
bool get_next_alignment_from_fastq(gzFile fp, char* buffer, size_t len, Alignment& alignment) {
alignment.Clear();
// handle name
if (0!=gzgets(fp,buffer,len)) {
buffer[strlen(buffer)-1] = '\0';
string name = buffer;
name = name.substr(1); // trim off leading @
// keep trailing /1 /2
alignment.set_name(name);
} else { return false; }
// handle sequence
if (0!=gzgets(fp,buffer,len)) {
buffer[strlen(buffer)-1] = '\0';
alignment.set_sequence(buffer);
} else {
cerr << "[vg::alignment.cpp] error: incomplete fastq record" << endl; exit(1);
}
// handle "+" sep
if (0!=gzgets(fp,buffer,len)) {
} else {
cerr << "[vg::alignment.cpp] error: incomplete fastq record" << endl; exit(1);
}
// handle quality
if (0!=gzgets(fp,buffer,len)) {
buffer[strlen(buffer)-1] = '\0';
string quality = string_quality_char_to_short(buffer);
//cerr << string_quality_short_to_char(quality) << endl;
alignment.set_quality(quality);
} else {
cerr << "[vg::alignment.cpp] error: incomplete fastq record" << endl; exit(1);
}
return true;
}
void alignment_quality_char_to_short(Alignment& alignment) {
alignment.set_quality(string_quality_char_to_short(alignment.quality()));
}
