void
addSupplementaryAlignmentEvidence(
bam_record& bamRead,
const std::string& svStr)
{
static const char svtag[] = {'S','A'};
bam_aux_append(bamRead.get_data(),svtag,'Z',(svStr.size()+1),
(const uint8_t*)(svStr.c_str()));
}
void
buildTestBamRecord(
bam_record& bamRead,
int targetID,
int pos,
int mateTargetID,
int matePos,
int fragmentSize,
int mapQ,
std::string cigarString,
std::string querySeq)
{
bam1_t& bamData(*(bamRead.get_data()));
// set qname
{
edit_bam_qname("buildTestBamRecord", bamData);
}
// set CIGAR
{
if (cigarString.empty())
{
cigarString = std::to_string(fragmentSize) + "M";
}
ALIGNPATH::path_t inputPath;
cigar_to_apath(cigarString.c_str(), inputPath);
edit_bam_cigar(inputPath, bamData);
}
// set read and qual
{
if ( querySeq.empty() )
{
querySeq = std::string(fragmentSize,'A');
}
const unsigned querySize(querySeq.length());
// initialize test qual array to all Q30's:
std::unique_ptr<uint8_t[]> qual(new uint8_t[querySize]);
for (unsigned i(0); i<querySize; ++i)
{
qual[i] = 30;
}
edit_bam_read_and_quality(querySeq.c_str(), qual.get(), bamData);
}
// Set some defaults for the read
bamRead.toggle_is_paired();
bamRead.toggle_is_mate_fwd_strand();
bamData.core.pos = pos;
bamData.core.isize = fragmentSize;
bamData.core.qual = mapQ;
bamRead.set_target_id(targetID);
// Set mate info
bamData.core.mtid = mateTargetID;
bamData.core.mpos = matePos;
static const char nhTag[] = {'N','H'};
static const char nmTag[] = {'N','M'};
static const char rgTag[] = {'R','G'};
bam_aux_append_unsigned(bamData, nhTag, 1);
bam_aux_append_unsigned(bamData, nmTag, 1);
bam_aux_append_unsigned(bamData, rgTag, 1);
}