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#include <alignment/datastructures/alignmentset/SAMSupplementalQVList.hpp>
const char *SupplementalQVList::qvNames[] = {"InsertionQV", "DeletionQV", "SubstitutionQV",
"MergeQV", "SubstitutionTag", "DeletionTag"};
const char *SupplementalQVList::qvTags[] = {"iq", "dq", "sq", "mq", "st", "dt"};
// Only the first 4 tags are quality values.
int SupplementalQVList::nqvTags = 4;
int SupplementalQVList::nTags = 6;
int SupplementalQVList::UseQV(std::vector<std::string> &qvList)
{
useqv = 0;
for (size_t i = 0; i < qvList.size(); i++) {
int j;
for (j = 0; j < nTags; j++) {
if (qvList[i] == qvNames[j]) {
useqv |= 1 << j;
break;
}
}
if (j == nTags) {
return 1;
}
}
return 0;
}
void SupplementalQVList::FormatQVOptionalFields(SMRTSequence &alignedSubsequence)
{
int i;
for (i = 0; i < nqvTags; i++) {
if (alignedSubsequence.GetQVPointerByIndex(i + 1)->data == NULL) {
// mask off this quality value since it does not exist
useqv = useqv & ~(1 << i);
}
}
for (i = 0; i < nqvTags; i++) {
if (useqv & (1 << i)) {
QualityVectorToPrintable(alignedSubsequence.GetQVPointerByIndex(i + 1)->data,
alignedSubsequence.length);
}
}
}
void SupplementalQVList::PrintQVOptionalFields(SMRTSequence &alignedSubsequence, std::ostream &out)
{
int i = 0;
for (i = 0; i < nqvTags; i++) {
if (alignedSubsequence.GetQVPointerByIndex(i + 1)->data == NULL) {
// mask off this quality value since it does not exist
useqv = useqv & ~(1 << i);
}
}
for (i = 0; i < nTags; i++) {
if (alignedSubsequence.GetQVPointerByIndex(i + 1) != NULL and (useqv & (1 << i))) {
out << "\t" << qvTags[i] << ":Z:";
alignedSubsequence.PrintAsciiRichQuality(out, i + 1, 0);
}
}
if (alignedSubsequence.substitutionTag != NULL and (useqv & SubstitutionTag)) {
out << "\t" << qvTags[I_SubstitutionTag - 1] << ":Z:";
alignedSubsequence.PrintAsciiRichQuality(out, I_SubstitutionTag, 0);
}
if (alignedSubsequence.deletionTag != NULL and (useqv & DeletionTag)) {
out << "\t" << qvTags[I_DeletionTag - 1] << ":Z:";
alignedSubsequence.PrintAsciiRichQuality(out, I_DeletionTag, 0);
}
}
void SupplementalQVList::clear()
{
for (int j = 0; j < nTags; j++) {
useqv &= 0 << j;
}
}
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