bool AlleleIdentity::CharacterizeVariantStatus(const LocalReferenceContext &reference_context,
const ReferenceReader &ref_reader, int chr_idx)
{
//cout << "Hello from CharacterizeVariantStatus; " << altAllele << endl;
bool is_ok = true;
status.isIndel = false;
status.isHPIndel = false;
status.isSNP = false;
status.isMNV = false;
status.isPaddedSNP = false;
status.doRealignment = false;
// Get Anchor length
ref_hp_length = reference_context.my_hp_length[0];
left_anchor = 0;
unsigned int a_idx = 0;
while (a_idx < altAllele.length() and a_idx < reference_context.reference_allele.length()
and altAllele[a_idx] == reference_context.reference_allele[a_idx]) {
a_idx++;
left_anchor++;
}
if (DEBUG > 0)
cout << "- Alternative Allele " << altAllele << " (anchor length " << left_anchor << ") ";
const string& ref_allele = reference_context.reference_allele;
const string& alt_allele = altAllele;
int ref_length = ref_allele.length();
int alt_length = alt_allele.length();
while (alt_length > 1 and ref_length > 1 and alt_allele[alt_length-1] == ref_allele[ref_length-1]) {
--alt_length;
--ref_length;
}
int prefix = 0;
while (prefix < alt_length and prefix < ref_length and alt_allele[prefix] == ref_allele[prefix])
++prefix;
ref_length -= prefix;
alt_length -= prefix;
// Change classification to better reflect what we can get with haplotyping
if (altAllele.length() != reference_context.reference_allele.length()) {
status.isIndel = true;
is_ok = SubCategorizeInDel(reference_context, ref_reader, chr_idx);
} else if ((int)altAllele.length() == 1) { // Categorize function only works with this setting
status.isSNP = true;
SubCategorizeSNP(reference_context);
if (DEBUG > 0) cout << " is a SNP." << endl;
} else {
status.isMNV = true;
ref_hp_length = reference_context.my_hp_length[left_anchor];
if (ref_length == 1 and alt_length == 1)
status.isPaddedSNP = true;
SubCategorizeMNP(reference_context);
if (DEBUG > 0)
cout << " is an MNP." << endl;
}
return (is_ok);
}
bool AlleleIdentity::CharacterizeVariantStatus(LocalReferenceContext &reference_context, int min_hp_for_overcall) {
//cout << "Hello from CharacterizeVariantStatus; " << altAllele << endl;
bool is_ok = true;
status.isIndel = false;
status.isHPIndel = false;
status.isSNP = false;
status.isMNV = false;
// Get Anchor length
anchor_length = 0;
unsigned int a_idx = 0;
while (a_idx < altAllele.length() and a_idx < reference_context.reference_allele.length()
and altAllele[a_idx] == reference_context.reference_allele[a_idx]) {
a_idx++;
anchor_length++;
}
if (DEBUG > 0)
cout << "- Alternative Allele " << altAllele << " (anchor length " << anchor_length << ")";
// Change classification to better reflect what we can get with haplotyping
if (altAllele.length() != reference_context.reference_allele.length()) {
status.isIndel = true;
is_ok = SubCategorizeInDel(reference_context);
}
else
if ((int)altAllele.length() == 1) { // Categorize function only works with this setting
status.isSNP = true;
SubCategorizeSNP(reference_context, min_hp_for_overcall);
}
else {
status.isMNV = true;
if (anchor_length < (int)reference_context.reference_allele.length())
ref_hp_length = reference_context.my_hp_length.at(anchor_length);
if (DEBUG > 0)
cout << " is an MNV." << endl;
}
return (is_ok);
}
