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update to have correct phasing with other unphased alleles #269

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merged 1 commit into from
Dec 18, 2024
Merged

update to have correct phasing with other unphased alleles #269

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9 changes: 5 additions & 4 deletions src/vcf/record.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -1218,15 +1218,16 @@ namespace ebi
void Record::get_phased_alleles(std::string GT, std::vector<std::string>& alleles) const
{
std::string delims("|/");
bool anyphased = false;
bool anyunphased = false;
std::vector<std::string> values;

if (!GT.size()) {
return;
}

if (GT.find('|') != std::string::npos) {
anyphased = true;
//search for other unphased allele, other than 1st one
if (GT.find('/', 1) != std::string::npos) {
anyunphased = true;
}

util::string_split_ex(GT, delims.c_str(), values, true);
Expand All @@ -1235,7 +1236,7 @@ namespace ebi
if (allele != values.end()) {
if (allele->at(0) != '/' && allele->at(0) != '|') {
//infer phasing based on other alleles phasing
allele->insert(0, anyphased ? "|" : "/");
allele->insert(0, anyunphased ? "/" : "|");
}
alleles.swap(values);
}
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1 change: 1 addition & 0 deletions test/input_files/v4.4/failed/failed_body_invalid_sample_PSL.vcf
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Expand Up @@ -17,3 +17,4 @@
1 1700 rs180734498 C <DEL>,T,<DUP> 100 PASS SVLEN=1,.,2;SVCLAIM=D,.,D GT:PSL 0|0:.,.
1 1800 rs180734498 C <CNV>,T,<DEL> 100 PASS SVLEN=2,.,1;SVCLAIM=D,.,DJ GT:PSL 0/0:T1,T2
1 1900 rs180734498 C <CNV>,T,<DUP> 100 PASS SVLEN=1,.,21;SVCLAIM=D,.,J GT:PSL 0/0|1:T1,T2,T3
1 1901 rs180734498 C T 100 PASS SVCLAIM=. GT:PSL /0:T1
4 changes: 3 additions & 1 deletion test/input_files/v4.4/passed/passed_body_samples_1.vcf
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Original file line number Diff line number Diff line change
Expand Up @@ -17,4 +17,6 @@
1 900 rs180734498 C <CNV>,T,<DUP> 100 PASS SVLEN=1,.,21;SVCLAIM=D,.,J GT:PSL:PSO /0|0|1:.,T2,T3:.,1,2
1 1700 rs180734498 C <DEL>,T,<DUP> 100 PASS SVLEN=1,.,2;SVCLAIM=D,.,D GT:PSL:PSO 0/0:.,.:.,.
1 1800 rs180734498 C <CNV>,T,<DEL> 100 PASS SVLEN=2,.,1;SVCLAIM=D,.,DJ GT:PSL:PSQ 0|0:T1,T2:1,2
1 1900 rs180734498 C <CNV>,T,<DUP> 100 PASS SVLEN=1,.,21;SVCLAIM=D,.,J GT:PSL:PSQ 0/0|1:T1,.,T3:1,.,3
1 1900 rs180734498 C <CNV>,T,<DUP> 100 PASS SVLEN=1,.,21;SVCLAIM=D,.,J GT:PSL:PSQ 0/0|1:.,.,T3:.,.,3
1 1901 rs180734498 C T 100 PASS SVCLAIM=. GT:PSL:PSQ 0:T1:3
1 1902 rs180734498 C T 100 PASS SVCLAIM=. GT:PSL:PSQ /0:.:.
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