private VariantOverlappingStatus processVariantFile(Variant variant, Set<Integer> missingSamples, Put put, Integer fileId,
VariantOverlappingStatus overlappingStatus, String gt) {
LinkedHashMap<String, Integer> samplePosition = getSamplePosition(fileId);
List<List<String>> samplesData = new ArrayList<>(samplePosition.size());
for (int i = 0; i < samplePosition.size(); i++) {
samplesData.add(Collections.singletonList(gt));
}
VariantBuilder builder = Variant.newBuilder(
variant.getChromosome(),
variant.getStart(),
variant.getEnd(),
variant.getReference(),
variant.getAlternate())
.setStudyId(String.valueOf(studyConfiguration.getStudyId()))
.setFormat("GT")
.setFileId(fileId.toString())
.setSamplesPosition(samplePosition)
.setSamplesData(samplesData);
studyConverter.convert(builder.build(), put, missingSamples, overlappingStatus);
return overlappingStatus;
}