void checkVarTypeField(String file, String varTypeExpected) {
SnpSiftCmdVarType varType = new SnpSiftCmdVarType(null);
VcfFileIterator vcf = new VcfFileIterator(file);
for (VcfEntry ve : vcf) {
// Annotate
varType.annotate(ve);
// Check that all variants are the ones expected
String varTypeAnnotated = ve.getInfo(SnpSiftCmdVarType.VARTYPE);
Assert.assertEquals(varTypeExpected, varTypeAnnotated);
}
}
/** Fill values for INFO fields requiring 'REF' value */
protected void findDbInfoRef(Map<String, String> info, Set<VcfEntry> uniqueVcfEntries) {
if (!useInfoFields || !hasVcfInfoPerAlleleRef) return; // Nothing to do
for (String infoFieldName : infoFields) {
// Does this field require 'REF' annotation?
if (!isVcfInfoPerAlleleRef(infoFieldName)) continue;
// Try to find 'REF' information in any entry
String val = null;
for (VcfEntry dbVcfEntry : uniqueVcfEntries) {
val = dbVcfEntry.getInfo(infoFieldName, dbVcfEntry.getRef());
if (VcfEntry.isEmpty(val)) val = null; // Only add non-empty
else break; // We need only one value
}
// Nothing found? Use 'MISSING' value
if (val == null) val = VcfFileIterator.MISSING;
// Store value
info.put(infoFieldName, val);
}
}