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);
}
}
/**
* Check that all variants in a file belong to a given type
*
* @param file
* @param varTypeExpected
*/
void checkAllVarType(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
if (verbose)
System.out.println(
ve //
+ "\n\tvarTypeExpected: "
+ varTypeExpected //
+ "\n\tINFO flag : "
+ ve.getInfoFlag(varTypeExpected) //
);
if (!ve.getInfoFlag(varTypeExpected))
System.err.println("Eror in file '" + file + "':\n" + ve);
Assert.assertEquals(true, ve.getInfoFlag(varTypeExpected));
}
}