void testAddHeaderAndTagToFile(const char* inputName, const char* outputName)
{
SamFile inSam, outSam;
assert(inSam.OpenForRead(inputName));
assert(outSam.OpenForWrite(outputName));
// Read the SAM Header.
SamFileHeader samHeader;
assert(inSam.ReadHeader(samHeader));
// Add a header line.
assert(samHeader.addHeaderLine("@RG\tID:myID\tSM:mySM") == false);
assert(samHeader.addHeaderLine("@RG\tID:myID3\tSM:mySM") == true);
// Write Header
assert(outSam.WriteHeader(samHeader));
SamRecord samRecord;
assert(inSam.ReadRecord(samHeader, samRecord));
// validateRead1(samRecord);
// Add two tags.
assert(samRecord.addIntTag("XA", 123));
assert(samRecord.addIntTag("XA", 456));
assert(samRecord.addTag("RR", 'Z', "myID1"));
assert(samRecord.addTag("RR", 'Z', "myID2"));
// Write as Sam.
assert(outSam.WriteRecord(samHeader, samRecord));
// TODO, add test to verify it was written correctly.
// Read a couple of records to make sure it properly can read them even
// if they are bigger than the original.
assert(inSam.ReadRecord(samHeader, samRecord));
assert(inSam.ReadRecord(samHeader, samRecord));
// Check the MD tag, which requires the reference.
GenomeSequence reference("testFiles/chr1_partial.fa");
assert(SamTags::isMDTagCorrect(samRecord, reference) == false);
String newMDTag;
SamTags::createMDTag(newMDTag, samRecord, reference);
assert(newMDTag == "2T1N0");
assert(SamTags::updateMDTag(samRecord, reference));
// Write as Sam.
assert(outSam.WriteRecord(samHeader, samRecord));
}
