void ReadContainerTest::test_ParseRead() {
map<pair<string,int>, string> ref_ext_nucleotides;
BamAlignment aln;
std::string rg = "test";
std::string repseq = "AC";
AlignedRead aligned_read;
float copynum = 10;
include_flank = false;
// Test valid allele length
aln.Name = "test";
aln.QueryBases = "NNNNN";
aln.Qualities = "NNNNN";
aln.SetIsReverseStrand(true);
aln.Position = 0;
aln.SetIsSecondMate(false);
aln.AddTag("RG","Z",rg);
aln.AddTag("XS","i",0);
aln.AddTag("XE","i",20);
aln.AddTag("XR", "Z", repseq);
aln.AddTag("XC", "f", copynum);
aln.RefID = 0;
// No XD
aln.RemoveTag("XD");
CPPUNIT_ASSERT(!(_read_container->ParseRead(aln, &aligned_read, ref_ext_nucleotides)));
// Test more valid allele lengths
aln.AddTag("XD","i",20);
CPPUNIT_ASSERT(_read_container->ParseRead(aln, &aligned_read, ref_ext_nucleotides));
aln.RemoveTag("XD");
aln.AddTag("XD","i",-19);
CPPUNIT_ASSERT(_read_container->ParseRead(aln, &aligned_read, ref_ext_nucleotides));
// Test invalid allele length
aln.RemoveTag("XD");
aln.AddTag("XD","i",-31);
CPPUNIT_ASSERT(!(_read_container->ParseRead(aln, &aligned_read, ref_ext_nucleotides)));
// Exceed max_diff_ref
aln.RemoveTag("XD");
aln.AddTag("XD","i",100);
CPPUNIT_ASSERT(!(_read_container->ParseRead(aln, &aligned_read, ref_ext_nucleotides)));
aln.RemoveTag("XD");
aln.AddTag("XD","i",0);
// Exceed max mate dist
aln.AddTag("XM","i",1000000);
CPPUNIT_ASSERT(!(_read_container->ParseRead(aln, &aligned_read, ref_ext_nucleotides)));
aln.RemoveTag("XM");
// Exceed max mapq
aln.AddTag("XQ","i",10000);
CPPUNIT_ASSERT(!(_read_container->ParseRead(aln, &aligned_read, ref_ext_nucleotides)));
aln.RemoveTag("XQ");
// Read is mate
aln.SetIsSecondMate(true);
CPPUNIT_ASSERT(!(_read_container->ParseRead(aln, &aligned_read, ref_ext_nucleotides)));
aln.SetIsSecondMate(false);
// Read is partial
aln.AddTag("XP","i",1);
CPPUNIT_ASSERT(!(_read_container->ParseRead(aln, &aligned_read, ref_ext_nucleotides)));
aln.RemoveTag("XP");
// Non-unit
unit = true;
aln.RemoveTag("XD");
aln.AddTag("XD","i",5);
CPPUNIT_ASSERT(!(_read_container->ParseRead(aln, &aligned_read, ref_ext_nucleotides)));
unit = false;
}
