inline static LibraryFormat formatFromID(uint8_t id) {
ReadType rt;
ReadOrientation ro;
ReadStrandedness rs;
switch (id & 0x01) {
case 0:
rt = ReadType::SINGLE_END;
break;
case 1:
rt = ReadType::PAIRED_END;
break;
}
switch ((id >> 1) & 0xB) {
case static_cast<uint8_t>(ReadOrientation::SAME):
ro = ReadOrientation::SAME;
break;
case static_cast<uint8_t>(ReadOrientation::AWAY):
ro = ReadOrientation::AWAY;
break;
case static_cast<uint8_t>(ReadOrientation::TOWARD):
ro = ReadOrientation::TOWARD;
break;
case static_cast<uint8_t>(ReadOrientation::NONE):
ro = ReadOrientation::NONE;
break;
}
switch ((id >> 3) & 0x6F) {
case static_cast<uint8_t>(ReadStrandedness::SA):
rs = ReadStrandedness::SA;
break;
case static_cast<uint8_t>(ReadStrandedness::AS):
rs = ReadStrandedness::AS;
break;
case static_cast<uint8_t>(ReadStrandedness::S):
rs = ReadStrandedness::S;
break;
case static_cast<uint8_t>(ReadStrandedness::A):
rs = ReadStrandedness::A;
break;
case static_cast<uint8_t>(ReadStrandedness::U):
rs = ReadStrandedness::U;
break;
}
return LibraryFormat(rt, ro, rs);
}
// Determine the library type of paired-end reads
LibraryFormat hitType(int32_t end1Start, bool end1Fwd, uint32_t len1,
int32_t end2Start, bool end2Fwd, uint32_t len2, bool canDovetail) {
// If the reads come from opposite strands
if (end1Fwd != end2Fwd) {
// and if read 1 comes from the forward strand
if (end1Fwd) {
// then if read 1 start < read 2 start ==> ISF
// NOTE: We can't really delineate between inward facing reads that stretch
// past each other and outward facing reads --- the purpose of stretch is to help
// make this determinateion.
int32_t stretch = canDovetail ? len2 : 0;
if (end1Start <= end2Start + stretch) {
return LibraryFormat(ReadType::PAIRED_END, ReadOrientation::TOWARD, ReadStrandedness::SA);
} // otherwise read 2 start < read 1 start ==> OSF
else {
return LibraryFormat(ReadType::PAIRED_END, ReadOrientation::AWAY, ReadStrandedness::SA);
}
}
// and if read 2 comes from the forward strand
if (end2Fwd) {
// then if read 2 start <= read 1 start ==> ISR
// NOTE: We can't really delineate between inward facing reads that stretch
// past each other and outward facing reads --- the purpose of stretch is to help
// make this determinateion.
int32_t stretch = canDovetail ? len1 : 0;
if (end2Start <= end1Start + stretch) {
return LibraryFormat(ReadType::PAIRED_END, ReadOrientation::TOWARD, ReadStrandedness::AS);
} // otherwise, read 2 start > read 1 start ==> OSR
else {
return LibraryFormat(ReadType::PAIRED_END, ReadOrientation::AWAY, ReadStrandedness::AS);
}
}
} else { // Otherwise, the reads come from the same strand
if (end1Fwd) { // if it's the forward strand ==> MSF
return LibraryFormat(ReadType::PAIRED_END, ReadOrientation::SAME, ReadStrandedness::S);
} else { // if it's the reverse strand ==> MSR
return LibraryFormat(ReadType::PAIRED_END, ReadOrientation::SAME, ReadStrandedness::A);
}
}
// SHOULD NOT GET HERE
spdlog::get("jointLog")->error("ERROR: Could not associate any known library type with read! "
"Please report this bug!\n");
std::this_thread::sleep_for(std::chrono::seconds(1));
std::exit(-1);
return LibraryFormat(ReadType::PAIRED_END, ReadOrientation::NONE, ReadStrandedness::U);
}
SCENARIO("Library types are encoded/decoded properly") {
GIVEN("A collection of library formats") {
std::unordered_map<std::string, LibraryFormat> fm =
{{"U", LibraryFormat(ReadType::SINGLE_END, ReadOrientation::NONE, ReadStrandedness::U)},
{"SF", LibraryFormat(ReadType::SINGLE_END, ReadOrientation::NONE, ReadStrandedness::S)},
{"SR", LibraryFormat(ReadType::SINGLE_END, ReadOrientation::NONE, ReadStrandedness::A)},
{"IU", LibraryFormat(ReadType::PAIRED_END, ReadOrientation::TOWARD, ReadStrandedness::U)},
{"ISF", LibraryFormat(ReadType::PAIRED_END, ReadOrientation::TOWARD, ReadStrandedness::S)},
{"ISR", LibraryFormat(ReadType::PAIRED_END, ReadOrientation::TOWARD, ReadStrandedness::A)},
{"OU", LibraryFormat(ReadType::PAIRED_END, ReadOrientation::AWAY, ReadStrandedness::U)},
{"OSF", LibraryFormat(ReadType::PAIRED_END, ReadOrientation::AWAY, ReadStrandedness::S)},
{"OSR", LibraryFormat(ReadType::PAIRED_END, ReadOrientation::AWAY, ReadStrandedness::A)},
{"MU", LibraryFormat(ReadType::PAIRED_END, ReadOrientation::SAME, ReadStrandedness::U)},
{"MSF", LibraryFormat(ReadType::PAIRED_END, ReadOrientation::SAME, ReadStrandedness::S)},
{"MSR", LibraryFormat(ReadType::PAIRED_END, ReadOrientation::SAME, ReadStrandedness::A)}};
for (auto& kv : fm) {
WHEN("type is " + kv.first) {
uint8_t id = kv.second.formatID();
THEN("decodes as " + kv.first) {
REQUIRE(kv.second == LibraryFormat::formatFromID(id));
}
}
}
}
}
SCENARIO("Paired-end library types have proper compatibility") {
