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Add make_randstrobe function #445

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Merged
marcelm merged 2 commits into from
Oct 1, 2024
Merged

Add make_randstrobe function #445

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063ecf8
Add RandstrobeIterator/-Generator tests
marcelm May 23, 2024
dc3af3b
Add make_randstrobe function
marcelm May 23, 2024
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13 changes: 11 additions & 2 deletions src/randstrobes.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -145,6 +145,14 @@ std::ostream& operator<<(std::ostream& os, const QueryRandstrobe& randstrobe) {
return os;
}

Randstrobe make_randstrobe(Syncmer strobe1, Syncmer strobe2) {
return Randstrobe{
randstrobe_hash(strobe1.hash, strobe2.hash),
static_cast<uint32_t>(strobe1.position),
static_cast<uint32_t>(strobe2.position)
};
}

Randstrobe RandstrobeIterator::get(unsigned int strobe1_index) const {
unsigned int w_end = std::min(static_cast<size_t>(strobe1_index + w_max), syncmers.size() - 1);

Expand All @@ -167,7 +175,7 @@ Randstrobe RandstrobeIterator::get(unsigned int strobe1_index) const {
}
}

return Randstrobe{randstrobe_hash(strobe1.hash, strobe2.hash), static_cast<uint32_t>(strobe1.position), static_cast<uint32_t>(strobe2.position)};
return make_randstrobe(strobe1, strobe2);
}

Randstrobe RandstrobeGenerator::next() {
Expand Down Expand Up @@ -198,7 +206,8 @@ Randstrobe RandstrobeGenerator::next() {
}
}
syncmers.pop_front();
return Randstrobe{randstrobe_hash(strobe1.hash, strobe2.hash), static_cast<uint32_t>(strobe1.position), static_cast<uint32_t>(strobe2.position)};

return make_randstrobe(strobe1, strobe2);
}

/*
Expand Down
35 changes: 35 additions & 0 deletions tests/tests.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -84,6 +84,41 @@ TEST_CASE("read_/write_vector") {
CHECK(y == expected);
}

TEST_CASE("RandstrobeGenerator is sane") {
auto references = References::from_fasta("tests/phix.fasta");
auto& seq = references.sequences[0];
auto parameters = IndexParameters::from_read_length(300);

RandstrobeGenerator iter{seq, parameters.syncmer, parameters.randstrobe};

Randstrobe randstrobe;
while ((randstrobe = iter.next()) != iter.end()) {
CHECK(randstrobe.hash > 0);
CHECK(randstrobe.strobe1_pos >= 0);
CHECK(randstrobe.strobe2_pos >= randstrobe.strobe2_pos);
CHECK(randstrobe.strobe1_pos < seq.length());
CHECK(randstrobe.strobe2_pos < seq.length());
}
}

TEST_CASE("RandstrobeIterator is sane") {
auto references = References::from_fasta("tests/phix.fasta");
auto& seq = references.sequences[0];
auto parameters = IndexParameters::from_read_length(300);

auto syncmers = canonical_syncmers(seq, parameters.syncmer);
RandstrobeIterator iter{syncmers, parameters.randstrobe};

while (iter.has_next()) {
auto randstrobe = iter.next();
CHECK(randstrobe.hash > 0);
CHECK(randstrobe.strobe1_pos >= 0);
CHECK(randstrobe.strobe2_pos >= randstrobe.strobe2_pos);
CHECK(randstrobe.strobe1_pos < seq.length());
CHECK(randstrobe.strobe2_pos < seq.length());
}
}

TEST_CASE("both randstrobes iterator implementations give same results") {
auto references = References::from_fasta("tests/phix.fasta");
auto& seq = references.sequences[0];
Expand Down