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Fixed missing decompress_map_ and added regression tests #1

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11b1adb
Fixed missing decompress map
May 25, 2024
811cec0
Added regression tests access_gappy_alphabet to ensure the implementa…
May 25, 2024
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4 changes: 3 additions & 1 deletion include/pasta/block_tree/block_tree.hpp
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Original file line number Diff line number Diff line change
Expand Up @@ -91,7 +91,7 @@ template <typename input_type, typename size_type> class BlockTree {
off = off % block_size;
blk_pointer = lvl_rs.rank1(blk_pointer) * tau_ + child;
}
return compressed_leaves_[blk_pointer * leaf_size + off];
return decompress_map_[compressed_leaves_[blk_pointer * leaf_size + off]];
};

int64_t select(input_type c, size_type j) {
Expand Down Expand Up @@ -401,12 +401,14 @@ template <typename input_type, typename size_type> class BlockTree {

void compress_leaves() {
compress_map_.resize(256, 0);
decompress_map_.resize(256, 0);
for (size_t i = 0; i < this->leaves_.size(); ++i) {
compress_map_[this->leaves_[i]] = 1;
}
for (size_t i = 0, cur_val = 0; i < this->compress_map_.size(); ++i) {
size_t tmp = compress_map_[i];
compress_map_[i] = cur_val;
decompress_map_[cur_val] = i;
cur_val += tmp;
}

Expand Down
14 changes: 14 additions & 0 deletions tests/block_tree/block_tree_fp_test.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -32,8 +32,10 @@ class BlockTreeFPTest : public ::testing::Test {
protected:

std::vector<uint8_t> text;
std::vector<uint8_t> gappy_alphabet_text;

pasta::BlockTreeFP<uint8_t, int32_t>* bt;
pasta::BlockTreeFP<uint8_t, int32_t>* gappy_alphabet_bt;

void SetUp() override {

Expand All @@ -43,16 +45,22 @@ class BlockTreeFPTest : public ::testing::Test {

size_t const string_length = 100000;
text.resize(string_length);
gappy_alphabet_text.resize(string_length);
for (size_t i = 0; i < text.size(); ++i) {
text[i] = dist(gen);
gappy_alphabet_text[i] = 2*dist(gen);
}

bt = pasta::make_block_tree_fp<uint8_t, int32_t>(text, 2, 1);
bt->add_rank_support();

gappy_alphabet_bt = pasta::make_block_tree_fp<uint8_t, int32_t>(gappy_alphabet_text, 2, 1);
gappy_alphabet_bt->add_rank_support();
}

void TearDown() override {
delete bt;
delete gappy_alphabet_bt;
}

};
Expand All @@ -63,6 +71,12 @@ TEST_F(BlockTreeFPTest, access) {
}
}

TEST_F(BlockTreeFPTest, access_gappy_alphabet) {
for (size_t i = 0; i < text.size(); ++i) {
ASSERT_EQ(gappy_alphabet_bt->access(i), gappy_alphabet_text[i]);
}
}

TEST_F(BlockTreeFPTest, rank) {
std::array<size_t, 256> hist = {0};

Expand Down
13 changes: 13 additions & 0 deletions tests/block_tree/block_tree_lpf_parallel_test.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -32,8 +32,10 @@ class BlockTreeLPFParallelTest : public ::testing::Test {
protected:

std::vector<uint8_t> text;
std::vector<uint8_t> gappy_alphabet_text;

pasta::BlockTreeLPF<uint8_t, int32_t>* bt;
pasta::BlockTreeLPF<uint8_t, int32_t>* gappy_alphabet_bt;

void SetUp() override {

Expand All @@ -43,16 +45,21 @@ class BlockTreeLPFParallelTest : public ::testing::Test {

size_t const string_length = 100000;
text.resize(string_length);
gappy_alphabet_text.resize(string_length);
for (size_t i = 0; i < text.size(); ++i) {
text[i] = dist(gen);
gappy_alphabet_text[i] = 2*dist(gen);
}

bt = pasta::make_block_tree_lpf_parallel<uint8_t, int32_t>(text, 2, 1, true, 4);
bt->add_rank_support_omp(4);
gappy_alphabet_bt = pasta::make_block_tree_lpf_parallel<uint8_t, int32_t>(gappy_alphabet_text, 2, 1, true, 4);
gappy_alphabet_bt->add_rank_support_omp(4);
}

void TearDown() override {
delete bt;
delete gappy_alphabet_bt;
}

};
Expand All @@ -63,6 +70,12 @@ TEST_F(BlockTreeLPFParallelTest, access) {
}
}

TEST_F(BlockTreeLPFParallelTest, access_gappy_alphabet) {
for (size_t i = 0; i < text.size(); ++i) {
ASSERT_EQ(gappy_alphabet_bt->access(i), gappy_alphabet_text[i]);
}
}

TEST_F(BlockTreeLPFParallelTest, rank) {
std::array<size_t, 256> hist = {0};

Expand Down
13 changes: 13 additions & 0 deletions tests/block_tree/block_tree_lpf_test.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -32,8 +32,10 @@ class BlockTreeLPFTest : public ::testing::Test {
protected:

std::vector<uint8_t> text;
std::vector<uint8_t> gappy_alphabet_text;

pasta::BlockTreeLPF<uint8_t, int32_t>* bt;
pasta::BlockTreeLPF<uint8_t, int32_t>* gappy_alphabet_bt;

void SetUp() override {

Expand All @@ -43,16 +45,21 @@ class BlockTreeLPFTest : public ::testing::Test {

size_t const string_length = 100000;
text.resize(string_length);
gappy_alphabet_text.resize(string_length);
for (size_t i = 0; i < text.size(); ++i) {
text[i] = dist(gen);
gappy_alphabet_text[i] = 2*dist(gen);
}

bt = pasta::make_block_tree_lpf<uint8_t, int32_t>(text, 2, 1, true);
bt->add_rank_support();
gappy_alphabet_bt = pasta::make_block_tree_lpf<uint8_t, int32_t>(gappy_alphabet_text, 2, 1, true);
gappy_alphabet_bt->add_rank_support();
}

void TearDown() override {
delete bt;
delete gappy_alphabet_bt;
}

};
Expand All @@ -63,6 +70,12 @@ TEST_F(BlockTreeLPFTest, access) {
}
}

TEST_F(BlockTreeLPFTest, access_gappy_alphabet) {
for (size_t i = 0; i < text.size(); ++i) {
ASSERT_EQ(gappy_alphabet_bt->access(i), gappy_alphabet_text[i]);
}
}

TEST_F(BlockTreeLPFTest, rank) {
std::array<size_t, 256> hist = {0};

Expand Down