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Initial implementation of NCHG cartesian-product #43

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merged 18 commits into from
Nov 13, 2024
Merged

Initial implementation of NCHG cartesian-product #43

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4fa45ac
Initial implementation of NCHG cartesian-product
robomics Nov 11, 2024
601e3b4
Fix typo
robomics Nov 11, 2024
a1ac243
Fix macOS builds
robomics Nov 11, 2024
fb367ff
Fix typos
robomics Nov 11, 2024
bb9032c
Add option to support processing domains for a single chromosome pair
robomics Nov 11, 2024
7424f75
Properly deal with \r\n line terminations on UNIX systems
robomics Nov 12, 2024
f2557a0
Bugfix
robomics Nov 12, 2024
ec95469
Update NCHG compute to accept a list of 2D domains in BEDPE format
robomics Nov 12, 2024
058275c
Update script to generate reference data for the integration tests
robomics Nov 12, 2024
4618352
Update validate_nchg_output.py to cover NCHG cartesian-product
robomics Nov 13, 2024
c68f8ca
Bugfix
robomics Nov 13, 2024
c125244
Fix typos
robomics Nov 13, 2024
c242b45
Bugfix
robomics Nov 13, 2024
6bb932f
Update test dataset
robomics Nov 13, 2024
59f115e
Update Ubuntu CI
robomics Nov 13, 2024
58acacf
Update codecov CI
robomics Nov 13, 2024
1f145db
Update macOS CI
robomics Nov 13, 2024
098f3e3
Fix CI
robomics Nov 13, 2024
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83 changes: 73 additions & 10 deletions .github/workflows/codecov.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -127,15 +127,6 @@ jobs:

cmake -DCMAKE_BUILD_TYPE=RelWithDebInfo \
-DCMAKE_PREFIX_PATH="$PWD/conan-env" \
-DENABLE_DEVELOPER_MODE=ON \
-DOPT_ENABLE_INTERPROCEDURAL_OPTIMIZATION=OFF \
-DOPT_ENABLE_SANITIZER_ADDRESS=OFF \
-DOPT_ENABLE_SANITIZER_LEAK=OFF \
-DOPT_ENABLE_SANITIZER_POINTER_COMPARE=OFF \
-DOPT_ENABLE_SANITIZER_POINTER_SUBTRACT=OFF \
-DOPT_ENABLE_SANITIZER_UNDEFINED_BEHAVIOR=OFF \
-DOPT_ENABLE_CPPCHECK=OFF \
-DOPT_ENABLE_CLANG_TIDY=OFF \
-DNCHG_ENABLE_TESTING=ON \
-DNCHG_DOWNLOAD_TEST_DATASET=OFF \
-DCMAKE_C_FLAGS="$cov_flags" \
Expand Down Expand Up @@ -379,6 +370,78 @@ jobs:
echo "DATA_DIR=$PWD/test/data/integration_tests" | tee -a "$GITHUB_ENV"
echo "OUT_PREFIX=ENCFF447ERX.1000000" | tee -a "$GITHUB_ENV"

- name: Test NCHG cartesian-product (gw)
run: |
LLVM_PROFILE_FILE="$PWD/nchg.cartesian-product-gw.profraw"

sudo -u devel \
-E env "LLVM_PROFILE_FILE=$LLVM_PROFILE_FILE" \
build/src/nchg/NCHG cartesian-product \
test/data/ENCFF447ERX.1000000.compartments.bed \
> "$OUT_PREFIX.bedpe"

test/scripts/validate_nchg_output.py cartesian-product \
"$OUT_PREFIX.bedpe" \
"$DATA_DIR/cartesian_product/$OUT_PREFIX.gw-domains.bedpe"

rm "$OUT_PREFIX"*

- name: Test NCHG cartesian-product (cis)
run: |
LLVM_PROFILE_FILE="$PWD/nchg.cartesian-product-cis.profraw"

sudo -u devel \
-E env "LLVM_PROFILE_FILE=$LLVM_PROFILE_FILE" \
build/src/nchg/NCHG cartesian-product \
--cis-only \
test/data/ENCFF447ERX.1000000.compartments.bed \
> domains.bedpe

test/scripts/validate_nchg_output.py cartesian-product \
domains.bedpe \
"$DATA_DIR/cartesian_product/$OUT_PREFIX.cis-domains.bedpe"

rm *.bedpe

- name: Test NCHG cartesian-product (trans)
run: |
LLVM_PROFILE_FILE="$PWD/nchg.cartesian-product-trans.profraw"

sudo -u devel \
-E env "LLVM_PROFILE_FILE=$LLVM_PROFILE_FILE" \
build/src/nchg/NCHG cartesian-product \
--trans-only \
test/data/ENCFF447ERX.1000000.compartments.bed \
> domains.bedpe

test/scripts/validate_nchg_output.py cartesian-product \
domains.bedpe \
"$DATA_DIR/cartesian_product/$OUT_PREFIX.trans-domains.bedpe"

rm *.bedpe

- name: Test NCHG cartesian-product (chr1:chr3)
run: |
LLVM_PROFILE_FILE="$PWD/nchg.cartesian-product-chr1-chr3.profraw"

sudo -u devel \
-E env "LLVM_PROFILE_FILE=$LLVM_PROFILE_FILE" \
build/src/nchg/NCHG cartesian-product \
--chrom1 chr1 \
--chrom2 chr3 \
test/data/ENCFF447ERX.1000000.compartments.bed \
> domains.bedpe

grep -E '\bchr1\b.*\bchr3\b' \
"$DATA_DIR/cartesian_product/$OUT_PREFIX.trans-domains.bedpe" \
> expected.bedpe

test/scripts/validate_nchg_output.py cartesian-product \
domains.bedpe \
expected.bedpe

rm *.bedpe

- name: Test NCHG compute (mt)
run: |
LLVM_PROFILE_FILE="$PWD/nchg.compute-mt.%$(nproc)m.profraw"
Expand Down Expand Up @@ -420,7 +483,7 @@ jobs:
test/data/ENCFF447ERX.1000000.cool \
"$OUT_PREFIX" \
--threads "$(nproc)" \
--domains test/data/ENCFF447ERX.1000000.compartments.bed
--domains "$DATA_DIR/cartesian_product/$OUT_PREFIX.gw-domains.bedpe"

test/scripts/validate_nchg_output.py compute \
"$OUT_PREFIX" \
Expand Down
58 changes: 57 additions & 1 deletion .github/workflows/macos-ci.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -455,6 +455,62 @@ jobs:
echo "DATA_DIR=$PWD/test/data/integration_tests" | tee -a "$GITHUB_ENV"
echo "OUT_PREFIX=ENCFF447ERX.1000000" | tee -a "$GITHUB_ENV"

- name: Test NCHG cartesian-product (gw)
run: |
bin/NCHG cartesian-product \
test/data/ENCFF447ERX.1000000.compartments.bed \
> "$OUT_PREFIX.bedpe"

test/scripts/validate_nchg_output.py cartesian-product \
"$OUT_PREFIX.bedpe" \
"$DATA_DIR/cartesian_product/$OUT_PREFIX.gw-domains.bedpe"

rm "$OUT_PREFIX"*

- name: Test NCHG cartesian-product (cis)
run: |
bin/NCHG cartesian-product \
--cis-only \
test/data/ENCFF447ERX.1000000.compartments.bed \
> domains.bedpe

test/scripts/validate_nchg_output.py cartesian-product \
domains.bedpe \
"$DATA_DIR/cartesian_product/$OUT_PREFIX.cis-domains.bedpe"

rm *.bedpe

- name: Test NCHG cartesian-product (trans)
run: |
bin/NCHG cartesian-product \
--trans-only \
test/data/ENCFF447ERX.1000000.compartments.bed \
> domains.bedpe

test/scripts/validate_nchg_output.py cartesian-product \
domains.bedpe \
"$DATA_DIR/cartesian_product/$OUT_PREFIX.trans-domains.bedpe"

rm *.bedpe

- name: Test NCHG cartesian-product (chr1:chr3)
run: |
bin/NCHG cartesian-product \
--chrom1 chr1 \
--chrom2 chr3 \
test/data/ENCFF447ERX.1000000.compartments.bed \
> domains.bedpe

grep -E '\bchr1\b.*\bchr3\b' \
"$DATA_DIR/cartesian_product/$OUT_PREFIX.trans-domains.bedpe" \
> expected.bedpe

test/scripts/validate_nchg_output.py cartesian-product \
domains.bedpe \
expected.bedpe

rm *.bedpe

- name: Test NCHG compute (mt)
run: |
bin/NCHG compute \
Expand Down Expand Up @@ -484,7 +540,7 @@ jobs:
test/data/ENCFF447ERX.1000000.cool \
"$OUT_PREFIX" \
--threads "$NPROC" \
--domains test/data/ENCFF447ERX.1000000.compartments.bed
--domains "$DATA_DIR/cartesian_product/$OUT_PREFIX.gw-domains.bedpe"

test/scripts/validate_nchg_output.py compute \
"$OUT_PREFIX" \
Expand Down
62 changes: 61 additions & 1 deletion .github/workflows/ubuntu-ci.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -499,6 +499,66 @@ jobs:
echo "DATA_DIR=$PWD/test/data/integration_tests" | tee -a "$GITHUB_ENV"
echo "OUT_PREFIX=ENCFF447ERX.1000000" | tee -a "$GITHUB_ENV"

- name: Test NCHG cartesian-product (gw)
run: |
sudo -u devel \
bin/NCHG cartesian-product \
test/data/ENCFF447ERX.1000000.compartments.bed \
> "$OUT_PREFIX.bedpe"

test/scripts/validate_nchg_output.py cartesian-product \
"$OUT_PREFIX.bedpe" \
"$DATA_DIR/cartesian_product/$OUT_PREFIX.gw-domains.bedpe"

rm "$OUT_PREFIX"*

- name: Test NCHG cartesian-product (cis)
run: |
sudo -u devel \
bin/NCHG cartesian-product \
--cis-only \
test/data/ENCFF447ERX.1000000.compartments.bed \
> domains.bedpe

test/scripts/validate_nchg_output.py cartesian-product \
domains.bedpe \
"$DATA_DIR/cartesian_product/$OUT_PREFIX.cis-domains.bedpe"

rm *.bedpe

- name: Test NCHG cartesian-product (trans)
run: |
sudo -u devel \
bin/NCHG cartesian-product \
--trans-only \
test/data/ENCFF447ERX.1000000.compartments.bed \
> domains.bedpe

test/scripts/validate_nchg_output.py cartesian-product \
domains.bedpe \
"$DATA_DIR/cartesian_product/$OUT_PREFIX.trans-domains.bedpe"

rm *.bedpe

- name: Test NCHG cartesian-product (chr1:chr3)
run: |
sudo -u devel \
bin/NCHG cartesian-product \
--chrom1 chr1 \
--chrom2 chr3 \
test/data/ENCFF447ERX.1000000.compartments.bed \
> domains.bedpe

grep -E '\bchr1\b.*\bchr3\b' \
"$DATA_DIR/cartesian_product/$OUT_PREFIX.trans-domains.bedpe" \
> expected.bedpe

test/scripts/validate_nchg_output.py cartesian-product \
domains.bedpe \
expected.bedpe

rm *.bedpe

- name: Test NCHG compute (mt)
run: |
sudo -u devel \
Expand Down Expand Up @@ -531,7 +591,7 @@ jobs:
test/data/ENCFF447ERX.1000000.cool \
"$OUT_PREFIX" \
--threads "$(nproc)" \
--domains test/data/ENCFF447ERX.1000000.compartments.bed
--domains "$DATA_DIR/cartesian_product/$OUT_PREFIX.gw-domains.bedpe"

test/scripts/validate_nchg_output.py compute \
"$OUT_PREFIX" \
Expand Down
4 changes: 2 additions & 2 deletions cmake/FetchTestDataset.cmake
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Original file line number Diff line number Diff line change
Expand Up @@ -18,8 +18,8 @@

# gersemi: off
file(
DOWNLOAD https://zenodo.org/records/14069775/files/nchg_test_data.tar.zst?download=1
EXPECTED_HASH SHA256=097eb7d6228f470000291ad4b83e0d8b7fd916ecfab74749833c01f13e8a882b
DOWNLOAD https://zenodo.org/records/14133677/files/nchg_test_data.tar.zst?download=1
EXPECTED_HASH SHA256=17d89d3d79996eadd5c9e60ed4411a5351abb87af8e0ab214856ea3bc9fab362
"${PROJECT_SOURCE_DIR}/test/data/nchg_test_data.tar.zst"
)
# gersemi: on
Expand Down
40 changes: 40 additions & 0 deletions src/libnchg/include/nchg/hash.hpp
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@@ -0,0 +1,40 @@
// Copyright (C) 2024 Roberto Rossini <[email protected]>
//
// SPDX-License-Identifier: GPL-3.0
//
// This library is free software: you can redistribute it and/or
// modify it under the terms of the GNU Public License as published
// by the Free Software Foundation; either version 3 of the License,
// or (at your option) any later version.
//
// This library is distributed in the hope that it will be useful,
// but WITHOUT ANY WARRANTY; without even the implied warranty of
// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
// Library General Public License for more details.
//
// You should have received a copy of the GNU Public License along
// with this library. If not, see
// <https://www.gnu.org/licenses/>.

#pragma once

#include <cstddef>
#include <functional>

namespace nchg::internal {
// Adapted from:
// https://www.boost.org/doc/libs/1_37_0/doc/html/hash/reference.html#boost.hash_combine

template <typename T>
[[nodiscard]] inline std::size_t hash_combine(std::size_t seed, const T &v) {
// NOLINTNEXTLINE(*-avoid-magic-numbers)
seed ^= std::hash<T>{}(v) + 0x9e3779b9 + (seed << 6U) + (seed >> 2U);
return seed;
}
template <typename T, typename... Args>
[[nodiscard]] inline std::size_t hash_combine(std::size_t seed, const T &v, const Args &...args) {
// NOLINTNEXTLINE(*-avoid-magic-numbers)
seed ^= std::hash<T>{}(v) + 0x9e3779b9 + (seed << 6U) + (seed >> 2U);
return hash_combine(seed, args...);
}
} // namespace nchg::internal
1 change: 1 addition & 0 deletions src/nchg/CMakeLists.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -33,6 +33,7 @@ add_executable(NCHG)
target_sources(
NCHG
PRIVATE
"${CMAKE_CURRENT_SOURCE_DIR}/cartesian_product/cartesian_product.cpp"
"${CMAKE_CURRENT_SOURCE_DIR}/common/io.cpp"
"${CMAKE_CURRENT_SOURCE_DIR}/compute/compute.cpp"
"${CMAKE_CURRENT_SOURCE_DIR}/expected/expected.cpp"
Expand Down
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