Step 1: Tailored camel's local for simplitigs

.github/workflows/ci.yml

@@ -0,0 +1,37 @@
+name: C++ CI
+
+on:
+  push:
+    branches: [ "main" ]
+  pull_request:
+    branches: [ "main" ]
+
+jobs:
+  build_with_unittests:
+
+    runs-on: ${{ matrix.os }}
+
+    strategy:
+      matrix:
+        os: [ubuntu-latest, macos-latest]
+
+    steps:
+    - uses: actions/checkout@v3
+    - name: make
+      run: make
+    - name: submodule
+      run: git submodule init; git submodule update
+    - name: cpptests
+      run: make cpptest
+
+  verify_ubuntu:
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v3
+    - name: make
+      run: make
+    - name: jellyfish
+      run: sudo apt install jellyfish
+    - name: verify
+      run: make quick-verify

.gitignore

@@ -1,3 +1,17 @@
+# Binaries
+prophasm
+prophasm2
+prophasmtest
+
+# Generated test files
+bin/
+
+# Generated version file
+src/version.h
+
+# IDE files
+.idea/
+
 # Prerequisites
 *.d
 

.gitmodules

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+[submodule "tests/googletest"]
+	path = tests/googletest
+	url = https://github.com/google/googletest

Makefile

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+.PHONY: all clean test cpptest verify quick-verify
+
+CXX=         g++
+CXXFLAGS=    -g -Wall -Wno-unused-function -std=c++17 -O2
+LDFLAGS=     -lz 
+SRC=         src
+SCRIPTS=     scripts
+DATA=        data
+TESTS=       tests
+GTEST=       $(TESTS)/googletest/googletest
+PROG=        prophasm2
+
+
+all: $(PROG)
+
+test: cpptest verify
+
+cpptest: prophasmtest
+	./prophasmtest
+
+verify: $(PROG) $(SCRIPTS)/verify.py $(DATA)/spneumoniae.fa
+	python $(SCRIPTS)/verify.py $(DATA)/spneumoniae.fa
+
+quick-verify: $(PROG) $(SCRIPTS)/verify.py $(DATA)/spneumoniae.fa
+	python $(SCRIPTS)/verify.py $(DATA)/spneumoniae.fa --quick
+
+$(PROG): $(SRC)/main.cpp $(SRC)/$(wildcard *.cpp *.h *.hpp) src/version.h
+	./create-version.sh
+	$(CXX) $(CXXFLAGS) $(SRC)/main.cpp -o $@ $(LDFLAGS)
+
+
+prophasmtest: $(TESTS)/unittest.cpp gtest-all.o $(SRC)/$(wildcard *.cpp *.h *.hpp) $(TESTS)/$(wildcard *.cpp *.h *.hpp)
+	$(CXX) $(CXXFLAGS) -isystem $(GTEST)/include -I $(GTEST)/include $(TESTS)/unittest.cpp gtest-all.o -pthread -o $@ $(LDFLAGS)
+
+gtest-all.o: $(GTEST)/src/gtest-all.cc $(wildcard *.cpp *.h *.hpp)
+	$(CXX) $(CXXFLAGS) -isystem $(GTEST)/include -I $(GTEST)/include -I $(GTEST) -DGTEST_CREATE_SHARED_LIBRARY=1 -c -pthread $(GTEST)/src/gtest-all.cc -o $@
+
+src/version.h: src/version
+	./create-version.sh
+
+clean:
+	rm -f $(PROG)
+	rm -f prophasmtest
+	rm -r -f ./bin
+	rm -f gtest-all.o
+	rm -f src/version.h

create-version.sh

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+#!/usr/bin/env bash
+cat <(echo "#define VERSION \"") <(git describe --abbrev=4 --dirty --always --tags 2> /dev/null || cat src/version) <(echo \") | tr -d '\n' > src/version.h

scripts/verify.py

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+#!/usr/bin/env python3
+import subprocess
+import sys
+import os
+import argparse
+
+
+def verify_instance(fasta_path: str, k: int, complements: bool) -> bool:
+    """
+    Check if running ProphAsm2 on given fasta file produces the same set of k-mers as the original one.
+    """
+    with open("./bin/simplitigs.fa", "w") as k_mers:
+        args = ["./prophasm2", "-p", fasta_path, "-k", f"{k}"]
+        if complements:
+            args.append("-c")
+        subprocess.run(args, stdout=k_mers)
+    # in result; in original sequence; in result without complements; in original without complements; in merged file
+    stats = [{}, {}, {}]
+    runs = [
+        (0, "./bin/simplitigs.fa", "simplitigs", complements),
+        (1, fasta_path, "original", complements),
+    ]
+    for i, path, result, pass_complements in runs:
+        args = ["jellyfish", "count", "-m", f"{k}", "-s", "100M", "-o", f"./bin/{result}.jf", path]
+        if pass_complements:
+            args.insert(2, "-C")
+        subprocess.run(args)
+        with open(f"./bin/{result}_stats.txt", "w") as f:
+            subprocess.run(["jellyfish", "stats", f"./bin/{result}.jf"], stdout=f)
+        with open(f"./bin/{result}_stats.txt", "r") as f:
+            for _ in range(4):
+                key, value = f.readline().split()
+                stats[i][key] = value
+    # Count k-mers on merged file.
+    subprocess.run(["jellyfish", "merge", "-o", f"./bin/merged.jf", "./bin/simplitigs.jf", "./bin/original.jf"])
+    with open(f"./bin/merged_stats.txt", "w") as f:
+        subprocess.run(["jellyfish", "stats", f"./bin/merged.jf"], stdout=f)
+    with open(f"./bin/merged_stats.txt", "r") as f:
+        for _ in range(4):
+            key, value = f.readline().split()
+            stats[2][key] = value
+    distinct_key = "Distinct:"
+    total_key = "Total:"
+    if stats[0][distinct_key] != stats[1][distinct_key] or stats[0][distinct_key] != stats[2][distinct_key]:
+        print("F")
+        print(f"Failed: k={k}: expected orginal_distinct_count={stats[1][distinct_key]}, result_distinct_count={stats[0][distinct_key]} and merged_distinct_count={stats[2][distinct_key]} to be equal.")
+        return False
+    elif complements and stats[0][distinct_key] != stats[0][total_key]:
+        print("W")
+        print(f"Warning: k={k}: number of masked k-mers={stats[0][total_key]} is not minimal possible (minimum is {stats[0][distinct_key]}).")
+    else:
+        print(".", end="")
+        sys.stdout.flush()
+    return True
+
+
+def main():
+    # Initialize.
+    if not os.path.exists("bin"):
+        os.makedirs("bin")
+
+    parser = argparse.ArgumentParser("check if ProphAsm2 outputs simplitigs which contain the same set of k-mers"
+                                     "as the original sequence")
+    parser.add_argument("--quick", help="if set do not check for full range of k", action="store_true")
+    parser.add_argument("path", help="path to the fasta file on which ProphAsm2 is verified")
+    args = parser.parse_args()
+
+    success = True
+    print("Testing ProphAsm2 outputs valid simplitigs on file " + args.path)
+    for complements in [True, False]:
+        for k in range(2, 33, 3 if args.quick else 1):
+            success &= verify_instance(args.path, k, complements)
+        print("")
+
+    # Print status.
+    if not success:
+        print("Tests failed")
+        exit(1)
+    print("OK")
+
+main()