added test

.github/workflows/test_n50.yml

@@ -0,0 +1,35 @@
+name: N50 Calculator CI
+
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main ]
+  workflow_dispatch:
+
+jobs:
+  build-and-test:
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v2
+
+    - name: Install dependencies
+      run: |
+        sudo apt-get update
+        sudo apt-get install -y gcc make zlib1g-dev
+
+    - name: Build N50 Calculator
+      run: make
+
+    - name: Run tests
+      run: make test
+
+    - name: Run simple test
+      run: make test-simple
+
+    - name: Archive binary
+      uses: actions/upload-artifact@v2
+      with:
+        name: n50-calculator
+        path: bin/n50

Makefile

@@ -0,0 +1,66 @@
+CC = gcc
+CFLAGS = -Wall -Wextra -O3
+LDFLAGS = -lz -lpthread
+
+SRC_DIR = src
+BIN_DIR = bin
+TEST_DIR = test
+TARGET = $(BIN_DIR)/n50
+
+.PHONY: all clean test
+
+all: $(TARGET)
+
+$(TARGET): $(SRC_DIR)/n50.c | $(BIN_DIR)
+	$(CC) $(CFLAGS) $< -o $@ $(LDFLAGS)
+
+$(BIN_DIR):
+	mkdir -p $(BIN_DIR)
+
+clean:
+	rm -rf $(BIN_DIR)
+
+test: $(TARGET)
+	@echo "Running tests..."
+	@passed=0; failed=0; \
+	for file in $(TEST_DIR)/*.*; do \
+		filename=$$(basename $$file); \
+		expected_n50=$${filename%%.*}; \
+		echo "Testing $$filename (Expected N50: $$expected_n50)"; \
+		output=$$($(TARGET) $$file); \
+		actual_n50=$$(echo "$$output" | cut -f4); \
+		if [ "$$actual_n50" = "$$expected_n50" ]; then \
+			echo "  Passed"; \
+			passed=$$((passed + 1)); \
+		else \
+			echo "  Failed. Expected N50: $$expected_n50, Got: $$actual_n50"; \
+			failed=$$((failed + 1)); \
+		fi; \
+	done; \
+	echo "Tests completed. Passed: $$passed, Failed: $$failed"; \
+	if [ $$failed -ne 0 ]; then exit 1; fi
+
+# Original simple test
+test-simple: $(TARGET)
+	@echo "Running simple test..."
+	@echo ">seq1" > test.fasta
+	@echo "ATCGATCGATCG" >> test.fasta
+	@echo ">seq2" >> test.fasta
+	@echo "ATCGATCGATCGATCGATCG" >> test.fasta
+	@echo ">seq3" >> test.fasta
+	@echo "ATCG" >> test.fasta
+	@output=$$($(TARGET) test.fasta); \
+	echo "Output: $$output"; \
+	total_bp=$$(echo "$$output" | cut -f2); \
+	total_seq=$$(echo "$$output" | cut -f3); \
+	n50=$$(echo "$$output" | cut -f4); \
+	if [ "$$total_bp" = "36" ] && [ "$$total_seq" = "3" ] && [ "$$n50" = "20" ]; then \
+		echo "Simple test passed successfully!"; \
+	else \
+		echo "Simple test failed!"; \
+		echo "Expected: 36 total bp, 3 sequences, N50 of 20"; \
+		echo "Got: $$total_bp total bp, $$total_seq sequences, N50 of $$n50"; \
+		exit 1; \
+	fi
+	@rm test.fasta
+	@echo "Simple test completed."

test/54.fa

@@ -0,0 +1,20 @@
+>Seq1 Description
+GATACTGACTGACTGATCGATCGTAGCTAGCTAGCTGATCTAGCTAGCTAGCTA
+>Seq2 Description
+GACTGATCGATCGTAGCTA
+>Seq3 Description
+GATACTGACTGACTGATCGATCGTAGCTAGCTAGCTGATCTAGCTAGCTAGCTA
+>Seq4 Description
+GACTGATCGATCGTAGCTA
+>Seq5 Description
+GATACTGACTGACTGATCGATCGTAGCTAGCTAGCTGATCTAGCTAGCTAGCTA
+>Seq6 Description
+GACTGATCGATCGTAGCTA
+>Seq7 Description
+GATACTGAGAGTATATACACACACGACTGACTGATCGATCGTAGCTAGCTAGCTGATCTAGCTAGCTAGCTA
+>Seq8 Description
+GACTGATCGATCGTAGCTA
+>Seq9 Description
+GATACTCTGATCGATCGTAGCTAGCTAGCTGATCTAGCTAGCTAGCTA
+>Seq10 Description
+GACTGATCGATCGTAGCTA

test/54.fq

@@ -0,0 +1,40 @@
+@Seq1 Description
+GATACTGACTGACTGATCGATCGTAGCTAGCTAGCTGATCTAGCTAGCTAGCTA
++
+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
+@Seq2 Description
+GACTGATCGATCGTAGCTA
++
+BBBBBBBBBBBBBBBBBBB
+@Seq3 Description
+GATACTGACTGACTGATCGATCGTAGCTAGCTAGCTGATCTAGCTAGCTAGCTA
++
+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
+@Seq4 Description
+GACTGATCGATCGTAGCTA
++
+BBBBBBBBBBBBBBBBBBB
+@Seq5 Description
+GATACTGACTGACTGATCGATCGTAGCTAGCTAGCTGATCTAGCTAGCTAGCTA
++
+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
+@Seq6 Description
+GACTGATCGATCGTAGCTA
++
+BBBBBBBBBBBBBBBBBBB
+@Seq7 Description
+GATACTGAGAGTATATACACACACGACTGACTGATCGATCGTAGCTAGCTAGCTGATCTAGCTAGCTAGCTA
++
+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
+@Seq8 Description
+GACTGATCGATCGTAGCTA
++
+BBBBBBBBBBBBBBBBBBB
+@Seq9 Description
+GATACTCTGATCGATCGTAGCTAGCTAGCTGATCTAGCTAGCTAGCTA
++
+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
+@Seq10 Description
+GACTGATCGATCGTAGCTA
++
+BBBBBBBBBBBBBBBBBBB