adding gc-percentage calculation and reporting

.github/workflows/test.yml

@@ -25,6 +25,9 @@ jobs:  # Define jobs for the workflow
           # Save the expected output to a file
           echo "Processing FASTQ file: ./data/sample.fastq" > expected_output.txt
           echo "Number of reads in ./data/sample.fastq: 2" >> expected_output.txt
+          echo "GC Count: 30" >> expected_output.txt
+          echo "Total number of bases: 60" >> expected_output.txt
+          echo "GC Percent : 50%" >> expected_output.txt
 
           # Capture the actual output of the script and save it to a file
           ./bin/fastq-peek.sh ./data/sample.fastq > actual_output.txt

bin/fastq-peek.sh

@@ -26,3 +26,19 @@ LINE_COUNT=$(wc -l < "$FASTQ_FILE")
 READ_COUNT=$((LINE_COUNT / 4))
 
 echo "Number of reads in $FASTQ_FILE: $READ_COUNT"
+
+
+# Calculate GC count
+GC_COUNT=$(cat "$FASTQ_FILE" | grep -o -E "G|C" | wc -l)
+
+echo "GC Count: $GC_COUNT"
+
+# Calculate total base count
+TOTAL_BASE_COUNT=$(cat "$FASTQ_FILE" | grep -o -E "A|T|G|C" |  wc -l)
+
+echo "Total number of bases: $TOTAL_BASE_COUNT"
+
+# Calculate GC Percent
+GC_PERCENT=$((100*$GC_COUNT/$TOTAL_BASE_COUNT))
+
+echo "GC Percent : $GC_PERCENT%"