add fastq-peak executable

bin/fastq-peak.sh

@@ -0,0 +1,32 @@
+#!/bin/bash
+
+# Get the directory of the current script
+SCRIPT_DIR=$(dirname "$0")
+
+# Source the library file for reusable functions
+source "$SCRIPT_DIR/../lib/utils.sh"
+
+# Check if a FASTQ file is provided
+if [ "$#" -ne 1 ]; then
+    echo "Usage: $0 <fastq_file>"
+    exit 1
+fi
+
+FASTQ_FILE=$1
+
+# Check if the provided file exists
+if [ ! -f "$FASTQ_FILE" ]; then
+    echo "Error: File '$FASTQ_FILE' not found!"
+    exit 1
+fi
+
+echo "Processing FASTQ file: $FASTQ_FILE"
+
+# Count the number of reads in the FASTQ file #
+# Count the number of lines in the FASTQ file
+LINE_COUNT=$(wc -l < "$FASTQ_FILE")
+#Calculate the number of reads (4 lines per read)
+READ_COUNT=$((LINE_COUNT / 4))
+# Output the number of reads
+echo "Number of reads in $FASTQ_FILE: $READ_COUNT"
+

data/sample.fastq

@@ -0,0 +1,8 @@
+@SEQ_ID_1
+GATTTGGGGTTTCCCAGTCACGACGTTGTA
++
+!''*((((***+))%%%++)(%%%%).1**-
+@SEQ_ID_2
+TGATTTGGGGTTTCCCAGTCACGACGTTGT
++
+!''*((((***+))%%%++)(%%%%).1**-