#!/bin/bash

# Define output files
HUB_FILE="hub.txt"
GENOME_FILE="genomes.txt"
TRACK_DB_FILE="trackDb.txt"

# Create hub.txt
cat <<EOF > $HUB_FILE
hub MyHg19Hub
shortLabel My Hg19 Hub
longLabel Custom Hg19 Track Hub
genomesFile genomes.txt
email your_email@example.com
EOF

# Create genomes.txt
cat <<EOF > $GENOME_FILE
genome hg19
trackDb trackDb.txt
EOF

# Create trackDb.txt
echo "" > $TRACK_DB_FILE  # Clear previous trackDb.txt

# Define colors for tracks
COLORS=("0,0,255" "255,0,0" "0,255,0" "255,165,0" "128,0,128" "0,255,255")

# Loop through all bigWig files ending with -HG19.bw
count=0
for file in *-HG19.bw; do
    # Extract the base filename without extension
    base_name=$(basename "$file" .bw)

    # Assign a color from the array (cycle through if more files)
    color=${COLORS[$((count % ${#COLORS[@]}))]}
    
    # Append track information to trackDb.txt
    cat <<EOF >> $TRACK_DB_FILE
track $base_name
bigDataUrl $file
shortLabel $base_name
longLabel $base_name bigWig Track
type bigWig
visibility full
color $color

EOF

    ((count++))
done

echo "✅ UCSC track hub files generated: hub.txt, genomes.txt, trackDb.txt"