#!/bin/bash
# Script to run BPP A00 analysis for coalescence network inference

# Set working directory
WORK_DIR=$(pwd)
SCRIPT_DIR="$(dirname "$0")"

# Check if BPP is installed and available
if ! command -v bpp &> /dev/null
then
    echo "Error: BPP is not installed or not in PATH"
    echo "Please install BPP and make sure it's accessible in your PATH"
    exit 1
fi

# Check if control file exists
CONTROL_FILE="${SCRIPT_DIR}/run_bpp_a00.ctl"
if [ ! -f "$CONTROL_FILE" ]; then
    echo "Error: Control file not found at $CONTROL_FILE"
    echo "Please make sure the control file exists"
    exit 1
fi

echo "Starting BPP A00 analysis..."
echo "Control file: $CONTROL_FILE"
echo "Working directory: $WORK_DIR"

# Run BPP analysis
bpp --cfile "$CONTROL_FILE"

# Check if the run was successful
if [ $? -eq 0 ]; then
    echo "BPP analysis completed successfully!"
    
    # Check for output files
    JOBNAME=$(grep -E "^jobname\s*=" "$CONTROL_FILE" | sed -E 's/^jobname\s*=\s*(.*)/\1/' | tr -d ' ')
    if [ -z "$JOBNAME" ]; then
        JOBNAME="out"
    fi
    
    echo "Output files:"
    echo "  Main output: ${JOBNAME}.txt"
    echo "  MCMC samples: ${JOBNAME}.mcmc.txt"
    
    if [ -f "${JOBNAME}.txt" ]; then
        echo "Main output file created successfully"
    else
        echo "Warning: Main output file not found"
    fi
    
    if [ -f "${JOBNAME}.mcmc.txt" ]; then
        echo "MCMC samples file created successfully"
    else
        echo "Warning: MCMC samples file not found"
    fi
    
else
    echo "Error: BPP analysis failed"
    exit 1
fi