#!/usr/bin/env python

"""Takes a bam file and sorts and indexes it with pysam"""

import os
import pysam

def prep(initial, final, threads):
    """Sorts and indexes bam files listed in dic"""

    if os.path.exists(initial):
        pysam.sort("-o", final, "-@", str(threads), initial)

    if os.path.exists(final):
        pysam.index(final)

    return final
