# Time-stamp: <2015-06-02 23:36:21 Tao Liu>

"""Description: Filter duplicate reads depending on sequencing depth.

Copyright (c) 2011 Tao Liu <taoliu@jimmy.harvard.edu>

This code is free software; you can redistribute it and/or modify it
under the terms of the BSD License (see the file COPYING included
with the distribution).

@status: release candidate
@version: $Id$
@author:  Yong Zhang, Tao Liu
@contact: taoliu@jimmy.harvard.edu
"""

# ------------------------------------
# python modules
# ------------------------------------

import os
import sys
import logging

# ------------------------------------
# own python modules
# ------------------------------------
from MACS2.OptValidator import opt_validate_pileup as opt_validate
from MACS2.OutputWriter import *
from MACS2.Pileup import pileup_and_write
from MACS2.Constants import *
# ------------------------------------
# Main function
# ------------------------------------
def run( o_options ):
    """The Main function/pipeline for duplication filter.
    
    """
    # Parse options...
    options = opt_validate( o_options )
    # end of parsing commandline options
    info = options.info
    warn = options.warn
    debug = options.debug
    error = options.error
    #0 output arguments
    assert options.format != 'BAMPE', "Pair-end data with BAMPE option currently doesn't work with pileup command. You can pretend your data to be single-end with -f BAM. Please try again!"

    #0 prepare output file
    outfile = os.path.join( options.outdir, options.outputfile )
    if os.path.isfile( outfile ):
        info("# Existing file %s will be replaced!" % outfile )
        os.unlink( outfile )

    #1 Read tag files
    info("# read alignment files...")
    (tsize, treat) = load_tag_files_options  (options)
    
    info("# tag size = %d", tsize)
    
    t0 = treat.total
    info("# total tags in alignment file: %d", t0)

    if options.bothdirection:
        info("# Pileup alignment file, extend each read towards up/downstream direction with %d bps" % options.extsize)
        pileup_and_write(treat, outfile, options.extsize * 2, 1, directional=False, halfextension=False)
    else:
        info("# Pileup alignment file, extend each read towards downstream direction with %d bps" % options.extsize)
        pileup_and_write(treat, outfile, options.extsize, 1, directional=True, halfextension=False)

    info("# Done! Check %s" % options.outputfile)

def load_tag_files_options ( options ):
    """From the options, load alignment tags.

    """
    options.info("# read treatment tags...")
    tp = options.parser(options.ifile[0])
    tsize = tp.tsize()
    treat = tp.build_fwtrack()
    #treat.sort()
    if len(options.ifile) > 1:
        # multiple input
        for tfile in options.ifile[1:]:
            tp = options.parser(tfile)
            treat = tp.append_fwtrack( treat )
            #treat.sort()
    treat.finalize()

    options.info("tag size is determined as %d bps" % tsize)
    return (tsize, treat)