Module Expr Str Import alias Import alias Import alias ImportFrom alias identifier ImportFrom alias ImportFrom alias ImportFrom alias FunctionDef arguments args NameParam defaults body Expr Str Assign NameStore Call NameLoad NameLoad Assign NameStore AttributeLoad NameLoad attr Assign NameStore AttributeLoad NameLoad attr Assign NameStore AttributeLoad NameLoad attr Assign NameStore AttributeLoad NameLoad attr Assert CompareNotEq AttributeLoad NameLoad attr Str Str Assign NameStore Call AttributeLoad AttributeLoad NameLoad attr attr AttributeLoad NameLoad attr AttributeLoad NameLoad attr If Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad body Expr Call NameLoad BinOpMod Str NameLoad Expr Call AttributeLoad NameLoad attr NameLoad Expr Call NameLoad Str Assign TupleStore NameStore NameStore Call NameLoad NameLoad Expr Call NameLoad Str NameLoad Assign NameStore AttributeLoad NameLoad attr Expr Call NameLoad Str NameLoad If AttributeLoad NameLoad attr body Expr Call NameLoad BinOpMod Str AttributeLoad NameLoad attr Expr Call NameLoad NameLoad NameLoad BinOpMult AttributeLoad NameLoad attr Num Num keyword NameLoad keyword NameLoad orelse Expr Call NameLoad BinOpMod Str AttributeLoad NameLoad attr Expr Call NameLoad NameLoad NameLoad AttributeLoad NameLoad attr Num keyword NameLoad keyword NameLoad Expr Call NameLoad BinOpMod Str AttributeLoad NameLoad attr decorator_list FunctionDef arguments args NameParam defaults body Expr Str Expr Call AttributeLoad NameLoad attr Str Assign NameStore Call AttributeLoad NameLoad attr SubscriptLoad AttributeLoad NameLoad attr Index Num Assign NameStore Call AttributeLoad NameLoad attr Assign NameStore Call AttributeLoad NameLoad attr If CompareGt Call NameLoad AttributeLoad NameLoad attr Num body For NameStore SubscriptLoad AttributeLoad NameLoad attr Slice Num body Assign NameStore Call AttributeLoad NameLoad attr NameLoad Assign NameStore Call AttributeLoad NameLoad attr NameLoad Expr Call AttributeLoad NameLoad attr Expr Call AttributeLoad NameLoad attr BinOpMod Str NameLoad Return TupleLoad NameLoad NameLoad decorator_list
N/A N/A 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
 N/A os N/A sys N/A logging MACS2.OptValidator opt_validate_pileup opt_validate MACS2.OutputWriter * MACS2.Pileup pileup_and_write MACS2.Constants * run N/A N/A o_options N/A N/A N/A The Main function/pipeline for duplication filter.
    
     N/A options N/A opt_validate o_options N/A info N/A options info N/A warn N/A options warn N/A debug N/A options debug N/A error N/A options error N/A N/A N/A 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! N/A outfile N/A N/A N/A os path join N/A options outdir N/A options outputfile N/A N/A N/A N/A os path isfile outfile N/A N/A N/A info N/A # Existing file %s will be replaced! outfile N/A N/A N/A os unlink outfile N/A N/A info # read alignment files... N/A N/A tsize treat N/A load_tag_files_options options N/A N/A info # tag size = %d tsize N/A t0 N/A treat total N/A N/A info # total tags in alignment file: %d t0 N/A N/A options bothdirection N/A N/A N/A info N/A # Pileup alignment file, extend each read towards up/downstream direction with %d bps N/A options extsize N/A N/A pileup_and_write treat outfile N/A N/A options extsize 2 1 directional False halfextension False N/A N/A N/A info N/A # Pileup alignment file, extend each read towards downstream direction with %d bps N/A options extsize N/A N/A pileup_and_write treat outfile N/A options extsize 1 directional True halfextension False N/A N/A info N/A # Done! Check %s N/A options outputfile N/A load_tag_files_options N/A N/A options N/A N/A N/A From the options, load alignment tags.

     N/A N/A N/A options info # read treatment tags... N/A tp N/A N/A options parser N/A N/A options ifile N/A 0 N/A tsize N/A N/A tp tsize N/A treat N/A N/A tp build_fwtrack N/A N/A N/A len N/A options ifile 1 N/A N/A tfile N/A N/A options ifile N/A 1 N/A N/A tp N/A N/A options parser tfile N/A treat N/A N/A tp append_fwtrack treat N/A N/A N/A treat finalize N/A N/A N/A options info N/A tag size is determined as %d bps tsize N/A N/A tsize treat N/A