varscan_somatic: varscan.py annotate

annotate varscan.py @ 3:7903598ccbaf draft

planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 79f2f0e89e74348cf18602e83762a0cb26131f17

author	iuc
date	Tue, 04 Dec 2018 05:50:31 -0500
parents	2fe9ebb98aad
children	2c66c4025db2

rev	line source
2 2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1 #!/usr/bin/env python3
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	2 from __future__ import print_function
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	3
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	4 import argparse
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	5 import io
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	6 import os
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	7 import subprocess
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	8 import sys
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	9 import tempfile
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	10 import time
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	11 from contextlib import ExitStack
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	12 from functools import partial
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	13 from threading import Thread
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	14
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	15 import pysam
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	16
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	17
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	18 class VariantCallingError (RuntimeError):
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	19 """Exception class for issues with samtools and varscan subprocesses."""
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	20
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	21 def __init__(self, message=None, call='', error=''):
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	22 self.message = message
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	23 self.call = call.strip()
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	24 self.error = error.strip()
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	25
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	26 def __str__(self):
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	27 if self.message is None:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	28 return ''
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	29 if self.error:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	30 msg_header = '"{0}" failed with:\n{1}\n\n'.format(
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	31 self.call, self.error
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	32 )
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	33 else:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	34 msg_header = '{0} failed.\n'
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	35 'No further information about this error is available.\n\n'.format(
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	36 self.call
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	37 )
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	38 return msg_header + self.message
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	39
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	40
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	41 class VarScanCaller (object):
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	42 def __init__(self, ref_genome, bam_input_files,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	43 max_depth=None,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	44 min_mapqual=None, min_basequal=None,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	45 threads=1, verbose=False, quiet=True
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	46 ):
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	47 self.ref_genome = ref_genome
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	48 self.bam_input_files = bam_input_files
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	49 self.max_depth = max_depth
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	50 self.min_mapqual = min_mapqual
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	51 self.min_basequal = min_basequal
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	52 self.threads = threads
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	53 self.verbose = verbose
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	54 self.quiet = quiet
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	55
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	56 with pysam.FastaFile(ref_genome) as ref_fa:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	57 self.ref_contigs = ref_fa.references
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	58 self.ref_lengths = ref_fa.lengths
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	59
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	60 self.pileup_engine = ['samtools', 'mpileup']
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	61 self.varcall_engine = ['varscan', 'somatic']
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	62 self.requires_stdout_redirect = False
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	63 self.TemporaryContigVCF = partial(
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	64 tempfile.NamedTemporaryFile,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	65 mode='wb', suffix='', delete=False, dir=os.getcwd()
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	66 )
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	67 self.tmpfiles = []
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	68
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	69 def _get_pysam_pileup_args(self):
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	70 param_dict = {}
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	71 if self.max_depth is not None:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	72 param_dict['max_depth'] = self.max_depth
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	73 if self.min_mapqual is not None:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	74 param_dict['min_mapping_quality'] = self.min_mapqual
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	75 if self.min_basequal is not None:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	76 param_dict['min_base_quality'] = self.min_basequal
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	77 param_dict['compute_baq'] = False
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	78 param_dict['stepper'] = 'samtools'
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	79 return param_dict
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	80
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	81 def varcall_parallel(self, normal_purity=None, tumor_purity=None,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	82 min_coverage=None,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	83 min_var_count=None,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	84 min_var_freq=None, min_hom_freq=None,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	85 p_value=None, somatic_p_value=None,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	86 threads=None, verbose=None, quiet=None
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	87 ):
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	88 if not threads:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	89 threads = self.threads
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	90 if verbose is None:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	91 verbose = self.verbose
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	92 if quiet is None:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	93 quiet = self.quiet
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	94 # mapping of method parameters to varcall engine command line options
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	95 varcall_engine_option_mapping = [
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	96 ('--normal-purity', normal_purity),
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	97 ('--tumor-purity', tumor_purity),
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	98 ('--min-coverage', min_coverage),
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	99 ('--min-reads2', min_var_count),
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	100 ('--min-var-freq', min_var_freq),
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	101 ('--min-freq-for-hom', min_hom_freq),
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	102 ('--p-value', p_value),
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	103 ('--somatic-p-value', somatic_p_value),
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	104 ('--min-avg-qual', self.min_basequal)
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	105 ]
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	106 varcall_engine_options = []
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	107 for option, value in varcall_engine_option_mapping:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	108 if value is not None:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	109 varcall_engine_options += [option, str(value)]
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	110 pileup_engine_options = ['-B']
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	111 if self.max_depth is not None:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	112 pileup_engine_options += ['-d', str(self.max_depth)]
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	113 if self.min_mapqual is not None:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	114 pileup_engine_options += ['-q', str(self.min_mapqual)]
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	115 if self.min_basequal is not None:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	116 pileup_engine_options += ['-Q', str(self.min_basequal)]
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	117
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	118 # Create a tuple of calls to samtools mpileup and varscan for
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	119 # each contig. The contig name is stored as the third element of
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	120 # that tuple.
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	121 # The calls are stored in the reverse order of the contig list so
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	122 # that they can be popped off later in the original order
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	123 calls = [(
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	124 self.pileup_engine + pileup_engine_options + [
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	125 '-r', contig + ':',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	126 '-f', self.ref_genome
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	127 ] + self.bam_input_files,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	128 self.varcall_engine + [
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	129 '-', '{out}', '--output-vcf', '1', '--mpileup', '1'
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	130 ] + varcall_engine_options,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	131 contig
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	132 ) for contig in self.ref_contigs[::-1]]
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	133
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	134 if verbose:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	135 print('Starting variant calling ..')
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	136
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	137 # launch subprocesses and monitor their status
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	138 subprocesses = []
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	139 error_table = {}
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	140 tmp_io_started = []
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	141 tmp_io_finished = []
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	142 self.tmpfiles = []
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	143
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	144 def enqueue_stderr_output(out, stderr_buffer):
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	145 for line in iter(out.readline, b''):
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	146 # Eventually we are going to print the contents of
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	147 # the stderr_buffer to sys.stderr so we can
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	148 # decode things here using its encoding.
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	149 # We do a 'backslashreplace' just to be on the safe side.
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	150 stderr_buffer.write(line.decode(sys.stderr.encoding,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	151 'backslashreplace'))
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	152 out.close()
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	153
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	154 try:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	155 while subprocesses or calls:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	156 while calls and len(subprocesses) < threads:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	157 # There are still calls waiting for execution and we
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	158 # have unoccupied threads so we launch a new combined
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	159 # call to samtools mpileup and the variant caller.
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	160
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	161 # pop the call arguments from our call stack
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	162 call = calls.pop()
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	163 # get the name of the contig that this call is going
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	164 # to work on
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	165 contig = call[2]
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	166 # Based on the contig name, generate a readable and
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	167 # file system-compatible prefix and use it to create
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	168 # a named temporary file, to which the call output
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	169 # will be redirected.
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	170 # At the moment we create the output file we add it to
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	171 # the list of all temporary output files so that we can
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	172 # remove it eventually during cleanup.
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	173 call_out = self.TemporaryContigVCF(
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	174 prefix=''.join(
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	175 c if c.isalnum() else '_' for c in contig
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	176 ) + '_',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	177 )
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	178 # maintain a list of variant call outputs
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	179 # in the order the subprocesses got launched
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	180 tmp_io_started.append(call_out.name)
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	181 if self.requires_stdout_redirect:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	182 # redirect stdout to the temporary file just created
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	183 stdout_p2 = call_out
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	184 stderr_p2 = subprocess.PIPE
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	185 else:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	186 # variant caller wants to write output to file directly
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	187 stdout_p2 = subprocess.PIPE
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	188 stderr_p2 = subprocess.STDOUT
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	189 call[1][call[1].index('{out}')] = call_out.name
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	190 call_out.close()
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	191 # for reporting purposes, join the arguments for the
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	192 # samtools and the variant caller calls into readable
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	193 # strings
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	194 c_str = (' '.join(call[0]), ' '.join(call[1]))
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	195 error_table[c_str] = [io.StringIO(), io.StringIO()]
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	196 # start the subprocesses
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	197 p1 = subprocess.Popen(
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	198 call[0],
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	199 stdout=subprocess.PIPE, stderr=subprocess.PIPE
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	200 )
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	201 p2 = subprocess.Popen(
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	202 call[1],
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	203 stdin=p1.stdout,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	204 stdout=stdout_p2,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	205 stderr=stderr_p2
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	206 )
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	207 # subprocess bookkeeping
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	208 subprocesses.append((c_str, p1, p2, call_out, contig))
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	209 # make sure our newly launched call does not block
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	210 # because its buffers fill up
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	211 p1.stdout.close()
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	212 t1 = Thread(
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	213 target=enqueue_stderr_output,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	214 args=(p1.stderr, error_table[c_str][0])
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	215 )
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	216 t2 = Thread(
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	217 target=enqueue_stderr_output,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	218 args=(
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	219 p2.stderr
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	220 if self.requires_stdout_redirect else
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	221 p2.stdout,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	222 error_table[c_str][1]
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	223 )
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	224 )
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	225 t1.daemon = t2.daemon = True
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	226 t1.start()
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	227 t2.start()
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	228
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	229 if verbose:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	230 print(
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	231 'Calling variants for contig: {0}'
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	232 .format(call[2])
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	233 )
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	234
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	235 # monitor all running calls to see if any of them are done
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	236 for call, p1, p2, ofo, contig in subprocesses:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	237 p1_stat = p1.poll()
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	238 p2_stat = p2.poll()
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	239 if p1_stat is not None or p2_stat is not None:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	240 # There is an outcome for this process!
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	241 # Lets see what it is
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	242 if p1_stat or p2_stat:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	243 print()
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	244 print(
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	245 error_table[call][0].getvalue(),
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	246 error_table[call][1].getvalue(),
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	247 file=sys.stderr
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	248 )
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	249 raise VariantCallingError(
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	250 'Variant Calling for contig {0} failed.'
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	251 .format(contig),
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	252 call='{0} \| {1}'.format(call[0], call[1])
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	253 )
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	254 if p1_stat == 0 and p2_stat is None:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	255 # VarScan is not handling the no output from
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	256 # samtools mpileup situation correctly so maybe
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	257 # that's the issue here
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	258 last_words = error_table[call][1].getvalue(
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	259 ).splitlines()[-4:]
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	260 if len(last_words) < 4 or any(
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	261 not msg.startswith('Input stream not ready')
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	262 for msg in last_words
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	263 ):
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	264 break
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	265 # lets give this process a bit more time
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	266 # VarScan is waiting for input it will never
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	267 # get, stop it.
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	268 p2.terminate()
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	269 subprocesses.remove((call, p1, p2, ofo, contig))
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	270 ofo.close()
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	271 break
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	272 if p2_stat == 0:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	273 # Things went fine.
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	274 # maintain a list of variant call outputs
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	275 # that finished successfully (in the order
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	276 # they finished)
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	277 tmp_io_finished.append(ofo.name)
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	278 if verbose:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	279 print()
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	280 print('Contig {0} finished.'.format(contig))
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	281 if not quiet:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	282 print()
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	283 print(
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	284 'stderr output from samtools mpileup/'
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	285 'bcftools:'.upper(),
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	286 file=sys.stderr
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	287 )
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	288 print(
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	289 error_table[call][0].getvalue(),
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	290 error_table[call][1].getvalue(),
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	291 file=sys.stderr
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	292 )
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	293 # Discard the collected stderr output from
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	294 # the call, remove the call from the list of
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	295 # running calls and close its output file.
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	296 del error_table[call]
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	297 subprocesses.remove((call, p1, p2, ofo, contig))
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	298 # Closing the output file is important or we
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	299 # may hit the file system limit for open files
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	300 # if there are lots of contigs.
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	301 ofo.close()
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	302 break
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	303 # wait a bit in between monitoring cycles
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	304 time.sleep(2)
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	305 finally:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	306 for call, p1, p2, ofo, contig in subprocesses:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	307 # make sure we do not leave running subprocesses behind
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	308 for proc in (p1, p2):
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	309 try:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	310 proc.terminate()
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	311 except Exception:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	312 pass
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	313 # close currently open files
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	314 ofo.close()
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	315 # store the files with finished content in the order that
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	316 # the corresponding jobs were launched
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	317 self.tmpfiles = [f for f in tmp_io_started if f in tmp_io_finished]
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	318 # Make sure remaining buffered stderr output of
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	319 # subprocesses does not get lost.
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	320 # Currently, we don't screen this output for real errors,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	321 # but simply rewrite everything.
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	322 if not quiet and error_table:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	323 print()
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	324 print(
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	325 'stderr output from samtools mpileup/bcftools:'.upper(),
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	326 file=sys.stderr
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	327 )
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	328 for call, errors in error_table.items():
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	329 print(' \| '.join(call), ':', file=sys.stderr)
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	330 print('-' * 20, file=sys.stderr)
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	331 print('samtools mpileup output:', file=sys.stderr)
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	332 print(errors[0].getvalue(), file=sys.stderr)
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	333 print('varscan somatic output:', file=sys.stderr)
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	334 print(errors[1].getvalue(), file=sys.stderr)
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	335
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	336 def _add_ref_contigs_to_header(self, header):
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	337 for chrom, length in zip(self.ref_contigs, self.ref_lengths):
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	338 header.add_meta(
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	339 'contig',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	340 items=[('ID', chrom), ('length', length)]
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	341 )
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	342
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	343 def _add_filters_to_header(self, header):
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	344 varscan_fpfilters = {
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	345 'VarCount': 'Fewer than {min_var_count2} variant-supporting reads',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	346 'VarFreq': 'Variant allele frequency below {min_var_freq2}',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	347 'VarAvgRL':
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	348 'Average clipped length of variant-supporting reads < '
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	349 '{min_var_len}',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	350 'VarReadPos': 'Relative average read position < {min_var_readpos}',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	351 'VarDist3':
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	352 'Average distance to effective 3\' end < {min_var_dist3}',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	353 'VarMMQS':
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	354 'Average mismatch quality sum for variant reads > '
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	355 '{max_var_mmqs}',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	356 'VarMapQual':
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	357 'Average mapping quality of variant reads < {min_var_mapqual}',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	358 'VarBaseQual':
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	359 'Average base quality of variant reads < {min_var_basequal}',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	360 'Strand':
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	361 'Strand representation of variant reads < {min_strandedness}',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	362 'RefAvgRL':
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	363 'Average clipped length of ref-supporting reads < '
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	364 '{min_ref_len}',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	365 'RefReadPos':
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	366 'Relative average read position < {min_ref_readpos}',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	367 'RefDist3':
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	368 'Average distance to effective 3\' end < {min_ref_dist3}',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	369 'RefMapQual':
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	370 'Average mapping quality of reference reads < '
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	371 '{min_ref_mapqual}',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	372 'RefBaseQual':
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	373 'Average base quality of ref-supporting reads < '
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	374 '{min_ref_basequal}',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	375 'RefMMQS':
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	376 'Average mismatch quality sum for ref-supporting reads > '
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	377 '{max_ref_mmqs}',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	378 'MMQSdiff':
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	379 'Mismatch quality sum difference (var - ref) > '
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	380 '{max_mmqs_diff}',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	381 'MinMMQSdiff':
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	382 'Mismatch quality sum difference (var - ref) < '
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	383 '{max_mmqs_diff}',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	384 'MapQualDiff':
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	385 'Mapping quality difference (ref - var) > {max_mapqual_diff}',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	386 'MaxBAQdiff':
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	387 'Average base quality difference (ref - var) > '
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	388 '{max_basequal_diff}',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	389 'ReadLenDiff':
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	390 'Average supporting read length difference (ref - var) > '
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	391 '{max_relative_len_diff}',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	392 }
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	393 for filter_id, description in varscan_fpfilters.items():
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	394 header.filters.add(filter_id, None, None, description)
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	395
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	396 def _add_indel_info_flag_to_header(self, header):
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	397 header.info.add(
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	398 'INDEL', 0, 'Flag', 'Indicates that the variant is an INDEL'
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	399 )
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	400
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	401 def _compile_common_header(self, varcall_template, no_filters=False):
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	402 # fix the header generated by VarScan
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	403 # by adding reference and contig information
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	404 common_header = pysam.VariantHeader()
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	405 common_header.add_meta('reference', value=self.ref_genome)
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	406 self._add_ref_contigs_to_header(common_header)
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	407 if not no_filters:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	408 # add filter info
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	409 self._add_filters_to_header(common_header)
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	410 # change the source information
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	411 common_header.add_meta('source', value='varscan.py')
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	412 # declare an INDEL flag for record INFO fields
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	413 self._add_indel_info_flag_to_header(common_header)
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	414 # take the remaining metadata from the template header produced by
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	415 # VarScan
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	416 with pysam.VariantFile(varcall_template, 'r') as original_data:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	417 varscan_header = original_data.header
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	418 for sample in varscan_header.samples:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	419 common_header.samples.add(sample)
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	420 common_header.merge(varscan_header)
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	421 return common_header
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	422
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	423 def pileup_masker(self, mask):
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	424 def apply_mask_on_pileup(piled_items):
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	425 for item, status in zip(piled_items, mask):
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	426 if status:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	427 yield item
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	428 return apply_mask_on_pileup
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	429
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	430 def get_allele_specific_pileup_column_stats(
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	431 self, allele, pile_column, ref_fetch
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	432 ):
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	433 # number of reads supporting the given allele on
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	434 # forward and reverse strand, and in total
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	435 var_reads_plus = var_reads_minus = 0
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	436 var_supp_read_mask = []
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	437 for base in pile_column.get_query_sequences():
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	438 if base == allele:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	439 # allele supporting read on + strand
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	440 var_reads_plus += 1
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	441 var_supp_read_mask.append(True)
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	442 elif base.upper() == allele:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	443 # allele supporting read on - strand
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	444 var_reads_minus += 1
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	445 var_supp_read_mask.append(True)
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	446 else:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	447 var_supp_read_mask.append(False)
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	448 var_reads_total = var_reads_plus + var_reads_minus
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	449
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	450 if var_reads_total == 0:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	451 # No stats without reads!
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	452 return None
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	453
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	454 var_supp_only = self.pileup_masker(var_supp_read_mask)
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	455
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	456 # average mapping quality of the reads supporting the
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	457 # given allele
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	458 avg_mapping_quality = sum(
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	459 mq for mq in var_supp_only(
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	460 pile_column.get_mapping_qualities()
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	461 )
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	462 ) / var_reads_total
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	463
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	464 # for the remaining stats we need access to complete
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	465 # read information
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	466 piled_reads = [
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	467 p for p in var_supp_only(pile_column.pileups)
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	468 ]
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	469 assert len(piled_reads) == var_reads_total
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	470 sum_avg_base_qualities = 0
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	471 sum_dist_from_center = 0
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	472 sum_dist_from_3prime = 0
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	473 sum_clipped_length = 0
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	474 sum_unclipped_length = 0
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	475 sum_num_mismatches_as_fraction = 0
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	476 sum_mismatch_qualities = 0
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	477
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	478 for p in piled_reads:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	479 sum_avg_base_qualities += sum(
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	480 p.alignment.query_qualities
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	481 ) / p.alignment.infer_query_length()
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	482 sum_clipped_length += p.alignment.query_alignment_length
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	483 unclipped_length = p.alignment.infer_read_length()
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	484 sum_unclipped_length += unclipped_length
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	485 read_center = p.alignment.query_alignment_length / 2
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	486 sum_dist_from_center += 1 - abs(
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	487 p.query_position - read_center
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	488 ) / read_center
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	489 if p.alignment.is_reverse:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	490 sum_dist_from_3prime += p.query_position / unclipped_length
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	491 else:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	492 sum_dist_from_3prime += 1 - p.query_position / unclipped_length
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	493
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	494 sum_num_mismatches = 0
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	495 for qpos, rpos in p.alignment.get_aligned_pairs():
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	496 if qpos is not None and rpos is not None:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	497 if p.alignment.query_sequence[qpos] != ref_fetch(
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	498 rpos, rpos + 1
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	499 ).upper(): # ref bases can be lowercase!
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	500 sum_num_mismatches += 1
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	501 sum_mismatch_qualities += p.alignment.query_qualities[
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	502 qpos
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	503 ]
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	504 sum_num_mismatches_as_fraction += (
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	505 sum_num_mismatches / p.alignment.query_alignment_length
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	506 )
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	507 avg_basequality = sum_avg_base_qualities / var_reads_total
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	508 avg_pos_as_fraction = sum_dist_from_center / var_reads_total
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	509 avg_num_mismatches_as_fraction = (
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	510 sum_num_mismatches_as_fraction / var_reads_total
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	511 )
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	512 avg_sum_mismatch_qualities = sum_mismatch_qualities / var_reads_total
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	513 avg_clipped_length = sum_clipped_length / var_reads_total
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	514 avg_distance_to_effective_3p_end = (
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	515 sum_dist_from_3prime / var_reads_total
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	516 )
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	517
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	518 return (
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	519 avg_mapping_quality,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	520 avg_basequality,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	521 var_reads_plus,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	522 var_reads_minus,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	523 avg_pos_as_fraction,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	524 avg_num_mismatches_as_fraction,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	525 avg_sum_mismatch_qualities,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	526 avg_clipped_length,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	527 avg_distance_to_effective_3p_end
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	528 )
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	529
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	530 def _postprocess_variant_records(self, invcf,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	531 min_var_count2, min_var_count2_lc,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	532 min_var_freq2, max_somatic_p,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	533 max_somatic_p_depth,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	534 min_ref_readpos, min_var_readpos,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	535 min_ref_dist3, min_var_dist3,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	536 min_ref_len, min_var_len,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	537 max_relative_len_diff,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	538 min_strandedness, min_strand_reads,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	539 min_ref_basequal, min_var_basequal,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	540 max_basequal_diff,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	541 min_ref_mapqual, min_var_mapqual,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	542 max_mapqual_diff,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	543 max_ref_mmqs, max_var_mmqs,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	544 min_mmqs_diff, max_mmqs_diff,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	545 **args):
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	546 # set FILTER field according to Varscan criteria
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	547 # multiple FILTER entries must be separated by semicolons
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	548 # No filters applied should be indicated with MISSING
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	549
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	550 # since posterior filters are always applied to just one sample,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	551 # a better place to store the info is in the FT genotype field:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	552 # can be PASS, '.' to indicate that filters have not been applied,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	553 # or a semicolon-separated list of filters that failed
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	554 # unfortunately, gemini does not support this field
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	555
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	556 with ExitStack() as io_stack:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	557 normal_reads, tumor_reads = (
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	558 io_stack.enter_context(
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	559 pysam.Samfile(fn, 'rb')) for fn in self.bam_input_files
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	560 )
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	561 refseq = io_stack.enter_context(pysam.FastaFile(self.ref_genome))
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	562 pileup_args = self._get_pysam_pileup_args()
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	563 for record in invcf:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	564 if any(len(allele) > 1 for allele in record.alleles):
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	565 # skip indel postprocessing for the moment
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	566 yield record
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	567 continue
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	568 # get pileup for genomic region affected by this variant
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	569 if record.info['SS'] == '2':
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	570 # a somatic variant => generate pileup from tumor data
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	571 pile = tumor_reads.pileup(
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	572 record.chrom, record.start, record.stop,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	573 **pileup_args
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	574 )
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	575 sample_of_interest = 'TUMOR'
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	576 elif record.info['SS'] in ['1', '3']:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	577 # a germline or LOH variant => pileup from normal data
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	578 pile = normal_reads.pileup(
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	579 record.chrom, record.start, record.stop,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	580 **pileup_args
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	581 )
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	582 sample_of_interest = 'NORMAL'
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	583 else:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	584 # TO DO: figure out if there is anything interesting to do
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	585 # for SS status codes 0 (reference) and 5 (unknown)
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	586 yield record
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	587 continue
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	588
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	589 # apply false-positive filtering a la varscan fpfilter
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	590 # find the variant site in the pileup columns
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	591 for pile_column in pile:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	592 if pile_column.reference_pos == record.start:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	593 break
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	594 # extract required information
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	595 # overall read depth at the site
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	596 read_depth = pile_column.get_num_aligned()
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	597 assert read_depth > 0
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	598 # no multiallelic sites in varscan
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	599 assert len(record.alleles) == 2
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	600 if record.samples[sample_of_interest]['RD'] > 0:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	601 ref_stats, alt_stats = [
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	602 self.get_allele_specific_pileup_column_stats(
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	603 allele,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	604 pile_column,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	605 partial(
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	606 pysam.FastaFile.fetch, refseq, record.chrom
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	607 )
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	608 )
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	609 for allele in record.alleles
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	610 ]
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	611 else:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	612 ref_stats = None
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	613 alt_stats = self.get_allele_specific_pileup_column_stats(
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	614 record.alleles[1],
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	615 pile_column,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	616 partial(pysam.FastaFile.fetch, refseq, record.chrom)
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	617 )
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	618 ref_count = 0
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	619 if ref_stats:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	620 ref_count = ref_stats[2] + ref_stats[3]
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	621 if ref_stats[1] < min_ref_basequal:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	622 record.filter.add('RefBaseQual')
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	623 if ref_count >= 2:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	624 if ref_stats[0] < min_ref_mapqual:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	625 record.filter.add('RefMapQual')
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	626 if ref_stats[4] < min_ref_readpos:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	627 record.filter.add('RefReadPos')
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	628 # ref_stats[5] (avg_num_mismatches_as_fraction
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	629 # is not a filter criterion in VarScan fpfilter
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	630 if ref_stats[6] > max_ref_mmqs:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	631 record.filter.add('RefMMQS')
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	632 if ref_stats[7] < min_ref_len:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	633 # VarScan fpfilter does not apply this filter
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	634 # for indels, but there is no reason
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	635 # not to do it.
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	636 record.filter.add('RefAvgRL')
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	637 if ref_stats[8] < min_ref_dist3:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	638 record.filter.add('RefDist3')
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	639 if alt_stats:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	640 alt_count = alt_stats[2] + alt_stats[3]
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	641 if (
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	642 alt_count < min_var_count2_lc
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	643 ) or (
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	644 read_depth >= max_somatic_p_depth and
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	645 alt_count < min_var_count2
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	646 ):
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	647 record.filter.add('VarCount')
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	648 if alt_count / read_depth < min_var_freq2:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	649 record.filter.add('VarFreq')
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	650 if alt_stats[1] < min_var_basequal:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	651 record.filter.add('VarBaseQual')
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	652 if alt_count > min_strand_reads:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	653 if (
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	654 alt_stats[2] / alt_count < min_strandedness
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	655 ) or (
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	656 alt_stats[3] / alt_count < min_strandedness
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	657 ):
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	658 record.filter.add('Strand')
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	659 if alt_stats[2] + alt_stats[3] >= 2:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	660 if alt_stats[0] < min_var_mapqual:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	661 record.filter.add('VarMapQual')
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	662 if alt_stats[4] < min_var_readpos:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	663 record.filter.add('VarReadPos')
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	664 # alt_stats[5] (avg_num_mismatches_as_fraction
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	665 # is not a filter criterion in VarScan fpfilter
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	666 if alt_stats[6] > max_var_mmqs:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	667 record.filter.add('VarMMQS')
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	668 if alt_stats[7] < min_var_len:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	669 # VarScan fpfilter does not apply this filter
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	670 # for indels, but there is no reason
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	671 # not to do it.
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	672 record.filter.add('VarAvgRL')
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	673 if alt_stats[8] < min_var_dist3:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	674 record.filter.add('VarDist3')
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	675 if ref_count >= 2 and alt_count >= 2:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	676 if (ref_stats[0] - alt_stats[0]) > max_mapqual_diff:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	677 record.filter.add('MapQualDiff')
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	678 if (ref_stats[1] - alt_stats[1]) > max_basequal_diff:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	679 record.filter.add('MaxBAQdiff')
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	680 mmqs_diff = alt_stats[6] - ref_stats[6]
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	681 if mmqs_diff < min_mmqs_diff:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	682 record.filter.add('MinMMQSdiff')
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	683 if mmqs_diff > max_mmqs_diff:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	684 record.filter.add('MMQSdiff')
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	685 if (
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	686 1 - alt_stats[7] / ref_stats[7]
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	687 ) > max_relative_len_diff:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	688 record.filter.add('ReadLenDiff')
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	689 else:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	690 # No variant-supporting reads for this record!
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	691 # This can happen in rare cases because of
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	692 # samtools mpileup issues, but indicates a
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	693 # rather unreliable variant call.
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	694 record.filter.add('VarCount')
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	695 record.filter.add('VarFreq')
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	696 yield record
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	697
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	698 def _indel_flagged_records(self, vcf):
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	699 for record in vcf:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	700 record.info['INDEL'] = True
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	701 yield record
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	702
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	703 def _merge_generator(self, vcf1, vcf2):
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	704 try:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	705 record1 = next(vcf1)
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	706 except StopIteration:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	707 for record2 in vcf2:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	708 yield record2
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	709 return
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	710 try:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	711 record2 = next(vcf2)
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	712 except StopIteration:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	713 yield record1
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	714 for record1 in vcf1:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	715 yield record1
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	716 return
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	717 while True:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	718 if (record1.start, record1.stop) < (record2.start, record2.stop):
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	719 yield record1
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	720 try:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	721 record1 = next(vcf1)
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	722 except StopIteration:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	723 yield record2
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	724 for record2 in vcf2:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	725 yield record2
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	726 return
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	727 else:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	728 yield record2
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	729 try:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	730 record2 = next(vcf2)
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	731 except StopIteration:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	732 yield record1
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	733 for record1 in vcf1:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	734 yield record1
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	735 return
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	736
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	737 def merge_and_postprocess(self, snps_out, indels_out=None,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	738 no_filters=False, **filter_args):
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	739 temporary_data = self.tmpfiles
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	740 self.tmpfiles = []
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	741 temporary_snp_files = [f + '.snp.vcf' for f in temporary_data]
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	742 temporary_indel_files = [f + '.indel.vcf' for f in temporary_data]
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	743
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	744 for f in temporary_data:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	745 try:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	746 os.remove(f)
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	747 except Exception:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	748 pass
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	749
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	750 def noop_gen(data, **kwargs):
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	751 for d in data:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	752 yield d
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	753
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	754 if no_filters:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	755 apply_filters = noop_gen
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	756 else:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	757 apply_filters = self._postprocess_variant_records
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	758
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	759 output_header = self._compile_common_header(
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	760 temporary_snp_files[0],
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	761 no_filters
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	762 )
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	763 if indels_out is None:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	764 with open(snps_out, 'w') as o:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	765 o.write(str(output_header).format(**filter_args))
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	766 for snp_f, indel_f in zip(
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	767 temporary_snp_files, temporary_indel_files
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	768 ):
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	769 with pysam.VariantFile(snp_f, 'r') as snp_invcf:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	770 # fix the input header on the fly
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	771 # to avoid Warnings from htslib about missing contig
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	772 # info
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	773 self._add_ref_contigs_to_header(snp_invcf.header)
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	774 self._add_filters_to_header(snp_invcf.header)
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	775 self._add_indel_info_flag_to_header(snp_invcf.header)
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	776 with pysam.VariantFile(indel_f, 'r') as indel_invcf:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	777 # fix the input header on the fly
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	778 # to avoid Warnings from htslib about missing
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	779 # contig info
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	780 self._add_ref_contigs_to_header(indel_invcf.header)
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	781 self._add_filters_to_header(indel_invcf.header)
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	782 self._add_indel_info_flag_to_header(
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	783 indel_invcf.header
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	784 )
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	785 for record in apply_filters(
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	786 self._merge_generator(
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	787 snp_invcf,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	788 self._indel_flagged_records(indel_invcf)
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	789 ),
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	790 **filter_args
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	791 ):
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	792 o.write(str(record))
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	793 try:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	794 os.remove(snp_f)
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	795 except Exception:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	796 pass
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	797 try:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	798 os.remove(indel_f)
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	799 except Exception:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	800 pass
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	801
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	802 else:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	803 with open(snps_out, 'w') as o:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	804 o.write(str(output_header).format(**filter_args))
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	805 for f in temporary_snp_files:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	806 with pysam.VariantFile(f, 'r') as invcf:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	807 # fix the input header on the fly
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	808 # to avoid Warnings from htslib about missing
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	809 # contig info and errors because of undeclared
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	810 # filters
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	811 self._add_ref_contigs_to_header(invcf.header)
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	812 self._add_filters_to_header(invcf.header)
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	813 for record in apply_filters(
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	814 invcf, **filter_args
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	815 ):
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	816 o.write(str(record))
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	817 try:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	818 os.remove(f)
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	819 except Exception:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	820 pass
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	821 with open(indels_out, 'w') as o:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	822 o.write(str(output_header))
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	823 for f in temporary_indel_files:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	824 with pysam.VariantFile(f, 'r') as invcf:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	825 # fix the input header on the fly
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	826 # to avoid Warnings from htslib about missing
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	827 # contig info and errors because of undeclared
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	828 # filters
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	829 self._add_ref_contigs_to_header(invcf.header)
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	830 self._add_filters_to_header(invcf.header)
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	831 self._add_indel_info_flag_to_header(invcf.header)
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	832 for record in apply_filters(
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	833 self._indel_flagged_records(invcf), **filter_args
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	834 ):
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	835 o.write(str(record))
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	836 try:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	837 os.remove(f)
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	838 except Exception:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	839 pass
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	840
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	841
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	842 def varscan_call(ref_genome, normal, tumor, output_path, **args):
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	843 """Preparse arguments and orchestrate calling and postprocessing."""
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	844
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	845 if args.pop('split_output'):
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	846 if '%T' in output_path:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	847 out = (
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	848 output_path.replace('%T', 'snp'),
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	849 output_path.replace('%T', 'indel')
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	850 )
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	851 else:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	852 out = (
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	853 output_path + '.snp',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	854 output_path + '.indel'
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	855 )
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	856 else:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	857 out = (output_path, None)
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	858
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	859 instance_args = {
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	860 k: args.pop(k) for k in [
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	861 'max_depth',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	862 'min_mapqual',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	863 'min_basequal',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	864 'threads',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	865 'verbose',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	866 'quiet'
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	867 ]
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	868 }
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	869 varscan_somatic_args = {
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	870 k: args.pop(k) for k in [
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	871 'normal_purity',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	872 'tumor_purity',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	873 'min_coverage',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	874 'min_var_count',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	875 'min_var_freq',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	876 'min_hom_freq',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	877 'somatic_p_value',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	878 'p_value'
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	879 ]
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	880 }
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	881
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	882 v = VarScanCaller(ref_genome, [normal, tumor], **instance_args)
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	883 v.varcall_parallel(**varscan_somatic_args)
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	884 v.merge_and_postprocess(out, *args)
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	885
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	886
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	887 if __name__ == '__main__':
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	888 p = argparse.ArgumentParser()
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	889 p.add_argument(
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	890 'ref_genome',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	891 metavar='reference_genome',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	892 help='the reference genome (in fasta format)'
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	893 )
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	894 p.add_argument(
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	895 '--normal',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	896 metavar='BAM_file', required=True,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	897 help='the BAM input file of aligned reads from the normal sample'
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	898 )
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	899 p.add_argument(
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	900 '--tumor',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	901 metavar='BAM_file', required=True,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	902 help='the BAM input file of aligned reads from the tumor sample'
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	903 )
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	904 p.add_argument(
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	905 '-o', '--ofile', required=True,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	906 metavar='OFILE', dest='output_path',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	907 help='Name of the variant output file. With --split-output, the name '
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	908 'may use the %%T replacement token or will be used as the '
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	909 'basename for the two output files to be generated (see '
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	910 '-s\|--split-output below).'
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	911 )
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	912 p.add_argument(
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	913 '-s', '--split-output',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	914 dest='split_output', action='store_true', default=False,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	915 help='indicate that separate output files for SNPs and indels '
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	916 'should be generated (original VarScan behavior). If specified, '
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	917 '%%T in the --ofile file name will be replaced with "snp" and '
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	918 '"indel" to generate the names of the SNP and indel output '
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	919 'files, respectively. If %%T is not found in the file name, it '
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	920 'will get interpreted as a basename to which ".snp"/".indel" '
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	921 'will be appended.'
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	922 )
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	923 p.add_argument(
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	924 '-t', '--threads',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	925 type=int, default=1,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	926 help='level of parallelism'
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	927 )
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	928 p.add_argument(
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	929 '-v', '--verbose',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	930 action='store_true',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	931 help='be verbose about progress'
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	932 )
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	933 p.add_argument(
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	934 '-q', '--quiet',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	935 action='store_true',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	936 help='suppress output from wrapped tools'
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	937 )
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	938 call_group = p.add_argument_group('Variant calling parameters')
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	939 call_group.add_argument(
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	940 '--normal-purity',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	941 dest='normal_purity', type=float,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	942 default=1.0,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	943 help='Estimated purity of the normal sample (default: 1.0)'
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	944 )
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	945 call_group.add_argument(
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	946 '--tumor-purity',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	947 dest='tumor_purity', type=float,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	948 default=1.0,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	949 help='Estimated purity of the tumor sample (default: 1.0)'
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	950 )
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	951 call_group.add_argument(
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	952 '--max-pileup-depth',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	953 dest='max_depth', type=int, default=8000,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	954 help='Maximum depth of generated pileups (samtools mpileup -d option; '
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	955 'default: 8000)'
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	956 )
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	957 call_group.add_argument(
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	958 '--min-basequal',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	959 dest='min_basequal', type=int,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	960 default=13,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	961 help='Minimum base quality at the variant position to use a read '
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	962 '(default: 13)'
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	963 )
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	964 call_group.add_argument(
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	965 '--min-mapqual',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	966 dest='min_mapqual', type=int,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	967 default=0,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	968 help='Minimum mapping quality required to use a read '
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	969 '(default: 0)'
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	970 )
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	971 call_group.add_argument(
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	972 '--min-coverage',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	973 dest='min_coverage', type=int,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	974 default=8,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	975 help='Minimum site coverage required in the normal and in the tumor '
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	976 'sample to call a variant (default: 8)'
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	977 )
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	978 call_group.add_argument(
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	979 '--min-var-count',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	980 dest='min_var_count', type=int,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	981 default=2,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	982 help='Minimum number of variant-supporting reads required to call a '
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	983 'variant (default: 2)'
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	984 )
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	985 call_group.add_argument(
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	986 '--min-var-freq',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	987 dest='min_var_freq', type=float,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	988 default=0.1,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	989 help='Minimum variant allele frequency for calling (default: 0.1)'
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	990 )
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	991 call_group.add_argument(
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	992 '--min-hom-freq',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	993 dest='min_hom_freq', type=float,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	994 default=0.75,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	995 help='Minimum variant allele frequency for homozygous call '
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	996 '(default: 0.75)'
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	997 )
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	998 call_group.add_argument(
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	999 '--p-value',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1000 dest='p_value', type=float,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1001 default=0.99,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1002 help='P-value threshold for heterozygous call (default: 0.99)'
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1003 )
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1004 call_group.add_argument(
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1005 '--somatic-p-value',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1006 dest='somatic_p_value', type=float,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1007 default=0.05,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1008 help='P-value threshold for somatic call (default: 0.05)'
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1009 )
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1010 filter_group = p.add_argument_group('Posterior variant filter parameters')
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1011 filter_group.add_argument(
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1012 '--no-filters',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1013 dest='no_filters', action='store_true',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1014 help='Disable all posterior variant filters. '
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1015 'If specified, all following options will be ignored'
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1016 )
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1017 filter_group.add_argument(
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1018 '--min-var-count2',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1019 dest='min_var_count2', type=int,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1020 default=4,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1021 help='Minimum number of variant-supporting reads (default: 4)'
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1022 )
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1023 filter_group.add_argument(
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1024 '--min-var-count2-lc',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1025 dest='min_var_count2_lc', type=int,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1026 default=2,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1027 help='Minimum number of variant-supporting reads when depth below '
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1028 '--somatic-p-depth (default: 2)'
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1029 )
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1030 filter_group.add_argument(
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1031 '--min-var-freq2',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1032 dest='min_var_freq2', type=float,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1033 default=0.05,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1034 help='Minimum variant allele frequency (default: 0.05)'
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1035 )
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1036 filter_group.add_argument(
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1037 '--max-somatic-p',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1038 dest='max_somatic_p', type=float,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1039 default=0.05,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1040 help='Maximum somatic p-value (default: 0.05)'
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1041 )
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1042 filter_group.add_argument(
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1043 '--max-somatic-p-depth',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1044 dest='max_somatic_p_depth', type=int,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1045 default=10,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1046 help='Depth required to run --max-somatic-p filter (default: 10)'
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1047 )
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1048 filter_group.add_argument(
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1049 '--min-ref-readpos',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1050 dest='min_ref_readpos', type=float,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1051 default=0.1,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1052 help='Minimum average relative distance of site from the ends of '
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1053 'ref-supporting reads (default: 0.1)'
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1054 )
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1055 filter_group.add_argument(
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1056 '--min-var-readpos',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1057 dest='min_var_readpos', type=float,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1058 default=0.1,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1059 help='Minimum average relative distance of site from the ends of '
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1060 'variant-supporting reads (default: 0.1)'
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1061 )
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1062 filter_group.add_argument(
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1063 '--min-ref-dist3',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1064 dest='min_ref_dist3', type=float,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1065 default=0.1,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1066 help='Minimum average relative distance of site from the effective '
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1067 '3\'end of ref-supporting reads (default: 0.1)'
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1068 )
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1069 filter_group.add_argument(
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1070 '--min-var-dist3',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1071 dest='min_var_dist3', type=float,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1072 default=0.1,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1073 help='Minimum average relative distance of site from the effective '
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1074 '3\'end of variant-supporting reads (default: 0.1)'
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1075 )
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1076 filter_group.add_argument(
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1077 '--min-ref-len',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1078 dest='min_ref_len', type=int,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1079 default=90,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1080 help='Minimum average trimmed length of reads supporting the ref '
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1081 'allele (default: 90)'
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1082 )
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1083 filter_group.add_argument(
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1084 '--min-var-len',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1085 dest='min_var_len', type=int,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1086 default=90,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1087 help='Minimum average trimmed length of reads supporting the variant '
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1088 'allele (default: 90)'
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1089 )
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1090 filter_group.add_argument(
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1091 '--max-len-diff',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1092 dest='max_relative_len_diff', type=float,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1093 default=0.25,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1094 help='Maximum average relative read length difference (ref - var; '
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1095 'default: 0.25)'
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1096 )
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1097 filter_group.add_argument(
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1098 '--min-strandedness',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1099 dest='min_strandedness', type=float,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1100 default=0.01,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1101 help='Minimum fraction of variant reads from each strand '
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1102 '(default: 0.01)'
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1103 )
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1104 filter_group.add_argument(
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1105 '--min-strand-reads',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1106 dest='min_strand_reads', type=int,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1107 default=5,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1108 help='Minimum allele depth required to run --min-strandedness filter '
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1109 '(default: 5)'
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1110 )
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1111 filter_group.add_argument(
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1112 '--min-ref-basequal',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1113 dest='min_ref_basequal', type=int,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1114 default=15,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1115 help='Minimum average base quality for the ref allele (default: 15)'
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1116 )
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1117 filter_group.add_argument(
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1118 '--min-var-basequal',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1119 dest='min_var_basequal', type=int,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1120 default=15,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1121 help='Minimum average base quality for the variant allele '
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1122 '(default: 15)'
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1123 )
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1124 filter_group.add_argument(
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1125 '--max-basequal-diff',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1126 dest='max_basequal_diff', type=int,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1127 default=50,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1128 help='Maximum average base quality diff (ref - var; default: 50)'
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1129 )
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1130 filter_group.add_argument(
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1131 '--min-ref-mapqual',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1132 dest='min_ref_mapqual', type=int,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1133 default=15,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1134 help='Minimum average mapping quality of reads supporting the ref '
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1135 'allele (default: 15)'
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1136 )
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1137 filter_group.add_argument(
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1138 '--min-var-mapqual',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1139 dest='min_var_mapqual', type=int,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1140 default=15,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1141 help='Minimum average mapping quality of reads supporting the variant '
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1142 'allele (default: 15)'
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1143 )
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1144 filter_group.add_argument(
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1145 '--max-mapqual-diff',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1146 dest='max_mapqual_diff', type=int,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1147 default=50,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1148 help='Maximum average mapping quality difference (ref - var; '
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1149 'default: 50)'
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1150 )
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1151 filter_group.add_argument(
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1152 '--max-ref-mmqs',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1153 dest='max_ref_mmqs', type=int,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1154 default=100,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1155 help='Maximum mismatch quality sum of reads supporting the ref '
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1156 'allele (default: 100)'
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1157 )
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1158 filter_group.add_argument(
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1159 '--max-var-mmqs',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1160 dest='max_var_mmqs', type=int,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1161 default=100,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1162 help='Maximum mismatch quality sum of reads supporting the variant '
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1163 'allele (default: 100)'
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1164 )
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1165 filter_group.add_argument(
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1166 '--min-mmqs-diff',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1167 dest='min_mmqs_diff', type=int,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1168 default=0,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1169 help='Minimum mismatch quality sum difference (var - ref; default: 0)'
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1170 )
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1171 filter_group.add_argument(
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1172 '--max-mmqs-diff',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1173 dest='max_mmqs_diff', type=int,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1174 default=50,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1175 help='Maximum mismatch quality sum difference (var - ref; default: 50)'
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1176 )
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1177 args = vars(p.parse_args())
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c iuc parents: diff changeset	1178 varscan_call(**args)

Mercurial > repos > iuc > varscan_somatic

annotate varscan.py @ 3:7903598ccbaf draft