comparison tools/naive_variant_caller.py @ 12:ac0235d2d459 draft

planemo upload for repository https://github.com/blankenberg/tools-blankenberg/tree/master/tools/naive_variant_caller commit ce964ed3ab7e390754fa03bb32a593fbe79dcf04

11:8af4e7a4d041

#Dan Blankenberg
import sys
import optparse

from pyBamParser.bam import Reader
from pyBamTools.genotyping.naive import VCFReadGroupGenotyper

def main():
    #Parse Command Line
    parser = optparse.OptionParser()
    parser.add_option( '-b', '--bam', dest='bam_file', action='append', type="string", default=[], help='BAM filename, optionally index filename. Multiple allowed.' )

    parser.add_option( '-m', '--min_mapping_quality', dest='min_mapping_quality', action='store', type="int", default=None, help='Minimum mapping.' )
    parser.add_option( '-t', '--coverage_dtype', dest='coverage_dtype', action='store', type="string", default=None, help='dtype to use for coverage array' )
    parser.add_option( '--allow_out_of_bounds_positions', dest='allow_out_of_bounds_positions', action='store_true', default = False, help='Allows out of bounds positions to not throw fatal errors' )
    parser.add_option( '--safe', dest='safe', action='store_true', default = False, help='Perform checks to prevent certain errors. Is slower.' )
    parser.add_option( '--region', dest='region', action='append', type="string", default=[], help='region' )
    (options, args) = parser.parse_args()
    
    if len( options.bam_file ) == 0:
        print >>sys.stderr, 'You must provide at least one bam (-b) file.'
        parser.print_help( sys.stderr )
        sys.exit( 1 )

12:ac0235d2d459

#!/usr/bin/env python
#Dan Blankenberg
import sys
import optparse

from pyBamParser.bam import Reader
from pyBamTools.genotyping.naive import VCFReadGroupGenotyper, PROGRAM_NAME, PROGRAM_VERSION

def main():
    #Parse Command Line
    parser = optparse.OptionParser()
    parser.add_option( '-b', '--bam', dest='bam_file', action='append', type="string", default=[], help='BAM filename, optionally index filename. Multiple allowed.' )

    parser.add_option( '-m', '--min_mapping_quality', dest='min_mapping_quality', action='store', type="int", default=None, help='Minimum mapping.' )
    parser.add_option( '-t', '--coverage_dtype', dest='coverage_dtype', action='store', type="string", default=None, help='dtype to use for coverage array' )
    parser.add_option( '--allow_out_of_bounds_positions', dest='allow_out_of_bounds_positions', action='store_true', default = False, help='Allows out of bounds positions to not throw fatal errors' )
    parser.add_option( '--safe', dest='safe', action='store_true', default = False, help='Perform checks to prevent certain errors. Is slower.' )
    parser.add_option( '--region', dest='region', action='append', type="string", default=[], help='region' )
    parser.add_option( '', '--version', dest='version', action='store_true', default = False, help='Report version and quit' )
    (options, args) = parser.parse_args()
    
    if options.version:
        print "%s version %s" % ( PROGRAM_NAME, PROGRAM_VERSION )
        sys.exit(0)
    
    if len( options.bam_file ) == 0:
        print >>sys.stderr, 'You must provide at least one bam (-b) file.'
        parser.print_help( sys.stderr )
        sys.exit( 1 )