def __init__(self):
CommandLineApp.__init__(self)
op = self.option_parser
op.set_usage('usage: filter-sam.py')
op.add_option('-i',
'--infile',
dest='infile',
type='string',
default=None,
help='Input .sam file')
op.add_option('-o',
'--outfile',
dest='outfile',
type='string',
default=None,
help='Output .sam file')
op.add_option('-a',
'--bwa_alg',
dest='bwa_alg',
type='string',
default='',
help='Output .sam file')
op.add_option('-s',
'--use_stampy',
dest='use_stampy',
type='int',
default=0,
help='SAM file was mapped with stampy')
def __init__(self):
CommandLineApp.__init__(self)
#self.force_exit = False #enable this when profiling
op = self.option_parser
op.set_usage('usage: extract_ref_alleles -i indiv -d samdir -o outdir --parent1 parent1_genome --parent2 parent2_genome --chroms csv_list --verbosity')
op.add_option('-i', '--individual', dest='indiv', type='string', default=None,
help='Name of individual. E.g. for sam file aln_indivA6_AACGAG_sec.sam.gz, indiv would be "indivA6_AACGAG"')
op.add_option('-d', '--samdir', dest='samdir', type='string', default='',
help='Directory containing SAM files')
op.add_option('-o', '--outdir', dest='outdir', type='string', default='',
help='Output directory')
op.add_option('--parent1', dest='parent1', type='string', default=None,
help='Parent 1 genome file to align against')
op.add_option('--parent2', dest='parent2', type='string', default=None,
help='Parent 2 genome file to align against')
op.add_option('--chroms', dest='chroms', type='string', default=None,
help='chromosomes desired')
op.add_option('--verbosity', action="store_true", dest='verbosity', default=False,
help="make lots of noise")
def __init__(self):
CommandLineApp.__init__(self)
op = self.option_parser
op.set_usage('usage: parse_and_map -[npm] -i reads.fq -b barcodes --parent1 parent1_genome --parent2 parent2_genome')
op.add_option('-i', '--raw-data', dest='raw_data_file', type='string', default=None,
help='Raw Illumina data file')
op.add_option('-b', '--barcodes', dest='barcodes_file', type='string', default=None,
help='Barcodes file')
op.add_option('--re_cutter', dest='re_cutter', type='string', default=None,
help='restriction enzyme')
op.add_option('--linker_system', dest='linker_system', type='string', default=None,
help='linker system')
op.add_option('--parent1', dest='parent1', type='string', default=None,
help='Parent 1 genome file to align against')
op.add_option('--parent2', dest='parent2', type='string', default=None,
help='Parent 2 genome file to align against')
op.add_option('-m', '--map-only', dest='map_only', default=False, action='store_true',
help='Just map data?')
op.add_option('-n', '--num-ind', dest='num_ind', default=None, type='int',
help='Number of individuals to map')
op.add_option('-p', '--parse-only', dest='parse_only', default=False, action='store_true',
help='Just parse data?')
def __init__(self):
CommandLineApp.__init__(self)
op = self.option_parser
op.set_usage('usage: parse_and_map -[npm] -i reads.fq -b barcodes --parent1 parent1_genome --parent2 parent2_genome')
op.add_option('-i', '--raw-data', dest='raw_data_file', type='string', default=None,
help='Raw Illumina data file')
op.add_option('-b', '--barcodes', dest='barcodes_file', type='string', default=None,
help='Barcodes file')
op.add_option('--re_cutter', dest='re_cutter', type='string', default=None,
help='restriction enzyme')
op.add_option('--linker_system', dest='linker_system', type='string', default=None,
help='linker system')
op.add_option('--parent1', dest='parent1', type='string', default=None,
help='Parent 1 genome file to align against')
op.add_option('--parent2', dest='parent2', type='string', default=None,
help='Parent 2 genome file to align against')
op.add_option('-m', '--map-only', dest='map_only', default=False, action='store_true',
help='Just map data?')
op.add_option('-n', '--num-ind', dest='num_ind', default=None, type='int',
help='Number of individuals to map')
op.add_option('-p', '--parse-only', dest='parse_only', default=False, action='store_true',
help='Just parse data?')
def __init__(self):
CommandLineApp.__init__(self)
op = self.option_parser
op.set_usage('usage: filter-sam.py')
op.add_option('-i', '--infile', dest='infile', type='string', default=None,
help='Input .sam file')
op.add_option('-o', '--outfile', dest='outfile', type='string', default=None,
help='Output .sam file')
def __init__(self):
CommandLineApp.__init__(self)
op = self.option_parser
op.set_usage(
'usage: extract_ref_alleles -i indiv -d samdir -o outdir --parent1 parent1_genome --parent2 parent2_genome --chroms csv_list --verbosity'
)
op.add_option(
'-i',
'--individual',
dest='indiv',
type='string',
default=None,
help=
'Name of individual. E.g. for sam file aln_indivA6_AACGAG_sec.sam.gz, indiv would be "indivA6_AACGAG"'
)
op.add_option('-d',
'--samdir',
dest='samdir',
type='string',
default='',
help='Directory containing SAM files')
op.add_option('-o',
'--outdir',
dest='outdir',
type='string',
default='',
help='Output directory')
op.add_option('--parent1',
dest='parent1',
type='string',
default=None,
help='Parent 1 genome file to align against')
op.add_option('--parent2',
dest='parent2',
type='string',
default=None,
help='Parent 2 genome file to align against')
op.add_option('--chroms',
dest='chroms',
type='string',
default=None,
help='chromosomes desired')
op.add_option('--verbosity',
action="store_true",
dest='verbosity',
default=False,
help="make lots of noise [default]")
def __init__(self):
CommandLineApp.__init__(self)
op = self.option_parser
op.set_usage('usage: stitchContigs.py')
op.add_option('-c',
'--chrom',
dest='chrom',
type='string',
default='X',
help='chromosome')
def __init__(self):
CommandLineApp.__init__(self)
op = self.option_parser
op.set_usage('usage: create_stats -i reads.fq -b barcodes')
op.add_option('-i', '--raw-data', dest='raw_data_file', type='string', default=None,
help='Raw Illumina data file')
op.add_option('-b', '--barcodes', dest='barcodes_file', type='string', default=None,
help='Barcodes file')
def __init__(self):
CommandLineApp.__init__(self)
op = self.option_parser
op.set_usage('usage: filter-sam.py')
op.add_option('-i', '--infile', dest='infile', type='string', default=None,
help='Input .sam file')
op.add_option('-o', '--outfile', dest='outfile', type='string', default=None,
help='Output .sam file')
op.add_option('-a', '--bwa_alg', dest='bwa_alg', type='string', default='',
help='Output .sam file')
op.add_option('-s', '--use_stampy', dest='use_stampy', type='int', default=0,
help='SAM file was mapped with stampy')
def __init__(self):
CommandLineApp.__init__(self)
argv = sys.argv
op = self.option_parser
usage = 'usage: %s tree1 tree2' % os.path.basename(argv[0])
op.set_usage(usage)
op.add_option('-n', '--dry-run', dest='dry_run', default=False, action='store_true',
help="Just print shell commands; don't actually do anything")
op.add_option('-d', '--delete', dest='delete', default=False, action='store_true',
help="Delete files from receiver that do not exist in sender")
op.add_option('--delete-only', dest='delete_only', default=False, action='store_true',
help="Delete files from receiver that do not exist in sender, and do not copy files.")
def __init__(self):
CommandLineApp.__init__(self)
op = self.option_parser
op.set_usage('usage: filter-sam.py')
op.add_option('-i',
'--infile',
dest='infile',
type='string',
default=None,
help='Input .sam file')
op.add_option('-o',
'--outfile',
dest='outfile',
type='string',
default=None,
help='Output .sam file')
def __init__(self):
CommandLineApp.__init__(self)
op = self.option_parser
usage = []
usage.append("%s --snptest --controls 58C --cases NBS --chrom '21 22' --local"
% __progname__)
usage.append('%s --cohorts "58C NBS POBI" --snpfile ~/wtccc2/celine-snps-ill'% __progname__)
op.set_usage('\n' + '\n'.join(usage))
op.add_option('--pca', dest='pca', default=False, action='store_true',
help='Perform PCA of selected cohorts')
op.add_option('', '--make-gen', dest='make_gen', default=False, action='store_true',
help="Convert to .gen input data format used by chiamo and related software")
op.add_option('--snptest', dest='snptest', default=False, action='store_true',
help='Perform association tests of selected cases & controls')
op.add_option('--sstat', dest='sstat', default=False, action='store_true',
help='Compute summary statistics for selected cohorts')
op.add_option('--cohorts', dest='cohorts', type='string', default='',
help='Space-separated list of cohorts')
op.add_option('--cases', dest='cases', type='string', default='',
help='Space-separated list of case cohorts')
op.add_option('--controls', dest='controls', type='string', default='',
help='Space-separated list of control cohorts')
op.add_option('--outfile', dest='outfile', type='string', default=None,
help='Name of output file')
op.add_option('--local', dest='local', default=False, action='store_true',
help='Run PCA / snptest locally, not on the cluster')
op.add_option('--chrom', dest='chroms', type='string', default=None,
help='Chromosomes to include (space-separated; default is 1-22)')
op.add_option('--snpfile', dest='snpfile', type='string', default=None,
help='File containing SNPs to use (.map format)')
op.add_option('--samplefile', dest='samplefile', type='string', default=None,
help='sample file to use (chiamo .sample format; defaults to WTCCC2 cohort sample file)')
op.add_option('--snptest-opts', dest='snptest_opts', type='string', default='',
help='Options to pass to snptest')
op.add_option('--factorfile', dest='factor_file', type='string', default=None,
help='File containing integer factor classifying individuals (minimum factor level is 1)')
op.add_option('--exclude', dest='excludefile', type='string', default=None,
help='File containing IDs of individuals to exclude' + \
'in addition to project exclusions (one ID per line)')
op.add_option('-n', dest='dry_run', default=False, action='store_true',
help="Don't actually do anything, just print commands")
op.add_option('', '--messy', dest='messy', default=False, action='store_true',
help="Do not remove intermediate files")
op.add_option('--platform', dest='platform', type='string', default=None)
def __init__(self):
CommandLineApp.__init__(self)
op = self.option_parser
usage = 'usage: %s file [file ...]' % os.path.basename(sys.argv[0])
op.set_usage(usage)
op.add_option('-f', '--field', dest='field', default=None, type='int',
help='Column index of field on which comparison of lines is to be based')
op.add_option('-d', '--delimiter', dest='delim', default=None, type='string',
help='Field delimiter (default is <TAB>)')
op.add_option('-i', '--inplace', dest='inplace', default=False, action='store_true',
help='Overwrite input files')
op.add_option('-o', '--out', dest='outdir', default='.', type='string',
help='Directory into which output files will be saved.' +\
'Defaults to current directory.' +\
'The output files are given the name of the corresponding ' + \
'input file, with the suffix .insect')
op.add_option('-u', '--unique', dest='unique', default=False, action='store_true',
help='Restrict keys to unique values before insecting. ' + \
'Duplicate keys result in an error unless this option is in force.')
def __init__(self):
CommandLineApp.__init__(self)
#self.force_exit = False #enable this when profiling
op = self.option_parser
op.set_usage('usage: extract_ref_alleles -i indiv -d samdir -o outdir --parent1 parent1_genome --parent2 parent2_genome --chroms csv_list --repeat_threshold AS-XS --verbosity')
op.add_option('-i', '--individual', dest='indiv', type='string', default=None,
help='Name of individual. E.g. for sam file aln_indivA6_AACGAG_sec.sam.gz, indiv would be "indivA6_AACGAG"')
op.add_option('-d', '--samdir', dest='samdir', type='string', default='',
help='Directory containing SAM files')
op.add_option('-o', '--outdir', dest='outdir', type='string', default='',
help='Output directory')
op.add_option('--parent1', dest='parent1', type='string', default=None,
help='Parent 1 genome file to align against')
op.add_option('--parent2', dest='parent2', type='string', default=None,
help='Parent 2 genome file to align against')
op.add_option('--chroms', dest='chroms', type='string', default=None,
help='chromosomes desired')
op.add_option('--verbosity', action="store_true", dest='verbosity', default=False,
help="make lots of noise")
op.add_option('--bwa_alg', dest='bwa_alg', type='string', default='',
help='BWA algorithm used to generate SAM files. It should be "aln" or "bwasw".')
op.add_option('--use_stampy', dest='use_stampy', type='int', default=0,
help='Was STAMPY used to generate SAM files? Set this to 1.')
op.add_option('--repeat_threshold', dest='AS_XS_threshold', type='int', default=6,
help='Minimum difference between top alignment and suboptimal alignment scores to keep')
def __init__(self):
CommandLineApp.__init__(self)
op = self.option_parser
usage = 'usage: [options] %s -i %s -o %s' % (
__progname__,
os.path.sep.join(['location','of','music', 'library']),
os.path.sep.join(['folder','to','receive','output']))
op.set_usage(usage)
op.add_option('-i', '--library', dest='libdir', type='string', default=None,
help='Location of root of music library')
op.add_option('-o', '--outdir', dest='outdir', type='string', default='.',
help='Folder to receive output, defaults to current folder.')
# op.add_option('-u', '--update', dest='update', default=False, action='store_true',
# help='Don\'t re-scan whole library; instead update saved dbm data base.')
op.add_option('-f', '--libfile', dest='savefile', type='string', default='library.dbm',
help="Saved library file, defaults to 'library.dbm'")
op.add_option('-r', '--rockbox', dest='path_to_rockbox', type='string', default=None,
help='Location of rockbox digital audio player.')
op.add_option('', '--mintracks', dest='minArtistTracks', default=0, type='int',
help='Playlists and linkfiles will only be generated for artists with' + \
' more than this number of tracks in the library.')
op.add_option('', '--numtries', dest='numtries', default=3, type='int',
help='Number of times to attempt web query for an artist before giving up.')
op.add_option('', '--noweb', dest='query_lastfm', default=True, action='store_false',
help="Don't query last.fm similar artists.")
op.add_option('-n', '', dest='create_files', default=True, action='store_false',
help='Don\'t create any playlists or link files')
op.add_option('', '--version', dest='show_version', default=False, action='store_true',
help='Print out version information and exit')
op.add_option('', '--show-library', dest='show_tree', default=False, action='store_true',
help='Print sparse representation of library, and exit')
op.add_option('', '--show-tracks', dest='show_tracks', default=False, action='store_true',
help='Include track information when using --show')
op.add_option('', '--show-artists', dest='show_artists', default=False, action='store_true',
help='Print information on artists in library, and exit')
op.add_option('-s', '--musicspace', dest='music_space_file', type='string', default=None,
help='Music space file')
op.add_option('', '--show-musicspace', dest='show_musicspace', default=False, action='store_true',
help="Print summary of neighbouring artists in musicspace, and exit")
op.add_option('', '--dropoff', dest='musicspace_dropoff_param', type='float', default=3.0,
help="Parameter controlling rate at which probability of inclusion falls away with distance in music space. When generating playlists for artist X, a value of 0 means that all other artists will be included with equal probability; a value of more than 5 or so means that you'll rarely get anybody but X. Default is 3.0")
op.add_option('', '--create-musicspace-skeleton', dest='write_music_space', default=False,
action='store_true',
help='create skeleton music space spreadsheet file and exit')
op.add_option('-t', '--target', dest='target', default='rockbox', type='string',
help="Specify target platform: defaults to rockbox; " +\
"in the future you will be able to use --target=native " +\
"to create playlists and links for use on the local machine.")
def __init__(self):
CommandLineApp.__init__(self)
op = self.option_parser
op.set_usage('usage: stitchContigs.py')
op.add_option('-c', '--chrom', dest='chrom', type='string', default='X', help='chromosome')
def __init__(self):
CommandLineApp.__init__(self)
op = self.option_parser
usage = 'usage: [options] %s -i %s -o %s' % (
__progname__,
os.path.sep.join(['location', 'of', 'music', 'library']),
os.path.sep.join(['folder', 'to', 'receive', 'output']))
op.set_usage(usage)
op.add_option('-i',
'--library',
dest='libdir',
type='string',
default=None,
help='Location of root of music library')
op.add_option(
'-o',
'--outdir',
dest='outdir',
type='string',
default='.',
help='Folder to receive output, defaults to current folder.')
# op.add_option('-u', '--update', dest='update', default=False, action='store_true',
# help='Don\'t re-scan whole library; instead update saved dbm data base.')
op.add_option('-f',
'--libfile',
dest='savefile',
type='string',
default='library.dbm',
help="Saved library file, defaults to 'library.dbm'")
op.add_option('-r',
'--rockbox',
dest='path_to_rockbox',
type='string',
default=None,
help='Location of rockbox digital audio player.')
op.add_option('', '--mintracks', dest='minArtistTracks', default=0, type='int',
help='Playlists and linkfiles will only be generated for artists with' + \
' more than this number of tracks in the library.')
op.add_option(
'',
'--numtries',
dest='numtries',
default=3,
type='int',
help=
'Number of times to attempt web query for an artist before giving up.'
)
op.add_option('',
'--noweb',
dest='query_lastfm',
default=True,
action='store_false',
help="Don't query last.fm similar artists.")
op.add_option('-n',
'',
dest='create_files',
default=True,
action='store_false',
help='Don\'t create any playlists or link files')
op.add_option('',
'--version',
dest='show_version',
default=False,
action='store_true',
help='Print out version information and exit')
op.add_option('',
'--show-library',
dest='show_tree',
default=False,
action='store_true',
help='Print sparse representation of library, and exit')
op.add_option('',
'--show-tracks',
dest='show_tracks',
default=False,
action='store_true',
help='Include track information when using --show')
op.add_option('',
'--show-artists',
dest='show_artists',
default=False,
action='store_true',
help='Print information on artists in library, and exit')
op.add_option('-s',
'--musicspace',
dest='music_space_file',
type='string',
default=None,
help='Music space file')
op.add_option(
'',
'--show-musicspace',
dest='show_musicspace',
default=False,
action='store_true',
help="Print summary of neighbouring artists in musicspace, and exit"
)
op.add_option(
'',
'--dropoff',
dest='musicspace_dropoff_param',
type='float',
default=3.0,
help=
"Parameter controlling rate at which probability of inclusion falls away with distance in music space. When generating playlists for artist X, a value of 0 means that all other artists will be included with equal probability; a value of more than 5 or so means that you'll rarely get anybody but X. Default is 3.0"
)
op.add_option(
'',
'--create-musicspace-skeleton',
dest='write_music_space',
default=False,
action='store_true',
help='create skeleton music space spreadsheet file and exit')
op.add_option('-t', '--target', dest='target', default='rockbox', type='string',
help="Specify target platform: defaults to rockbox; " +\
"in the future you will be able to use --target=native " +\
"to create playlists and links for use on the local machine.")
def __init__(self):
CommandLineApp.__init__(self)
op = self.option_parser
op.set_usage('usage: parse_and_map -[npm] -i reads.fq -b barcodes --parent1 parent1_genome --parent2 parent2_genome')
op.add_option('-i', '--raw-data', dest='raw_data_file', type='string', default=None,
help='Raw Illumina data file')
op.add_option('-b', '--barcodes', dest='barcodes_file', type='string', default=None,
help='Barcodes file')
op.add_option('--re_cutter', dest='re_cutter', type='string', default=None,
help='restriction enzyme')
op.add_option('--linker_system', dest='linker_system', type='string', default=None,
help='linker system')
op.add_option('--parent1', dest='parent1', type='string', default=None,
help='Parent 1 genome file to align against')
op.add_option('--parent2', dest='parent2', type='string', default=None,
help='Parent 2 genome file to align against')
op.add_option('-m', '--map-only', dest='map_only', default=False, action='store_true',
help='Just map data?')
op.add_option('-n', '--num-ind', dest='num_ind', default=None, type='int',
help='Number of individuals to map')
op.add_option('-p', '--parse-only', dest='parse_only', default=False, action='store_true',
help='Just parse data?')
op.add_option('--bwa_alg', dest='bwa_alg', type='string', default="aln",
help='Algorithm for BWA mapping. Use aln or bwasw. This is ignored is use_stampy is 1.')
op.add_option('--bwa_threads', dest='bwa_threads', type='int', default=1,
help='Number of threads in the BWA multi-threading mode')
op.add_option('--use_stampy', dest='use_stampy', type='int', default=0,
help='Use stampy for mapping')
op.add_option('--stampy_premap_w_bwa', dest='stampy_premap_w_bwa', type='int', default=1,
help='Use BWA before running stampy for a speed boost.')
op.add_option('--stampy_pseudo_threads', dest='stampy_pseudo_threads', type='int', default=0,
help='Use qsub commands to split up stampy processes during mapping. NOT currently used.')
op.add_option('--dbg', dest='debug', default=False, action='store_true',
help='More verbose output and leaves temporary files instead of cleaning up')
op.add_option('--quality_trim_reads_thresh', dest='quality_trim_reads_thresh', default=None, type='int',
help='Illumina parsing only - what level should split files be quality trimmed at')
op.add_option('--quality_trim_reads_consec', dest='quality_trim_reads_consec', default=None, type='int',
help='Illumina parsing only - Minimum number of consecutive bases passing threshold values')
#Set divergence for mapping to a foreign reference (note: this is
#strongly recommended for divergences >3%, as it will automatically
#shut down BWA pre-mapping which otherwise cause occasional segfaults)
#(stampy default if .001)
op.add_option('--indiv_stampy_substitution_rate', dest='stampy_substitution_rate', type='float', default=0.001,
help='Set divergence for mapping to a foreign reference')
op.add_option('--indiv_mapq_filter', dest='mapq_filter', type='int', default=0,
help='Filter out poor alignments. Set this to 0 to skip.')
op.add_option('--new_parser', dest='new_parser', type='int', default=0,
help='Use a faster, experimental parser')
op.add_option('--new_parser_offset', dest='new_parser_offset', type='int', default=0,
help='When using new parser, how many base pairs after barcode to omit')
op.add_option('--new_parser_filter_out_seq', dest='new_parser_filter_out_seq', type='string',
default=None, help='A sequence to remove from parsed reads')
#Illumina indexing only
op.add_option('--index_file', dest='index_file', type='string', default=None,
help='When using Illumina indexes, this is the fastq/fasta file with the indexes.')
op.add_option('--index_barcodes', dest='index_barcodes', type='string', default=None,
help='When using Illumina indexes, this the the file with a listing of index sequences and labels')
def __init__(self):
CommandLineApp.__init__(self)
op = self.option_parser
op.set_usage(
'usage: parse_and_map -[npm] -i reads.fq -b barcodes --parent1 parent1_genome --parent2 parent2_genome'
)
op.add_option('-i',
'--raw-data',
dest='raw_data_file',
type='string',
default=None,
help='Raw Illumina data file')
op.add_option('-b',
'--barcodes',
dest='barcodes_file',
type='string',
default=None,
help='Barcodes file')
op.add_option('--re_cutter',
dest='re_cutter',
type='string',
default=None,
help='restriction enzyme')
op.add_option('--linker_system',
dest='linker_system',
type='string',
default=None,
help='linker system')
op.add_option('--parent1',
dest='parent1',
type='string',
default=None,
help='Parent 1 genome file to align against')
op.add_option('--parent2',
dest='parent2',
type='string',
default=None,
help='Parent 2 genome file to align against')
op.add_option('-m',
'--map-only',
dest='map_only',
default=False,
action='store_true',
help='Just map data?')
op.add_option('-n',
'--num-ind',
dest='num_ind',
default=None,
type='int',
help='Number of individuals to map')
op.add_option('-p',
'--parse-only',
dest='parse_only',
default=False,
action='store_true',
help='Just parse data?')
op.add_option(
'--bwa_alg',
dest='bwa_alg',
type='string',
default='aln',
help=
'Algorithm for BWA mapping. Use aln or bwasw. This is ignored is use_stampy is 1.'
)
op.add_option('--bwa_threads',
dest='bwa_threads',
type='int',
default=1,
help='Number of threads in the BWA multi-threading mode')
op.add_option('--use_stampy',
dest='use_stampy',
type='int',
default=0,
help='Use stampy for mapping')
op.add_option('--stampy_premap_w_bwa',
dest='stampy_premap_w_bwa',
type='int',
default=1,
help='Use BWA before running stampy for a speed boost.')
op.add_option(
'--stampy_pseudo_threads',
dest='stampy_pseudo_threads',
type='int',
default=0,
help=
'Use qsub commands to split up stampy processes during mapping. NOT currently used.'
)
op.add_option(
'--dbg',
dest='debug',
default=False,
action='store_true',
help=
'More verbose output and leaves temporary files instead of cleaning up'
)
op.add_option(
'--quality_trim_reads_thresh',
dest='quality_trim_reads_thresh',
default=None,
type='int',
help=
'Illumina parsing only - what level should split files be quality trimmed at'
)
op.add_option(
'--quality_trim_reads_consec',
dest='quality_trim_reads_consec',
default=None,
type='int',
help=
'Illumina parsing only - Minimum number of consecutive bases passing threshold values'
)
op.add_option(
'-S',
'--samtools_path',
dest='samtools_path',
default='samtools',
type='string',
help=
'Path to samtools 0.1.9 including the name of the binary at the end of the string'
)
#Set divergence for mapping to a foreign reference (note: this is
#strongly recommended for divergences >3%, as it will automatically
#shut down BWA pre-mapping which otherwise cause occasional segfaults)
#(stampy default if .001)
op.add_option('--indiv_stampy_substitution_rate',
dest='stampy_substitution_rate',
type='float',
default=0.001,
help='Set divergence for mapping to a foreign reference')
op.add_option(
'--indiv_mapq_filter',
dest='mapq_filter',
type='int',
default=0,
help='Filter out poor alignments. Set this to 0 to skip.')
op.add_option('--new_parser',
dest='new_parser',
type='int',
default=0,
help='Use a faster, experimental parser')
op.add_option(
'--new_parser_offset',
dest='new_parser_offset',
type='int',
default=0,
help=
'When using new parser, how many base pairs after barcode to omit')
op.add_option('--new_parser_filter_out_seq',
dest='new_parser_filter_out_seq',
type='string',
default=None,
help='A sequence to remove from parsed reads')
#Illumina indexing only
op.add_option(
'--index_file',
dest='index_file',
type='string',
default=None,
help=
'When using Illumina indexes, this is the fastq/fasta file with the indexes.'
)
op.add_option(
'--index_barcodes',
dest='index_barcodes',
type='string',
default=None,
help=
'When using Illumina indexes, this the the file with a listing of index sequences and labels'
)
