Method: Cheripic::Cmd#argument_parser

Defined in:
lib/cheripic/cmd.rb

#argument_parser ⇒ Hash

trollop argument_parser for input args string and

Returns:

  • (Hash) —

    a hash of trollop option names as keys and user or default setting as values



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# File 'lib/cheripic/cmd.rb', line 40

def argument_parser
  cmds = self
  Trollop::Parser.new do
    version Cheripic::VERSION
    banner cmds.help_message
    opt :assembly, 'Assembly file in FASTA format',
        :short => '-f',
        :type => String
    opt :input_format, 'bulk and parent alignment file format types - set either pileup or bam or vcf',
        :short => '-F',
        :type => String,
        :default => 'pileup'
    opt :mut_bulk, 'Pileup or sorted BAM file alignments from mutant/trait of interest bulk 1',
        :short => '-a',
        :type => String
    opt :mut_bulk_vcf, 'vcf file for variants from mutant/trait of interest bulk 1',
        :type => String,
        :default => ''
    opt :bg_bulk, 'Pileup or sorted BAM file alignments from background/wildtype bulk 2',
        :short => '-b',
        :type => String
    opt :bg_bulk_vcf, 'vcf file for variants from background/wildtype bulk 2',
        :type => String,
        :default => ''
    opt :output, 'custom name tag to include in the output file name',
        :default => 'cheripic_results'
    opt :loglevel, 'Choose any one of "info / warn / debug" level for logs generated',
        :default => 'info'
    opt :hmes_adjust, 'factor added to snp count of each contig to adjust for hme score calculations',
        :type => Float,
        :default => 0.5
    opt :htlow, 'lower level for categorizing heterozygosity',
        :type => Float,
        :default => 0.25
    opt :hthigh, 'high level for categorizing heterozygosity',
        :type => Float,
        :default => 0.75
    opt :mindepth, 'minimum read depth at a position to consider for variant calls',
        :type => Integer,
        :default => 6
    opt :max_d_multiple, "multiplication factor for average coverage to calculate maximum read coverage
if set zero no calculation will be made from bam file.\nsetting this value will override user set max depth",
        :type => Integer,
        :default => 5
    opt :maxdepth, 'maximum read depth at a position to consider for variant calls
if set to zero no user max depth will be used',
        :type => Integer,
        :default => 0
    opt :min_non_ref_count, 'minimum read depth supporting non reference base at each position',
        :type => Integer,
        :default => 3
    opt :min_indel_count_support, 'minimum read depth supporting an indel at each position',
        :type => Integer,
        :default => 3
    opt :ambiguous_ref_bases, 'including variant at completely ambiguous bases in the reference',
        :type => String,
        :default => 'false'
    opt :mapping_quality, 'minimum mapping quality of read covering the position',
        :short => '-q',
        :type => Integer,
        :default => 20
    opt :base_quality, 'minimum base quality of bases covering the position',
        :short => '-Q',
        :type => Integer,
        :default => 15
    opt :noise, 'praportion of reads for a variant to conisder as noise',
        :type => Float,
        :default => 0.1
    opt :cross_type, 'type of cross used to generated mapping population - back or out',
        :type => String,
        :default => 'back'
    opt :use_all_contigs, 'option to select all contigs or only contigs containing variants for analysis',
        :type => String,
        :default => 'false'
    opt :include_low_hmes, 'option to include or discard variants from contigs with
low hme-score or bfr score to list in the final output',
        :type => String,
        :default => 'false'
    opt :polyploidy, 'Set if the data input is from polyploids',
        :type => String,
        :default => 'false'
    opt :mut_parent, 'Pileup or sorted BAM file alignments from mutant/trait of interest parent',
        :short => '-p',
        :type => String,
        :default => ''
    opt :bg_parent, 'Pileup or sorted BAM file alignments from background/wildtype parent',
        :short => '-r',
        :type => String,
        :default => ''
    opt :repeats_file, 'repeat masker output file for the assembly ',
        :short => '-R',
        :type => String,
        :default => ''
    opt :bfr_adjust, 'factor added to hemi snp frequency of each parent to adjust for bfr calculations',
        :type => Float,
        :default => 0.05
    opt :sel_seq_len, 'sequence length to print from either side of selected variants',
        :type => Integer,
        :default => 50
    opt :examples, 'shows some example commands with explanation'
  end
end