casts = []
casts << {long: 'beg', short: 'b', type: 'uint', mandatory: false, default: nil, allowed: nil, disallowed: "0"}
casts << {long: 'end', short: 'e', type: 'uint', mandatory: false, default: nil, allowed: nil, disallowed: "0"}
casts << {long: 'forward', short: 'f', type: 'string', mandatory: false, default: nil, allowed: nil, disallowed: nil}
casts = []
casts << {long: 'beg', short: 'b', type: 'uint', mandatory: false, default: nil, allowed: nil, disallowed: "0"}
casts << {long: 'end', short: 'e', type: 'uint', mandatory: false, default: nil, allowed: nil, disallowed: "0"}
casts << {long: 'forward', short: 'f', type: 'string', mandatory: false, default: nil, allowed: nil, disallowed: nil}
casts << {long: 'reverse', short: 'r', type: 'string', mandatory: false, default: nil, allowed: nil, disallowed: nil}
casts << {long: 'reverse_rc', short: 'R', type: 'string', mandatory: false, default: nil, allowed: nil, disallowed: nil}
casts << {long: 'template_file', short: 't', type: 'file!', mandatory: false, default: nil, allowed: nil, disallowed: nil}
casts << {long: 'reverse', short: 'r', type: 'string', mandatory: false, default: nil, allowed: nil, disallowed: nil}
casts << {long: 'reverse_rc', short: 'R', type: 'string', mandatory: false, default: nil, allowed: nil, disallowed: nil}
casts << {long: 'template_file', short: 't', type: 'file!', mandatory: false, default: nil, allowed: nil, disallowed: nil}
Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
input.each_record do |record|
if record[:SEQ]
entry = Seq.new(seq: record[:SEQ])
unless options[:beg]
Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
input.each_record do |record|
if record[:SEQ]
entry = Seq.new(seq: record[:SEQ])
unless options[:beg]
compact.seq.delete! "-.~"
fmatch = compact.patmatch(options[:forward],
compact.seq.delete! "-.~"
fmatch = compact.patmatch(options[:forward],