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ZMUGHAL

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Emmanouil "Manolis" Maragkakis
and 1 contributors

NAME

CLIPSeqTools::Role::Option::ReferenceLibrary - Role to enable reading reference libraries with reads from the command line

SYNOPSIS

Role to enable reading reference libraries with reads from the command line

  Defines options.
      -r_driver <Str>          driver for database connection  for reference
                               library(eg. mysql, SQLite).
      -r_database <Str>        database name or path for reference library
                               (eg. SQLite).
      -r_table <Str>           database table for reference library.
      -r_host <Str>            hostname for database connection for reference
                               library.
      -r_user <Str>            username for database connection for reference
                               library.
      -r_password <Str>        password for database connection for reference
                               library.
      -r_records_class <Str>   type of records stored in database for
                               reference library (Default: GenOO::Data::DB::
                               DBIC::Species::Schema::SampleResultBase::v3).
      -r_filter <Filter>       filter library. Option can be given multiple
                               times.
                               Syntax: column_name="pattern"
                                 e.g. -filter deletion="def"
                                      -filter rmsk="undef"
                                 to keep reads with deletions and not repeat
                                 masked.
                                 e.g. -filter query_length=">31"
                                      -filter query_length="<=50"
                                 to keep reads longer than 31 and shorter or
                                 equal to 50.
                               Supports: >, >=, <, <=, =, !=, def, undef.

  Provides attributes.
      r_reads_collection      reads collection that is read from the specified
                              source.