NAME

annotate_db_sample_with_rmsk.pl

SYNOPSIS

annotate_db_sample_with_rmsk.pl [options/parameters]

Annotate a database table that contains alignments with Repeat Masker info. Add a column named rmsk which will be null if the alignment is not contained in a repeat region and not null otherwise..

  Input options for library.
      -driver <Str>          driver for database connection (eg. mysql, SQLite).
      -database <Str>        database name or path to database file for file based databases.
      -table <Str>           database table.
      -host <Str>            hostname for database connection.
      -user <Str>            username for database connection.
      -password <Str>        password for database connection.
      -records_class <Str>   type of records stored in database (Default: GenOO::Data::DB::DBIC::Species::Schema::SampleResultBase::v3).

  Other Input.
      -rmsk_file <Str>       BED file with the repeat masker regions.

  Flags.
      -drop                  flag that if set the program will attempt to drop the column if it already exists (not working for SQlite).

  Other options.
      -v                     verbosity. If used progress lines are printed.
      -h                     print help message
      -man                   show man page

DESCRIPTION

Annotate a database table that contains alignments with Repeat Masker info. Add a column named rmsk which will be null if the alignment is not contained in a repeat region and not null otherwise..