NAME

annotate_db_sample_with_deletion.pl

SYNOPSIS

annotate_db_sample_with_deletion.pl [options/parameters]

Annotate a database table that contains alignments with Repeat Masker info. Add a column named deletion 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).

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 deletion which will be null if the alignment is not contained in a repeat region and not null otherwise..