NAME

load_sam_to_sqlite_database.pl

SYNOPSIS

load_sam_to_sqlite_database.pl [options/parameters]

Store alignments from a SAM file into and SQlite database. If exists tag XC:i is used as copy number for the record.

Input options.
    -sam_file <Str>          sam file that will be stored in the database. If not specified STDIN is used.
    -sam_record_class <Str>  type of records stored in the SAM file (Default: GenOOx::Data::File::SAMstar::Record)
    
Output options.
    -database <Str>        database name or path to database file for file based databases.
    -table <Str>           database table.
    -drop <Str>            flag that if set drops the database table if it already exists.

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

DESCRIPTION

Store alignments from a SAM file into and SQlite database. If exists tag XC:i is used as copy number for the record.