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.