NAME

CLIPSeqTools::PreprocessApp::sam_to_sqlite - Load a SAM file in an SQLite database.

SYNOPSIS

clipseqtools-preprocess sam_to_sqlite [options/parameters]

DESCRIPTION

Store alignments from a SAM file into and SQLite database. If SAM tag XC:i exists it will be used as the copy number of the record.

OPTIONS

Input options.
  --sam_file <Str>       sam file to be stored in database. If not
                         specified STDIN is used.
  --records_class <Str>  type of records stored in SAM file. [Default:
                         GenOOx::Data::File::SAMstar::Record]

Database options.
  --database <Str>       database name or path. Will be created.
  --table <Str>          database table. Will be created.
  --drop <Str>           drop table if it already exists.

Other options.
  -v --verbose           print progress lines and extra information.
  -h -? --usage --help   print help message