NAME

       repair - a component of subread suite

USAGE

       repair [options] -i <input_file> -o <output_file>

       Required arguments:

       -i <string>
              Name of input file. BAM format by default.

       -o <string>
              Name of output file. The output file is in BAM format.

       Optional arguments:

       -S     The input file is in SAM format.

       -c     Compress  the  output  BAM  file.  This  will reduce the size of BAM file, but will
              increase the time of retrieving reads from BAM file.

       -T <int>
              Number of CPU threads. 8 by default.

       -d     Do not add dummy reads for singleton reads.

       -t     Do not include sequences and quality scores of reads in the output file.