NAME

       repair  -  Find reads that are from the same pair in the input and then place them next to
       each other in the output. A dummy read is added for each singleton read that does not have
       a pair. The output file is compatible with featureCounts program

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.

       repair Version 2.0.0

              Find reads that are from the same pair in the input and then place them next

       to each other in the output. A dummy read is added for each singleton read that  does  not
       have a pair. The output file is compatible with featureCounts program.