repair(1) a component of subread suite


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:

The input file is in SAM format.
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.
Do not add dummy reads for singleton reads.
Do not include sequences and quality scores of reads in the output file.