repair(1) 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.