repair1

Overview

repair Version 2.0.4

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.