14 	SUBREADputs("  Find reads that are from the same pair in the input and then place them next");  in print_usage_pairer()
15 	SUBREADputs("to each other in the output. A dummy read is added for each singleton read");  in print_usage_pairer()
16 	SUBREADputs("that does not have a pair. The output file is compatible with featureCounts");  in print_usage_pairer()
17 	SUBREADputs("program.");  in print_usage_pairer()
18 	SUBREADputs("");  in print_usage_pairer()
19 	SUBREADputs("Usage:");  in print_usage_pairer()
20 	SUBREADputs("");  in print_usage_pairer()
21 	SUBREADputs("  ./repair [options] -i <input_file> -o <output_file>\n");  in print_usage_pairer()
22 	SUBREADputs("");  in print_usage_pairer()
23 	SUBREADputs("Required arguments:");  in print_usage_pairer()
24 	SUBREADputs("");  in print_usage_pairer()
25 	SUBREADputs("  -i <string>  Name of input file. BAM format by default.");  in print_usage_pairer()
26 	SUBREADputs("");  in print_usage_pairer()
27 	SUBREADputs("  -o <string>  Name of output file. The output file is in BAM format.");  in print_usage_pairer()
28 	SUBREADputs("");  in print_usage_pairer()
29 	SUBREADputs("Optional arguments:");  in print_usage_pairer()
30 	SUBREADputs("");  in print_usage_pairer()
31 	SUBREADputs("  -S           The input file is in SAM format.");  in print_usage_pairer()
32 	SUBREADputs("");  in print_usage_pairer()
33 	SUBREADputs("  -c           Compress the output BAM file. This will reduce the size of BAM");  in print_usage_pairer()
34 	SUBREADputs("               file, but will increase the time of retrieving reads from BAM");  in print_usage_pairer()
35 	SUBREADputs("               file.");  in print_usage_pairer()
36 	SUBREADputs("");  in print_usage_pairer()
37 	SUBREADputs("  -T <int>     Number of CPU threads. 8 by default.");  in print_usage_pairer()
38 	SUBREADputs("");  in print_usage_pairer()
39 	SUBREADputs("  -d           Do not add dummy reads for singleton reads.");  in print_usage_pairer()
40 	SUBREADputs("");  in print_usage_pairer()
41 	SUBREADputs("  -t           Do not include sequences and quality scores of reads in the");  in print_usage_pairer()
42 	SUBREADputs("               output file.");  in print_usage_pairer()
43 	SUBREADputs("");  in print_usage_pairer()