This mode is used to extract reads from a SAM/BAM file. It is implemented by edu.cornell.med.icb.goby.modes.SamExtractReadsMode.java.
Mode Parameters
The following options are available in this mode
| Flag | Arguments | Required | Description |
|---|---|---|---|
(-o|--output) | output | no | Where the output will be written. |
n/a | input | yes | The SAM input file. |
--quality-encoding | quality-encoding | no | The encoding for quality scores. The default quality encoding is to not convert the characters (BAM encoding). Valid encodings include BAM, Illumina, Sanger and Solexa. Default value: BAM |
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