This mode is used to converts a compact alignment to to plain text. It is implemented by edu.cornell.med.icb.goby.modes.AlignmentToTextMode.java.
Mode Parameters
The following options are available in this mode
| Flag | Arguments | Required | Description |
|---|---|---|---|
(-o|--output) | output | no | The alignments in text format |
n/a | input | yes | The compact alignment file to read as input. |
(-f|--format) | format | no | Format of the output file (plain, SAM). |
(-l|--constant-read-length) | constant-read-length | no | Use this number as read length for every read when the query length is not included in the alignment header. |
(-r|--include-reference-names) | include-reference-names | no | When provided, only write counts for reference identifiers listed in this comma separated list. To process only counts for chromosome 19 and 1, if sequences are identified by 1 and 19, use: --include-reference-names 1,19 |
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