This mode is used to convert a Last MAF file to the alignment compact format. Also converts the
associated Last COUNTS file (one line per query and count) to the alignment too-many-hits format. It is implemented by edu.cornell.med.icb.goby.modes.LastToCompactMode.java.
Mode Parameters
The following options are available in this mode
| Flag | Arguments | Required | Description |
|---|---|---|---|
(-i|--input) | input | yes | The LAST alignment file to convert to compact alignment format. By default, both the MAF and COUNTS files associated with this parameter are converted. No extension is required; it is assumed to be either “.maf” or “.counts”. |
(-o|--output) | output | yes | The output path and basename to write the compact format to. |
(-g|--genome-cache) | genome-cache | no | The genome cache basename. This argument is required when aligning color space with last, in order to translate color-space variations to base space variations. |
(-q|--query-ids) | query-reads-ids | no | A compact file describing reads which provides identifiers for each read. If provided, read identifiers are propagated to the alignment header. |
(-t|--target-ids) | target-reference-ids | no | A compact file describing targets which provides identifiers for each target sequence. If provided, target identifiers are propagated to the alignment header. |
--propagate-query-ids | n/a | no | When this switch is provided, propagate query ids if provided in the compact file designated by the query-ids option. The default is false since query ids are generally not useful and can consume a large amount of storage. |
--propagate-target-ids | propagate-target-ids | no | When this switch is provided, propagate target ids if provided in the compact file designated by the target-ids option. The default is true since target ids are quite useful and not very many. |
(-f|--read-index-filter) | read-index-filter | no | The name of a read index set with multiplicy information. When provided, last-to-compact appends exactly m identical entries for a read with index |
--ambiguity-threshold | ambiguity-threshold | no | Maximum number of locations that a read can match to be included in the alignment entries. |
(-p|--quality-filter-parameters) | quality-filter-parameters | no | Parameters to configure the quality filter. |
--only-maf | n/a | no | When this switch is provided, only convert the MAF file. |
--only-counts | n/a | no | When this switch is provided, only convert the COUNTS file. |
--third-party-input | third-party-input | no | Use to import files not produced by Goby. |
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