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

FlagArgumentsRequiredDescription
(-i|--input)inputyesThe 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)outputyesThe output path and basename to write the compact format to.
(-g|--genome-cache)genome-cachenoThe 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-idsnoA 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-idsnoA compact file describing targets which provides identifiers for each target sequence. If provided, target identifiers are propagated to the alignment header.
--propagate-query-idsn/anoWhen 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-idspropagate-target-idsnoWhen 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-filternoThe 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-thresholdambiguity-thresholdnoMaximum number of locations that a read can match to be included in the alignment entries.
(-p|--quality-filter-parameters)quality-filter-parametersnoParameters to configure the quality filter.
--only-mafn/anoWhen this switch is provided, only convert the MAF file.
--only-countsn/anoWhen this switch is provided, only convert the COUNTS file.
--third-party-inputthird-party-inputnoUse to import files not produced by Goby.