This mode is used to convert binary BWA alignments in the SAM format to the compact alignment format. It is implemented by edu.cornell.med.icb.goby.modes.SAMToCompactMode.java.
See this tutorial for details about how to use sam-to-compact.
Mode Parameters
The following options are available in this mode
| Flag | Arguments | Required | Description |
|---|---|---|---|
(-i|--input) | input | yes | The SAM binary file to convert to compact alignment format. |
(-o|--output) | output | yes | The output path and basename to write the compact format to. |
(-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. Default value: FALSE |
--sorted | n/a | no | Indicates that the input file is sorted. When true, the Goby alignment file is written sorted and indexed. Default value: FALSE |
--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. Default value: true |
(-f|--read-index-filter) | read-index-filter | no | The name of a read index set with multiplicity 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. Default value: 2 |
(-p|--quality-filter-parameters) | quality-filter-parameters | no | Parameters to configure the quality filter. Default value: threshold=0.05 |
--number-of-reads | number-of-reads | no | The number of reads in the input file. The number is determined from the argument to the -q option when provided. Use this option when importing an alignment not generated with Goby (see samtools flagstat to get the number of reads in a SAM/BAM file). Default value: -1 |
--third-party-input | third-party-input | no | Use to import files not produced by Goby. Default value: true |
--bsmap | bsmap | no | If the input sam file came from the bsmap aligner which is special in that it provides the reference string and how it handles reverse strand. Default value: false |
--quality-encoding | quality-encoding | no | The encoding for quality scores. The default quality encoding is that used by the Illumina pipeline 1.3+. Valid encodings include Illumina, Sanger and Solexa. Default value: Illumina |
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