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.
The following options are available in this mode
|input||yes||The SAM binary file to convert to compact alignment format.|
|output||yes||The output path and basename to write the compact format to.|
|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.
|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.
|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
|n/a||no||Indicates that the input file is sorted. When true, the Goby alignment file is written sorted and|
Default value: FALSE
|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
|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||no||Maximum number of locations that a read can match to be included in the alignment entries. Default value: 2|
|quality-filter-parameters||no||Parameters to configure the quality filter. Default value: threshold=0.05|
|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||no||Use to import files not produced by Goby. Default value: true|
|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||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