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

FlagArgumentsRequiredDescription
(-i|--input)inputyesThe SAM binary file to convert to compact alignment format.
(-o|--output)outputyesThe output path and basename to write the compact format to.
(-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.
Default value: FALSE
--sortedn/anoIndicates that the input file is sorted. When true, the Goby alignment file is written sorted and
indexed.
Default value: FALSE
--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.
Default value: true
(-f|--read-index-filter)read-index-filternoThe 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-thresholdambiguity-thresholdnoMaximum number of locations that a read can match to be included in the alignment entries. Default value: 2
(-p|--quality-filter-parameters)quality-filter-parametersnoParameters to configure the quality filter. Default value: threshold=0.05
--number-of-readsnumber-of-readsnoThe 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-inputthird-party-inputnoUse to import files not produced by Goby. Default value: true
--bsmapbsmapnoIf 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-encodingquality-encodingnoThe 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