alignment-to-read-set

This mode is used to converts a compact alignment to a read set file. It is implemented by edu.cornell.med.icb.goby.modes.CompactAlignmentToReadSetMode.java.

Mode Parameters

The following options are available in this mode

Flag	Arguments	Required	Description
`n/a`	input	yes	The compact alignment file(s) to read as input.
`(-s\|--suffix)`	suffix	no	The suffix to use to construct the read set filename with the input basename. Together with input basename, will determine where the output is written.
`--matching-reads`	n/a	no	When provided, output reads that matched the reference.
`--non-matching-reads`	n/a	no	When provided, output reads that did not match the reference.
`--ambiguous-reads`	n/a	no	When provided, output reads that matched more than k locations in the reference.
`--non-ambiguous-reads`	n/a	no	When provided, output reads that matched more than k locations in the reference.
`--ambiguity-threshold`	ambiguity-threshold	no	The parameter k, threshold used to determine if a read should be considered ambiguous. The value of k is the number of locations that a read matches in the reference.
`(-f\|--pre-filter)`	pre-filter	no	A read set to use as pre-filter. Reads must be in the pre-filter to be in the written to the output read set.