Goby/Alignment-to-read-set

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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	matching-reads	no	When provided, output reads that matched the reference.
--non-matching-reads	non-matching-reads	no	When provided, output reads that did not match the reference.
--ambiguous-reads	ambiguous-reads	no	When provided, output reads that matched more than k locations in the reference.
--non-ambiguous-reads	non-ambiguous-reads	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.