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

FlagArgumentsRequiredDescription
n/ainputyesThe compact alignment file(s) to read as input.
(-s|--suffix)suffixnoThe 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-readsn/anoWhen provided, output reads that matched the reference.
--non-matching-readsn/anoWhen provided, output reads that did not match the reference.
--ambiguous-readsn/anoWhen provided, output reads that matched more than k locations in the reference.
--non-ambiguous-readsn/anoWhen provided, output reads that matched more than k locations in the reference.
--ambiguity-thresholdambiguity-thresholdnoThe 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-filternoA read set to use as pre-filter. Reads must be in the pre-filter to be in the written to the output read set.