This mode is used to converts a compact alignment to to plain text. It is implemented by edu.cornell.med.icb.goby.modes.AlignmentToTextMode.java.

Mode Parameters

The following options are available in this mode

FlagArgumentsRequiredDescription
(-o|--output)outputnoThe alignments in text format
n/ainputyesThe compact alignment file to read as input.
(-f|--format)formatnoFormat of the output file (plain, SAM).
(-l|--constant-read-length)constant-read-lengthnoUse this number as read length for every read when the query length is not included in the alignment header.
(-r|--include-reference-names)include-reference-namesnoWhen provided, only write counts for reference identifiers listed in this comma separated list. To process only counts for chromosome 19 and 1, if sequences are identified by 1 and 19, use: --include-reference-names 1,19