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.
The following options are available in this mode
|output||no||The alignments in text format|
|input||yes||The compact alignment file to read as input.|
|format||no||Format of the output file (plain, SAM).|
|constant-read-length||no||Use this number as read length for every read when the query length is not included in the alignment header.|
|include-reference-names||no||When 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|