This mode is used to sort a compact alignment by reference position. The output alignment is sorted and indexed. It is implemented by  edu.cornell.med.icb.goby.modes.SortMode. See the sorting tutorial for examples of use.

Mode Parameters

The following options are available in this mode

FlagArgumentsRequiredDescription
(-o|--output)outputyesThe basename where to write the sorted alignment.
n/ainputyesThe compact alignment file to read as input.
(-r|--include-reference-names)include-reference-namesnoWhen provided, only output alignment entries that match the provided reference identifiers listed in this comma separated list. To process only entries matching chromosome 19 and 1, if sequences are identified by 1 and 19, use: –include-reference-names 1,19
(-s|--start-position)start-positionnoThe start position within the file, which should be number of bytes into the file to start reading from. Reading will start at the first record on or after start-position.
(-e|--end-position)end-positionnoThe end position within the file, which should be number of bytes into the file to end reading from. Reading will end at the end of the record on or after end-position.