This mode is used to concatenate compact alignment files. Concatenation preserves sorting when every input alignment is already sorted.Reference sequences must match exactly across the input alignments.  Queries are assumed to be entirely distinct and will be treated as independent observations (e.g., reads from multiple independent samples). To this effect, alignment entries read from different input basenames, which would otherwise share an identical query index, are renumbered with distinct query indices (this behaviour can be turned off with the adjust-query-indices option).

The mode is implemented by edu.cornell.med.icb.goby.modes.ConcatenateAlignmentMode.java.

Mode Parameters

The following options are available in this mode

FlagArgumentsRequiredDescription
(-o|--output)outputnoThe basename of the output alignment.
n/ainputyesThe basenames of the input alignments to concatenate.
--adjust-query-indicesadjust-query-indicesnoIndicates that the query indices should be adjusted to remove clashes among alignment inputs. Use this options to concatenate alignments built from different split of a large read file (such splits can be created with reformat-compact-reads). Default value: true
--genomegenomenoA genome basename. The genome must have been processed by build-sequence-cache mode to produce the compressed, random access files this mode needs.
(-p|--processor)processornoThe name of the alignment processor. An alignment processor can be configured to scan alignment entries before calling variants. By default, no processor is used. If you specify realign_near_indels, a processor that realigns reads in the proximity of indels will be used. Please note that this feature is experimental (Since Goby 1.9.7). Default value: NONE