sortByName: Produce sorted and indexed BAM file(s) from BAM file(s); this...

In HenrikBengtsson/aroma.seq: High-Throughput Sequence Analysis using the Aroma Framework

Description

Produce sorted and indexed BAM file(s) from BAM file(s); this method will likely be superseded shortly by a SamTransform method.

Usage

sortByName(...)

Arguments

pathD	The destination path.
bIndex	If TRUE, index file created after sort.
suffix	Filename suffix for sorted output.
skip	If TRUE, already converted files are skipped, otherwise not.
overwrite	If TRUE, already converted files are ignored and overwritten.
verbose	See Verbose.
...	Not used.

Value

Returns a BamDataFile (BamDataSet).

Author(s)

Taku Tokuyasu

See Also

Internally asBam is utilized.

HenrikBengtsson/aroma.seq documentation built on Feb. 15, 2021, 2:21 a.m.