readBaseQuality: (Legacy) Read short reads and their quality scores into R representations
Description
readBaseQuality reads all base call files in a directory
dirPath whose file name matches seqPattern and all quality
score files whose name matches prbPattern, returning a compact
internal representation of the sequences, and quality scores in the files.
Methods read all files into a single R object.
A character vector (or other object; see methods
defined on this generic) giving the directory path (relative or
absolute) of files to be input.
seqPattern
The (grep-style) pattern describing
base call file names to be read. The default (character(0))
results in (attempted) input of all files in the directory.
prbPattern
The (grep-style) pattern describing
quality score file names to be read. The default (character(0))
results in (attempted) input of all files in the directory.
type
The type of file to be parsed. Supported types include:
Solexa: parse reads and their qualities from _seq.txt
and _prb.txt-formatted files, respectively.
...
Additional arguments, perhaps used by methods.
Value
A single R object (e.g., ShortReadQ) containing
sequences and qualities of all files in dirPath matching
seqPattern and prbPattern respectively. There is no
guarantee of order in which files are read.