read.SeqFolder: Read contents of a sequencing folder and make a SimpleList...
In hiReadsProcessor: Functions to process LM-PCR reads from 454/Illumina data

Description Usage Arguments Value Note See Also Examples

Given a sequencing folder path, sample information file path, and sequence file extension pattern, the function returns a list of variables required to process the data. The function also calls read.sampleInfo which reads in sample processing metadata and formats it if needed.

1 2	read.SeqFolder(sequencingFolderPath = NULL, sampleInfoFilePath = NULL, seqfilePattern = NULL)

`sequencingFolderPath`	full or relative path to the sequencing folder
`sampleInfoFilePath`	full or relative path to the sample information file, which holds samples to quadrant/lane associations along with other metadata required to trim sequences or process it. Default to NULL, where the function tries to find xls/xlsx or tab deliminated txt file in the sequencing folder which sounds similar to 'sampleinfo' and present you with choices of file to select from.
`seqfilePattern`	regex/string to describe sequence file endings. See examples. Default is NULL.

a SimpleList list which is used by other functions to process and decode the data.

One must make sure that each sequencing file has sector name/number prefixed at the beginning, else findBarcodes will fail trying to find the filename.
For paired end Illumina runs, make sure the filenames include R1, R2, and I1 somewhere in the name denoting pair1, pair2, and index/barcode reads, respectively.

read.sampleInfo, findBarcodes, splitByBarcode

runData <- system.file("extdata/FLX_sample_run/", 
package = "hiReadsProcessor")
read.SeqFolder(runData, seqfilePattern=".+fna.gz$")
## Not run: 
read.SeqFolder(".", seqfilePattern = "\\.TCA.454Reads.fna$")
read.SeqFolder(".", seqfilePattern = ".+fastq$")

## End(Not run)