readFastqFile: Read and write FASTQ Files

Description Usage Arguments Value Note

Description

Read a FASTQ file into a data frame, or write a data frame to a FASTQ file.

Usage

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readFastq(filein, maxReads = NULL, verbose = TRUE)
writeFastq(x, fileout, compress = FALSE, verbose = TRUE)

Arguments

filein

full pathname to one existing, optionally compressed, FASTQ file. Compression and .gz file extension are automatically detected.

fileout

full pathname for newly created, optionally compressed, FASTQ file. Compression and .gz file extension are automatically coordinated.

maxReads

integer count of the maximum number of reads wanted, where NULL means read the entire file.

compress

logical, explicitly compress the created file and adjust filename accordingly.

Value

For readFastq, a data frame, with 3 columns:

READ_ID

the ReadID for each short read

READ_SEQ

the nucleotide sequence of each short read

SCORE

the cryptic ASCII Phred score string for each short read

For writeFastq, the name of the created file.

Note

FASTQ data can get quite large. This routine can easily exceed available memory for large maxReads.


robertdouglasmorrison/DuffyTools documentation built on Dec. 14, 2018, 3:05 p.m.