fixFastq: fix a corrupted fastq file (if fastq-like)
In sagrudd/nanopoRe: Accessory Methods for the Analysis of Oxford Nanopore Technologies DNA Sequence Data
Description
Usage
Arguments
Value
Examples
Description
fixFastq parses a fastq (or fastq.gz) file for compliant fastq entries
and writes these to the file specified in newfastq parameter. Any
non-compliant reads are dropped
Usage
1
fixFastq(fastq, newfastq)
Arguments
fastq
file location of fastq source
newfastq
location of file to write content to
Value
path to new fastq file (same as newfastq provided)
Examples
1
2
3
4
5
6
badFastq <- system.file("extdata", "frankenFastq.fastq.gz", package =
"nanopoRe")
fastqValidator(badFastq)
tempFile <- tempfile(pattern="fastq", fileext=".fq")
fixFastq(badFastq, tempFile)
fastqValidator(tempFile)
sagrudd/nanopoRe documentation built on June 7, 2020, 10:20 p.m.
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Description Usage Arguments Value Examples
Description
fixFastq parses a fastq (or fastq.gz) file for compliant fastq entries and writes these to the file specified in newfastq parameter. Any non-compliant reads are dropped
Usage
1 | fixFastq(fastq, newfastq)
|
Arguments
fastq |
file location of fastq source |
newfastq |
location of file to write content to |
Value
path to new fastq file (same as newfastq provided)
Examples
1 2 3 4 5 6 | badFastq <- system.file("extdata", "frankenFastq.fastq.gz", package =
"nanopoRe")
fastqValidator(badFastq)
tempFile <- tempfile(pattern="fastq", fileext=".fq")
fixFastq(badFastq, tempFile)
fastqValidator(tempFile)
|
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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