harp: Perform allele-specific alignment with fastq files
In dvera/harp:

Description Usage Arguments Value

View source: R/harp.R

Perform allele-specific alignment with fastq files

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harp(fastqFiles1, fastqFiles2 = NULL, index1prefix, index2prefix,
  minAS = -20, minQual = 20, threads = getOption("threads", 1L),
  fields = c("AS", "XM", "XO", "XG", "NM"), ...)

`fastqFiles1`	A vector of relative/absolute paths to fastq files. Each fastq file provided is parsed independently.
`fastqFiles2`	A vector of read2 fastq files corresponding to the mate-pairs of the files defined in fastqFiles1.
`index1prefix`	A relative/absolute path to a bowtie2 index of one of the reference haplotypes. Note that the prefix of reference 1 and 2 should be different (e.g., not both be "genome")
`index2prefix`	A relative/absolute path to a bowtie2 index of the second reference haplotype.
`minAS`	An integer specifying the minimum alignment score to consider a read as aligned.
`minQual`	A positive integer specifying the nimimum alignment score to parse a read.
`threads`	A positive integer specifying the number of threads to use for alignment and parsing.
`fields`	A vector of optional sam fields to preserve in the output sam files.