dot-grepData: Helper function for parsing output of samtools stats

In mcjmigdal/sumsamstats: Summarizing Samtools Stats Output With ATAC-seq QC in mind

Description

As readSamtoolsStats parses output of samtools stat this function is used to grep relevant parts of the output.

Usage

.grepData(input, section, columns, col.names = "")

Arguments

input	A character vector containing output of samtools stats, each line as one element.
section	Pattern to extract from the report. Each section of samtools stats report is uniquley labeled, for example Summary Numbers are labeled as SN.
columns	A integer vector containing numbers of columns to extract from specified section of samtools stats report.
col.names	A character vector containing names of extracted columns. Optional.

Value

data frame holding data from selected section of samtools stat output.

Examples

file <- system.file('extdata', 'sample1', package = 'sumsamstats')
inputFile <- readLines(file)
.grepData(input=inputFile, section='SN', columns=c(2,3), col.names=c('description', 'value'))

mcjmigdal/sumsamstats documentation built on July 11, 2021, 10:47 a.m.