testPairedEndBam: Quickly test if a BAM file has paired end reads

In Rsamtools: Binary alignment (BAM), FASTA, variant call (BCF), and tabix file import

Description

Iterate through a BAM file until a paired-end read is encountered or the end of file is reached; report the occurrence of paired-end reads to the user.

Usage

testPairedEndBam(file, index=file, ...)

Arguments

file	character(1) BAM file name, or a BamFile instance. Open BamFiles are closed; their yield size is respected when iterating through the file.
index	(optional) character(1) name of the index file of the 'BAM' file being processed; this is given without the '.bai' extension.
...	Additional arguments, currently unused.

Value

A logical vector of length 1 containing TRUE is returned if BAM file contained paired end reads, FALSE otherwise.

Author(s)

Martin Morgan mailto:[e-mail], Sonali Arora mailto:[e-mail]

Examples

fl <- system.file("extdata", "ex1.bam", package="Rsamtools")
testPairedEndBam(fl)

Example output

Loading required package: GenomeInfoDb
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

The following object is masked from 'package:base':

    strsplit

[1] TRUE

Rsamtools documentation built on Nov. 8, 2020, 8:11 p.m.