read.bam: Read BAM file into GRanges or data.table

In mskilab/bamUtils: Utility functions for manipulating BAMs

Read BAM file into GRanges or data.table

Description

Wrapper around Rsamtools BAM scanning functions By default, returns GRangesList of read pairs for which <at least one> read lies in the supplied interval

Usage

read.bam(
  bam,
  intervals = NULL,
  gr = intervals,
  all = FALSE,
  bai = NULL,
  pairs.grl = TRUE,
  stripstrand = TRUE,
  what = scanBamWhat(),
  unpack.flag = FALSE,
  verbose = FALSE,
  tag = NULL,
  tagFilter = list(),
  isPaired = NA,
  isProperPair = NA,
  isUnmappedQuery = NA,
  hasUnmappedMate = NA,
  isNotPassingQualityControls = NA,
  isDuplicate = FALSE,
  isValidVendorRead = TRUE,
  pairs.grl.split = TRUE,
  as.data.table = FALSE,
  ignore.indels = FALSE,
  size.limit = 1e+06,
  ...
)

Arguments

bam	string Input BAM file. Advisable to make BAM a BamFile instance instead of a plain string, so that the index does not have to be reloaded.
intervals	GRanges of intervals to retrieve. If left unspecified with 'all = TRUE', will try to pull down entire BAM file
gr	Granges (default = intervals)
all	boolean Flag to read in all of BAM as a GRanges via 'si2gr(seqinfo())' (default = FALSE)
bai	string Input BAM index file.
pairs.grl	boolean Flag if TRUE will return GRangesList of read pairs in which at least one read falls in the supplied interval (default = FALSE)
stripstrand	boolean Flag to ignore strand information on the query intervals (default = TRUE)
what	vector What fields to pull down from BAM. (default = scanBamWhat())
verbose	boolean verbose flag (default = FALSE)
tag	vector Additional tags to pull down from the BAM (e.g. 'R2')
isPaired	boolean Flag indicates whether unpaired (FALSE), paired (TRUE), or any (NA) read should be returned. See documentation for Rsamtools::scanBamFlag(). (default = NA)
isProperPair	boolean Flag indicates whether improperly paired (FALSE), properly paired (TRUE), or any (NA) read should be returned. A properly paired read is defined by the alignment algorithm and might, e.g., represent reads aligning to identical reference sequences and with a specified distance. See documentation for Rsamtools::scanBamFlag(). (default = NA)
isUnmappedQuery	boolean Flag indicates whether unmapped (TRUE), mapped (FALSE), or any (NA) read should be returned. See documentation for Rsamtools::scanBamFlag(). (default = NA)
hasUnmappedMate	boolean Flag indicates whether reads with mapped (FALSE), unmapped (TRUE), or any (NA) mate should be returned. See documentation for Rsamtools::scanBamFlag(). (default = NA)
isNotPassingQualityControls	boolean Flag indicates whether reads passing quality controls (FALSE), reads not passing quality controls (TRUE), or any (NA) read should be returned. See documentation for Rsamtools::scanBamFlag(). (default = NA)
isDuplicate	boolean Flag indicates that un-duplicated (FALSE), duplicated (TRUE), or any (NA) reads should be returned. 'Duplicated' reads may represent PCR or optical duplicates. See documentation for Rsamtools::scanBamFlag(). (default = FALSE)
pairs.grl.split	boolean Return reads as GRangesList. Controls whether get.pairs.grl() does split (default = TRUE)
as.data.table	boolean Return reads in the form of a data.table rather than GRanges/GRangesList (default = FALSE)
ignore.indels	boolean Flag messes with cigar to read BAM with indels removed. Useful for breakpoint mapping on contigs (default = FALSE)
...	futher arguments passed to Rsamtools::scanBamFlag()

Value

Reads in one of GRanges, GRangesList or data.table

mskilab/bamUtils documentation built on Sept. 28, 2022, 3:45 p.m.