fetchBam: fetch a bam file pileup with the ability to consider read...

In jrboyd/seqsetvis: Set Based Visualizations for Next-Gen Sequencing Data

fetch a bam file pileup with the ability to consider read extension to fragment size (fragLen)

Description

fetch a bam file pileup with the ability to consider read extension to fragment size (fragLen)

Usage

fetchBam(
  bam_f,
  qgr,
  fragLen = NULL,
  target_strand = c("*", "+", "-")[1],
  max_dupes = Inf,
  splice_strategy = c("none", "ignore", "add", "only", "splice_count")[1],
  flip_strand = FALSE,
  return_unprocessed = FALSE,
  ...
)

Arguments

bam_f	character or BamFile to load
qgr	GRanges regions to fetchs
fragLen	numeric, NULL, or NA. if numeric, supplied value is used. if NULL, value is calculated with fragLen_calcStranded (default) if NA, raw bam pileup with no cross strand shift is returned.
target_strand	character. if one of "+" or "-", reads are filtered to match. ignored if any other value.
max_dupes	numeric >= 1. duplicate reads by strandd start position over this number are removed, Default is Inf.
splice_strategy	character, one of c("none", "ignore", "add", "only"). Default is "none" and split read alignments are asssumed not present. fragLen must be NA for any other value to be valid. "ignore" will not count spliced regions. "add" counts spliced regions along with others, "only" will only count spliced regions and ignore others.
flip_strand	if TRUE, strand alignment is flipped prior to fragLen extension. Default is FALSE.
return_unprocessed	boolean. if TRUE returns read alignment in data.table. Default is FALSE.
...	passed to ScanBamParam(), can't be which or what.

Value

GRanges containing tag pileup values in score meta column. tags are optionally extended to fragment length (fragLen) prior to pile up.

jrboyd/seqsetvis documentation built on Oct. 15, 2024, 11:28 p.m.