getGAlignmentsPairs: Internal GAlignmentPairs loader from fst data.frame

In JokingHero/ORFik: Open Reading Frames in Genomics

Internal GAlignmentPairs loader from fst data.frame

Description

Internal GAlignmentPairs loader from fst data.frame

Usage

getGAlignmentsPairs(df, strandMode = 0, seqinfo = NULL)

Arguments

df	a data.frame with columns minimum 6 columns: seqnames, start1/start2 (integers), cigar1/cigar2 and strand Additional columns will be assigned as meta columns
strandMode	numeric, default 0. Only used for paired end bam files. One of (0: strand = *, 1: first read of pair is +, 2: first read of pair is -). See ?strandMode. Note: Sets default to 0 instead of 1, as readGAlignmentPairs uses 1. This is to guarantee hits, but will also make mismatches of overlapping transcripts in opposite directions.
seqinfo	Seqinfo object, defaul NULL (created from ranges). Add to avoid warnings later on differences in seqinfo.

Value

GAlignmentPairs object

JokingHero/ORFik documentation built on Dec. 21, 2024, 12:01 a.m.