getGAlignmentsPairs {ORFik} | R Documentation

## 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

[Package ORFik version 1.12.13 Index]