cigar-utilities {AllelicImbalance} | R Documentation

## realCigarPosition

### Description

From a GAlignments calculate the real corresponding position for each read based on its cigar.

### Usage

    realCigarPosition.old(RleCigar, BpPos)

    realCigarPositions.old(RleCigar)

    realCigarPositionsList.old(RleCigarList)

### Arguments

`RleCigar` | An `Rle` containing cigar information
`BpPos` | the absolute position on the chromosome of interest
`RleCigarList` | An `RleList` containing cigar information

### Details

The main intention for these functions are to be the internal functions for `scanForHeterozygotes` and `getAlleleCount`.

### Value

realCigarPosition returns the new position realCigarPositions returns a vector with the corrected positions to be subsetted from a read. `realCigarPositionsList` returns a list where each element i a vector with the corrected positions to be subsetted from a read.

### Author(s)

Jesper R. Gadin

### Examples

      RleCigarList <-  cigarToRleList('3M4I93M')
      BpPos <- 5

      newPos <- realCigarPosition.old(RleCigar=RleCigarList[[1]], BpPos)
      newPositions <- realCigarPositions.old(RleCigar=RleCigarList[[1]])
      newPositionsList <- realCigarPositionsList.old(RleCigarList=RleCigarList)

[Package AllelicImbalance version 1.22.0 Index]