AllelicImbalance (version 1.10.2)

cigar-utilities: 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

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.

Details

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

See Also

• The scanForHeterozygotes which is a function to find possible heterozygote sites in a GAlignmentsList object

Examples

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

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