cigar-utilities: realCigarPosition
In AllelicImbalance: Investigates Allele Specific Expression

Description Usage Arguments Details Value Author(s) Examples

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

realCigarPosition.old(RleCigar, BpPos)

realCigarPositions.old(RleCigar)

realCigarPositionsList.old(RleCigarList)

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

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

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.

Jesper R. Gadin

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

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