Fix the coordinates in Axt object

Description

In ‘axt’ file and Axt object, the coordinates of negative query alignments are relative to the reverse-complemented coordinates of its chromosome. This is different from the convention in Bioconductor. This function fixes the coordinates which are always relative to the positive strand.

Usage

1

Arguments

x

Axt object.

Details

In Axt, the ‘strand’ is for the aligning organism. If the strand value is “-”, the values of the aligning organism's start and end fields are relative to the reverse-complemented coordinates of its chromosome.

Value

A Axt object.

Author(s)

Ge Tan

Examples

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  axtFnDanRer10Hg38 <- file.path(system.file("extdata", package="CNEr"),
                                 "danRer10.hg38.net.axt")
  qAssemblyFn <- file.path(system.file("extdata",
                                       package="BSgenome.Hsapiens.UCSC.hg38"),
                           "single_sequences.2bit")
  tAssemblyFn <- file.path(system.file("extdata",
                                       package="BSgenome.Drerio.UCSC.danRer10"),
                           "single_sequences.2bit")
  axtDanRer10Hg38 <- readAxt(axtFnDanRer10Hg38, tAssemblyFn=tAssemblyFn,
                             qAssemblyFn=qAssemblyFn)
  ## Fix the coordinates
  fixCoordinates(axtDanRer10Hg38)
  
  ## Restore it
  fixCoordinates(fixCoordinates(axtDanRer10Hg38))

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