Computes the coverage restricted to the target region.
This method computes the approximate coverage of each base in a given region.
A list as returned by
The target region as a
The detailed alignment information given by the CIGAR strings in .bam files are ignored by the function. Instead, it is assumed that the whole read alignes to the reference without indels. This is often not true for longer read (e.g. generated with Roche 454 Sequencing), but saves computation time.
A list of the same length as the
alnReads argument. Each list
element is an integer vector of the same length as the target region (in
bases) and stores the coverage generated by the reads from the
corresponding list element of
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