[BioC] BAM files to Genomic Ranges object

[Dario Strbenac]

> the first argument is supposed to be the path to the bam file, not to the directory in which the bam file is located.

That's right. Also, note the help page.

path : A character vector of length 1. The path of the BAM file.

Notice there is another method BAM2GRangesList described on the help page for processing multiple BAM file paths into a GRangesList.

Hervé Pagès makes a good point. Although this package isn't for the analysis of RNA-seq data, and the output of Tophat is not relevant, this code was written when everyone was using the original Bowtie to do ChIP-seq alignments, which doesn't perform gapped alignments. This will be updated.