[BioC] BAM files to Genomic Ranges object

[Dario Strbenac]

>That code looks correct, but I would rather do:
>
>   bam_files <- list.files(pattern="*.bam")
>   gr_list <- lapply(bam_files,
>                     function(bam_file)
>                       as(readGappedAlignments(bam_file), "GRanges"))
>   names(gr_list) <- bam_files

Is it possible to add an option to the coercion to keep the metadata columns ? For example, if the user specifies they also want to read the quality scores, the coercion to GRanges currently discards that.