[BioC] export a GappedAlignment object to a BAM file

Yue Li gorillayue at gmail.com
Tue May 8 15:24:05 CEST 2012

Dear List,

I wonder if there's a way to export a GappedAlignment object to a bam file.

rtracklayer 'export' function exports gff, bed, bed15, bedGraph but not bam. It also does not recognize GappedAlignment class.

One could reformat the GappedAlignment object into a SAM-like table, write.table it to a local disk, and then use 'asBAM' to convert that file to BAM. But that seems a little cumbersome.

Thanks much,

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