[Bioc-sig-seq] Another ScanBamParam suggestion

Ivan Gregoretti ivangreg at gmail.com
Fri Sep 30 16:48:32 CEST 2011

Following Janet's example, I would also like to propose an upgrade to

It would be great if we could tell ScanBamPram that we want to load
only the reads that passed the vendor's quality filter.

In other words, the functionality I am suggesting is analogous to the
filter in readAligned() from the ShortRead library.

With the new release of Illumina sequencing reagents (version 3) you
get 200 million reads per lane from the HiSeq 2000. In my view, with
samples that big becoming popular, any investment in "read in"
efficiency is a good investment. I would be happy to provide a sample
BAM for those interested in addressing this suggestion.

It is also my humble opinion that we should start considering
parallelisation for reading in. I hope that I am not just wishing too

Thank you,


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