[Bioc-devel] Rsamtools quitting ungracefully when indexing unsorted BAM file

Martin Morgan mtmorgan at fhcrc.org
Mon Jan 3 06:05:21 CET 2011

On 12/16/2010 02:38 AM, florian.hahne at novartis.com wrote:
> Hi List, Martin,


> Another suggestion: wouldn't it be super cool to expose parts of the
> samtools view functionality to convert between SAM and BAM files? It
> seem a bit odd that you can sort and index BAM files but can't convert
> them from SAM files, which still seem to be the preferred file type for
> many applications.

Rsamtools devel version 1.3.15 introduces asBam, allowing the equivalent
of samtools view -Sb in.sam > out.bam (plus sort and index); this
implies that reference sequence info (@SQ tags) are encoded in the first
lines of the SAM files. Happy to make further additions...


> Best regards, Mit freundlichen Grüssen, Meilleures salutations,
> *Florian Hahne
> Novartis Institute For Biomedical Research**
> Translational Sciences / PreClinical Safety / investigativeToxicology
> (iTOX)*
> Expert Data Integration and Modeling Bioinformatics
> CHBS, WKL-135.1.67
> Novartis Institute For Biomedical Research, Werk Klybeck
> Klybeckstrasse 141
> CH-4057 Basel
> Switzerland
> Phone: +41 61 6967127
> Email : _florian.hahne at novartis.com_ <mailto:florian.hahne at novartis.com>

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