On 1 Jul 2014, at 16:06, Marcel Martin <marcel.mar...@tu-dortmund.de> wrote:
> Interestingly, at least in my samtools version (0.1.19-96b5f2294a,
> Ubuntu 14.04), the EOF marker check is also done (and fails) when you
> pipe in a BAM file from stdin:
>
> $ samtools view -b merged.bam | samtools view - > /dev/null
> [bam_header_read] EOF marker is absent. The input is probably truncated.
This bug was refixed for htslib-based samtools a while back:
https://github.com/samtools/samtools/issues/18
John
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