Hi Dario,
There's no point to using "samtools cat" with a single file...there'd be
nothing to concatenate. Just use "samtools view -c test.bam" directly.
BTW, the regular "cat" command is also typically only needed with more than
one file (otherwise, just use redirection "<" and save typing two
characters).
Best,
Devon
--
Devon Ryan, Ph.D.
Email: dpr...@dpryan.com
Laboratory for Molecular and Cellular Cognition
German Centre for Neurodegenerative Diseases (DZNE)
Ludwig-Erhard-Allee 2
53175 Bonn
Germany
<devon.r...@dzne.de>
On Wed, Dec 3, 2014 at 1:39 PM, Dario Beraldi <dario.bera...@gmail.com>
wrote:
> Hello,
>
> I realized that samtools cat doesn't work if only one input file is
> supplied. Is this behavior intentional? I would prefer if one input file
> was allowed, just like in Unix cat. Example:
>
> ## Two files, OK:
> samtools cat test.bam test.bam | samtools view -c -
> 352
>
> ## One file:
> samtools cat test.bam
> Usage: samtools cat [-h header.sam] [-o out.bam] <in1.bam> <in2.bam> [...]
>
> samtools --version
> samtools 1.1
> Using htslib 1.1
> Copyright (C) 2014 Genome Research Ltd.
>
> Thanks!
> Dario
>
>
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