On Wed, Feb 25, 2015 at 2:07 PM, Roberto Alonso CIPF <ralo...@cipf.es> wrote:
> Hello again :),
> I have found the problem, the code that merge the files is this:
> galaxy/datatypes/tabular.py:484:            cmd = 'egrep -v "^@" %s >> %s' %
> ( ' '.join(split_files[1:]), output_file )
> This concatenates the file name into the sam file. Just adding "h" it is
> enough, so it will be like this:
> galaxy/datatypes/tabular.py:484:            cmd = 'egrep -hv "^@" %s >> %s'
> % ( ' '.join(split_files[1:]), output_file )
> Thanks all for your help, best regards

Well done :)

It looks like the SAM merge needs fixing then,

$ man egrep
       -h, --no-filename
              Suppress  the  prefixing  of  file  names  on  output.
This is the default when there is only one file (or only standard
input) to

I filed a pull request adding the -h option to egrep, crediting you:

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