On Wed, Feb 25, 2015 at 2:07 PM, Roberto Alonso CIPF <ralonso@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 search. I filed a pull request adding the -h option to egrep, crediting you: https://github.com/galaxyproject/galaxy/pull/4 Peter