demultiplex.py put_output error

[MagnificaScience]

Hello Thomas,

There appear to be 3 bugs in put_output within demultiplex.py
Line 656

seq1_name = '%(code)s_%(Flowcell)s_s_%(lane)s_fastq.txt' % \
            ({'code': 'R1samplecode123', 'Flowcell': Flowcell, 'lane': Lane})

Should be

seq1_name = '%(code)s_%(Flowcell)s_s_%(lane)s_fastq.txt' % \
            ({'code': 'R1_%s' % opts.output.split('/')[-2], 'Flowcell': Flowcell, 'lane': Lane})

With the a similar change required on line 658.

Line 660 is
if not os.exists(os.path.join(dir_in, seq1_name)):
which does not work, but this does:
if not os.path.exists(os.path.join(dir_in, seq1_name)):

With these changes made, the output for --match1 and --match2 end up with the right filename in the right place.

Thanks,
Jason