bam2bam usage in pipeline_bamstats

[IanSudbery]

pipeline_bamstats uses bam2bam in order add back peduoquality/seqeuence to a bam file.

if does with the following command:

cat Aly-IN-2.bam     | cgat bam2bam -v 0     --method=set-sequence > BamFiles.dir/Aly-IN-2.bam 

I.e. output is sent to stdout, but the log is not redirected. bam2bam doesn't like this, even though -v0 is set, which should probably be okay (see cgat-developers/cgat-apps#30), but it isn't currently..

[Acribbs]

#82 should fix this