Treat input filenames in the same way as perl if the last non-space character is a pipe character (i.e., fork a shell, execute the command, and read from it through a pipe)
Extend pipe capabilities to output files
Update with partially completed support for multiple output streams.  Not currenty compiling
Fix compile errors - needs testing
Correct problem with check for no output file
merge bug fix from develop
Correct a few bugs with dual output files and scoring
merge from develop
Extend output support from gt.scorereads to FASTQ/FASTQ
Fix spelling error in define
Merge bug fix from develop
Fix memory leak in generating SAM tags SA and MD
Merge branch 'develop' into pipeio

Merging bug fixed from develop
Merge branch 'develop' into pipeio

Conflicts:
	GEMTools/tools/gt.scorereads.c
Merge branch 'develop' into pipeio
Merge branch 'pipeio' into develop

Add ability to have multiple output files in gt.scorereads with different formats
Input and Output filenames are checked for pipe characters and interpreted in a
similar way to pipes in perl filenames if present
Pipeline description correction.
Merge branch 'develop' of ssh://fenris.ti00a1.pcb.ub.es:7999/gt/gemtools into develop
fixed JIP compatability
Patched to be compatible with JIP changes