Added BC_READ and SEC_BC_READ command line options
delete temporary files
Merge pull request #64 from jenniferliddle/devel

Added BC_READ and SEC_BC_READ command line options
Update versions ready for release
Merge pull request #65 from jenniferliddle/devel

Update versions ready for release
Seems to produce correct bam files for secondary and supplementary alignments.
Just the metrics to correct now...
Metrics now work for regression tests
Remove debug code
Name change
Merge remote-tracking branch 'js10-remote/devel' into devel
Peekable iterator implements SAMRecordIterator

and so avoid need for extra class (at expense of adding a few methods)