fixes #271
fixes #272

- consistent use of /usr/bin/env perl shebangs
- consistent use of 'use warnings;' in favor of perl -w
Clean after fix in e3d4eee

- free allocated memory
- strncmp not necessary with hts_readlist
Fix fixmates for supplementary reads

Currently samtools fixmate will incorrectly perceive supplementary reads as
primaries and consequently mess up the pairing information for the primaries.
This commit fixes this by passing supplementary reads through unmodified.
This also updates flagstat to separate out the statistics for supplementary
and secondary reads.

Signed-off-by: Martin Pollard <mp15@sanger.ac.uk>
Merge #! fixes to misc/ scripts

Use "#!/usr/bin/env (perl|python)" throughout, to get the interpreter
from $PATH.  Use "use strict; use warnings;" in Perl scripts (this merge
commit also re-adds strict in novo2sam.pl).  Fixes #273.

(These small changes are not legally significant for copyright purposes,
so years in the copyright notices have not been updated.)