fixes #271
fixes #272

- consistent use of /usr/bin/env perl shebangs
- consistent use of 'use warnings;' in favor of perl -w
Replace bcftools+bcf_filter.sh with new vcf-miniview

Add new vcf-miniview test utility, which reads BCF or VCF and outputs
VCF optionally filtered in the same way that the old bcf_filter.sh did.
The sed -r option used by bcf_filter.sh was not available on OS X, and
an installation of bcftools will not necessarily be available on test
machines, notably when testing via travis.
Insulate test case from $GREP_OPTIONS

Prevent e.g. GREP_OPTIONS='--binary-files=without-match' from
subverting the expected output.

Perhaps we ought to add 'unalias egrep' somewhere too...
Update expected output with symbolic "<X>" alleles

Since b14b21933b08ccdf7a777ed4a3529edbb03114e9 mpileup outputs a
symbolic allele rather than a plain "X".
Update QS values in expected output, and don't truncate them

Following the lead of f85ac7d492ddf7fd54e9849733c2d66adf874938
(around the time of which the QS computation changed), we should be
regression testing the full values emitted for QS.
Merge minimal MD5 reference area for mpileup tests

Provide a local reference area via $REF_PATH for mpileup/regression.sh
tests (cf 38eda28b81fd3c176f90a0f03d2645fc891167f0's commit message).
(Note that these MD5 files are truncated versions of their full
sequences; just enough to pass the tests.)

Set REF_PATH to an empty value (but not the empty string, as that
produces the default setting), or in general to point within the test
suite, for tests that exercise it -- currently test.pl and regression.sh.

This makes the test suite self-contained for reference areas, and
in particular prevents travis build testing from trying to access
the EBI reference server.  Fixes #279.
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.)
Formatting fixes for better grinding into HTML

In particular, the removed .RE was incorrectly nested.
Also use fancy >= and arrow characters where available.
Recanonicalise test/test.pl whitespace -- USE -b/-w TO DIFF/BLAME

This file had a mixture of 4-space and 8-space tabs, which previously
went unnoticed.  Manually re-expand tabs to spaces using the right
number of spaces for each tab.

See notes in fcb8af08a6fd3bfcf195407c4ba5bae528ee326d.
mpileup: conform to VCFv4.2 spec, version string should be quoted