* MANTA-30

Refactored in VCF reader from PUMA.
* MANTA-30

Refactored in VCF reader from PUMA.
Merge branch 'MANTA-30' of https://github.com/StructuralVariants/manta into MANTA-30
* MANTA-30

Added support for multiple (e.g. T + N) samples.
Added --truth-vcf option to GenerateSVCandidates.

Temporary checkpoint: reads in a single VCF line and dumps it out before
bailing.
MANTA-30

Now reads all variants in the VCF (second lines of translocs are skipped,
as are unknown/compound types).
* MANTA-30

TruthTracker with initial stats (currently to stderr).
* MANTA-30

Committing previously omitted files.
* MANTA-30

Stats on what happened to SVs derived from Edges now stored in and logged
by TruthTracker
Sync to 2013_10_29 master

Fixed conflicts:
	src/c++/lib/applications/GenerateSVCandidates/GenerateSVCandidates.cpp
	src/c++/lib/blt_util/log.hh
	src/c++/lib/svgraph/SVLocus.hh
* MANTA-30

cppcheck fixes & astyle reformatting
* MANTA-30

VCF input files moved from format to common as requested.
Merge MANTA-30 onto master
MANTA-30 close clang 3.3 warnings
MANTA-30 cleanup warnOnce

Note using a non-const static like this won't scale as a library
function -- what happens if another unrelated class were to call
this before the vcf parser? Even in it's new form, this is
dodgey (ie. it's not thread safe) consider a generic 'exception
or warn' object to generalize the case in a safe way.
MANTA-30 incidental replication with MANTA-25
MANTA-30 unfinished assembles contian many contigs
MANTA-30 remove a map copy
MANTA-30 shift more tt logic into object
* MANTA-30

Fixed a fix that was causing a build failure for me.
spelling