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
tweak usage
add sequence pretty printer
MANTA-58 improve debug msg
MANTA-58 additional debug info
MANTA-58 add new min edge check
MANTA-61 tranfer markdown manual code from isaac

Still need to add content!
MANTA-60 add version to python config/run scripts
MANTA-58 fix off-by-one error
MANTA-58 demo a new split edge size check
MANTA-58 first pass at a fix

add 100 bases of flanking refernece seqeunce at the assembly stage
which is reserved for split read alignment and not available for
breakend discovery (ie. not part of the contig alignment)
MANTA-58 debug msg
MANTA-58 fix off-by-one in scanEnd, assert conditions