ensure the paired files are different

thanks to Nelli Talo for the report
Merge pull request #73 from pradosj/master

A small change that make the project compilable with c++11
improving haplotype construction by continuing until ambiguous
Do not branch from join nodes
Turn off consequentive k-mer quality check.

Now that we use alignment-based filtering, this check is no longer necessary.
move the variant filtering into an sga submodule
Merge branch 'extended-dbg'
rename file
consider VCF files with "." in the filter column as PASS
make graph-concordance quieter
Fix PASS/. check
Move dbsnp script to sga-extra repo
calculate dust and hplens if they are not tagged in the VCF
Merge branch 'master' of git://github.com/pradosj/sga into pradosj-master
Merge branch 'pradosj-master'
Merge branch 'master' of https://github.com/jts/sga
add quality-based filter
Merge branch 'master' of https://github.com/jts/sga

Conflicts:
	src/SGA/sga.cpp
fix description of somatic-variant-filters
fix indentation