MANTA-17 possible implementation for getSemiAlignedMetric
MANTA-17 switching debug messages off, slow-down not tolerable
MANTA-17 Including reads which are either semi-aligned or clipped
MANTA-17 resync with master
Merge branch 'master' into MANTA-17
MANTA-17 Fixing small variant assembly routine
MANTA-17 Reverting semi-aligned read check
MANTA-17 re-sync with master, pulling small SV changes
SVTYPE and SVLEN only written for small variants
Merge branch 'master' of github.com:StructuralVariants/manta
MANTA-31 workflow fails when no tumor bam file is provided
update cl
Merge branch 'master' into MANTA-17
MANTA-17 some post-merging fixes
Adding SVLEN and END tags to vcf header
Adding vcf id also for non-translocation calls
MANTA-17 Adding rudimentary singleton/shaodow test
MANTA-17 Adding verbose debug out
Fix for previous commit
add tabix-compressed vcf iterator from starka, and update build to link against tabix lib/include