Fix three GCC warnings
[Savepoint] Updating breakpoint/bubble file format and start work on calls2vcf
Update simulation script files

1. Added read correction using path information to simulation in results/correction
2. replace `zcat` with `gzip -dc` since zcat is broken on OSX 10.10
Fix simulation output paths [skip CI]
kmer-agnostic: Fix bug in generating err free reads [skip CI]
Add ecoli error correction; fix status output bug
Set path to ctxK properly [skip CI]
Added test to show how links behave in loops
calls2vcf can now produce a VCF from a breakpoint file
Added flanks too far apart check
calls2vcf: Added bubble decomposition
pview reports junction positions in path output
Add script to plot link trees. Filtering coming soon.
Fix missed API change in tests
Added option to turn off additional path info output
ctx-contigs: add --confid-min option
ctx-contigs: Added --confid-step option
Fix multithreading bug in hash table insert
Improvements to thresholding links

1. Fix ecoli error correction to run simulation with link info
2. perl scripts now start with: #!/usr/bin/env perl
3. scripts/CortexLinkCleaning.pm: Add perl module to threshold links
4. ctx_pjoin.c adds full header
Added prototype path pruning. New options for pview.