Sniffles

Sniffles:
* Added sequence resolved calls.
* Changed -n parameter (-n -1) reports now all read names.

Parameter added
--report_seq : Reports the sequences of Indels in the VCF output
--min_homo_af: Adapt the threshold to infer a homozygous variant
--min_het_af: Adapt the threshold to infer a heterozygous variant
--Ivcf: Enabling Recalling/force calling given a VCF file.

Bug fixes
* Bugs corrected in genotype estimation
* BND flag

Fixes
- Avoid calling SV in N stretches of certain sizes .
- Included genome header in vcf and BND type support.

Fixes
- More constrained calling of InvDup.
- Increased sensitivity for small indels.

Extension
- Parameter introduced: --ignore_std disable the filtering based on std.

Fixes
- Seg. fault sometimes occurring at the end of the run
- Enhanced resolution for smaller indel in noisy regions
- Constrained calling of INVDUP

Extention
- Parameter introduced: Min segment length

New features:
1. Automatic distance computation
2. STD computations and filtering of breakpoints to detect artifacts
3. Detection of small translocated elements
4. New SV type
5. Enhanced small indel calling

Bug Fixes:
1. Merging of SVs within the tree