Add all project VCF file merge into 1 global merge file

Seqstat reporting read length histogram

Added reporting of readlength histogram as `stats > reads > len_histogram`
Simplified / Scalafied some of the SeqStat code

Adding more unit tests

Fixes #284 

See merge request !331

Added reporting of readlength histogram as `stats > reads > len_histogram`
Simplified / Scalafied some of the SeqStat code

Feature report core testing



See merge request !330

Fixed target variant plot

Fixes #285 

See merge request !329

Add output tests to gvcf2bed.

Fixes #282.
Also fixes previously unseen bug in the GvcfToBed extension.

See merge request !328

Fixes #282.
Also fixes previously unseen bug in the GvcfToBed extension.

Fix and test #280



See merge request !327

Add testcode to accept merged VCFs

Change tests to accept pindel
Add testcode to accept merged VCFs

Adding the pindel wrapper to the extensions. Updated to support v0.2.5b8

Adding the pindel wrapper

Updates:

- [x] Pindel wrapper update to support version v0.2.5b8
- [x] Adding tool to create pindel-config (aka bam list for pindel)
- [x] VCF output for pindel (using the pindel2vcf)
- [x] Insertsize estimation tool (not using bammetrics, is done in mapping pipeline, but not accesible from shivasvcalling->pindel)

Closes #240
Closes #263

See merge request !304

Feature sv unit tests

This is some basic unit testing for sv calling

@wyleung can merge this and then add pindel on that other branch to this?

See merge request !323

Add some more to the test to vcf filter

Fixes #273 

See merge request !324