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Feature skip abort

This adds the possibility to force the pipeline to continue with a config value even when the Fastqvalidator finds a problem.

This merge request depends on !326 

See merge request !333

Added fix mpileup for bcftools

fixes #278 

See merge request !326

bow authored Mar 01, 2016 and Peter van 't Hof committed Mar 02, 2016

As mentioned in the documentation[1], the `--custom` flag can
be specified multiple times.

[1] http://www.ensembl.org/info/docs/tools/vep/script/vep_options.html#opt_custom
(cherry picked from commit 5204f4f)

Added check on sequence dictionary

Fixes #283 

See merge request !325

Feature tagging

Fixes #254 

See merge request !334

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