Slamdunk

*Changes:*

* Sample information can now be set by user.
* VCF file can be supplied instead of calling SNPs within Slamdunk.

**Bugfixes:**

* Fixed version check bug in **map** module.
* Attribute retrieval fix in core **count** module.
* Adaptation of **splash** to raw numbers and more lenient on `RA:Z` tags
* Bugfix in read length checking step from `sys.maxint` to `sys.maxsize`

*Bugfixes:*

* *float* to *int* fix in multithreaded *snp* step

*Major refactoring:*

* Rewriting source for full **python3** compatibility
* All dependencies now provided externally, **environment.yml* file added to pull in dependencies from [Bioconda](https://bioconda.github.io/)
* NextGenMap v0.5.2 -> v0.5.5. Takes care of flipped basequalities in supplementary alignments.
* Varscan2 v2.4.1 -> v2.4.4
* Samtools v1.9 -> v1.10
* [RNASeqReadSimulator](https://github.com/davidliwei/RNASeqReadSimulator) by [Wei Li](https://weililab.org) added as subtree
* Dockerfile moved and updated to run with [miniconda](https://hub.docker.com/r/continuumio/miniconda3)
* Travis-CI testset updated.

*Bugfixes:*

* Reverse strand A->G SNP coordinates offset fixed.

* Mismatch of string to int in key search fixed for summary.

*Bugfixes:*

* Mutation type bugfix in MPTagToConversion fixed
* Deduplicated bam file properly closed for indexing
* alleyoop snpeval also works now without snp sets
* Chromosome retreival fix for pysam
* dplyr dependencies removed (Bioconda)