Slamdunk

*Changes:*

* [Bioconda](https://bioconda.github.io/recipes/slamdunk/README.html): Slamdunk recipe added. **Slamdunk now available via conda from v0.3.2!**
* Symlink ngm -> nextgenmap/bin/ngm-0.5.2/ngm replaced by hard copy for bioconda-utils build compatibility.

*Changes:*

* Upgrade Samtools 1.3.1 -> Samtools 1.9 for upcoming bioconda build.

*Bugfixes:*

* pysam-0.15.0.1 region retreival fix. (dashed chromosomes allowed now)
* NGM permission fix to allow Singularity image build directly from Docker hub.

*Changes:*

* Travis-CI testing added.
* Automated versionable Docker container builds.
* Static 2 T>C conversion cutoff multiTCSTringency parameter replaced by dynamic conversion-threshold parameter
* Positional track module added to Alleyoop to produce genome-wide positional T>C conversion rate bigWigtracks
* Read-separator module added to Alleyoop to separated T>C reads from non T>C reads into bam-files.
* Docker base image set to ubuntu:18.04

*Bugfixes:*

* Supplementary alignment flags unset in filtered bam
* Fixed numpy version removed to satisfy pandas dependency
* Minimum baseQ filter now inclusive which is the expected behaviour
* Reference check for short chromosomes introduced
* Backwards compatibility to pysam 0.8.3 introduced

*Changes:*

* License updated to AGPLv3
* Deduplicator now only marks duplicates instead of removing them. Useful for deduplication QA like [dupRadar](https://bioconductor.org/packages/release/bioc/html/dupRadar.html). Allows for deduplication of T>C-fraction of reads only.
* [Singularity](http://singularity.lbl.gov) build-file branch added.

*Bugfixes:*

* readInRegion fixed: Switched from fetch(region="chr:start-end" (1-based) to fetch(reference=chr, start=start, end=end) (0-based). Intervals close to the ends of a chromosome are now correctly handeled and not skipped.
* Hotfix to fix executable permissions on some R plotting scripts
* Fixed alleyoop collapse to ignore all MLE columns for now
* R package dependencies fixed for IMP cluster
* include_package_data removed for proper contrib import

_Bugfixes:_
- Hotfix to include README.md in sdist packaging
- Hotfix to fix executable permissions on some R plotting scripts
- Fixed alleyoop collapse to ignore all MLE columns for now

_Changes:_
- Slamdunk supports now `MultiQC <http://multiqc.info/>`_ report creation
- Default set to local mapping
- Base-quality cutoff implemented throughout the entire _slamdunk_ / _alleyoop_ workflow
- BAQ computation disabled for samtools mpileup
- Dedup now supports selection of reads containing a defined T>C conversions
- All documentation moved to gh-pages branch for slicker repo
- CPMs now normalized to filtered reads
- Docker image now build automatically to head revision
- Official webpage introduced instead of readthedocs.org hosting
- Evaluation module for count files added to splash

_Bugfixes:_
- PCAs for single sample working now
- Dedup working again
- Sample files may contain empty lines now