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* Update test data output and allow `:`
* Add edlib to requirements in setup.py
* Add softclip finder test
* Build on python-3.6
* Make futures library conditional for python2
* Drop temporary from requirements
* Extend testcoverage
* Drop `external_bin` from BamAlignmentWriter
* Many small simplifications, bugfixes and enhaced tests
* Improve reporting of 5p and 3p clips
* Add some wigglespace for finding the most likely TSD position
* Keep insertions associated with deletion intact
* Add testcase for a cluster that should not be split
* Fix if/else logic for genotypes
* Skip "genomic sinks" with lots of TE evidence
* Continue on RuntimeError
* Improve splitting of input file
* Need to `fetch` reads in the specified region if using `external_bin=False`
* Don't use external samtools when finding clusters
* Identify decoy regions based on cluster density
* Drop reraise_with_stack, doesn't work on py3
* Fix outdated min/max coordinates leading to dropped chunks
* Re-raise any exceptions when processing chunks
* Fix OrderedDict syntax for py2 compatibility
* Improve logging when splitting input into chunks
* Don't remove read that isn't present anymore
* Fix return value when assembling too many reads
* Fix limiting of region when using multiple threads
* Report maximum MAPQ of read evidence for a cluster
* Bump minimum MAPQ to 4 by default and make it configurable
* Refactor cap3 assembly (so it can be exchanged more easily) and add limit to how many reads it will assemble
* Fix and apply read_is_compatible to all read with BD tag
* Generalize marking clusters as compatible or incompatible and apply at every cluster split or join
* Estimate nref/nalt using overlap of start and end if start and end are more than 50nt apart
* Skip clusters of reads that are inconsistent
* Remove redundant parenthesis, fix typo
* Allow non-proper pairs when counting evidence
* Account for max. mate distance when joining cluster
* Add new dependencies to conda recipe
* Prevent joining clusters that we previously split explicitly
* Don't thread/cache joining of cluster
* Use lru_cache for some cigar operations
* Use cigar_to_max function consistently
* Make use of new AlignmentHeader object (old method now very slow)
* Use edlib align instead of Cap3Assembly
* Fix evidence_against functionality
* Output reads that count as non-support
* Allow picking up location of reference_fasta via env var for quicker test execution
* Fix 3p evidence bam, fix nref with 1 breakpoint
* Update test-data
* Assign left/right based on AD if AD and BD are set
* Make counting more accurate, cleanup various Cluster counts and write out split reads found via `evidence_for_five/three_p`
* Collect evidence for insertions
* Fix a typo in `get_breakpoint_sequence`
* Fix resolving consensus ties if tie contains `N`
* Upgrade to pysam 0.14
* Make split_ads a property since the splits can update
* Fix typo in dumb_consensus help
* Add IUPAC to nucleotides dict
* Restructure non_evidence so that evidence for and against can be counted
* Use `reference_start` instead of deprecated `pos`
* Implement `get_breakpoint_sequence` as a method of TargetSiteDuplication
* Add `evidence_for` function
* Update planemo from 0.46.1 to 0.48.0
* Refine the cluster merging logic
* Fix the overlap calculation, in case the re-aligned contig ends up at a different position
* Update test data output, genotype outputs with higher precision (sigh)
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