Readtagger

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* Fixes for CRAM input and output
* Adjust chunk-size in readtagger based on readlength (for pacbio/nanopore reads)
* Cleanup temporary bwa indexes
* Dependency updates

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* Refine cluster coordinates using an Assembly strategy
* Fix GFF sorting on python 3
* Improve BWA alignment settings (default to intractg plus -Y) and add align_contigs method to SimpleAligner
* Add pysamtools_view command
* Improve cluster-splitting
* Add multiprocessing-logging recipe
* Only output BWA stderr if the exit code is not zero
* Add a function to sort gff files
* Close open file descriptors
* Make imprecise insertion sites more realistic
* Fix read_index property
* Adapt readtagger to higher coverage datasets
* Fix readtagger crash when not producing discard tag file.
* Add number of mates for left and right support to GFF
* Split clusters that start with reverse reads conatining only BD tags

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* Split cluster if there are multiple polarity switches between Forward and Reverse orientation
* Manipulate copy of cigarlist to avoid numpy issue

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* Expose reference fasta option in bam_readtagger.xml

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* Move readtagger CLI form argparse to click
* Index bamfile if neccesary
* Replace multipocessing pool with ProcessPoolExecutor
* Set the matesequence while tagging reads
* Fix false positives in readtagger module
* Do cap3 assembly in shared memory if passing --shm_dir or if SHM_DIR environment variable is defined
* Parallelize findlcluster by splitting input bam
* Add check_call.py script for rapidly verifying IGV screenshots

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* Fix crash when determining reference name

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