version 2.0.0 #78
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version 2.0.0 #78
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…y to alignmentpreset.py for clearer filenaming refactor: restructure the alignmentpreset functionalities to have a better call-order refactor: reduce the complexity of the functions in alignmentpreset significantly perf: perform most alignment-preset related calculations in parallel (multiprocessing with concurrent.futures)
…but static imports to improve stability fix: add an explicit import for IUPACData from Bio.Data (instead of the implicit import that didn't always work depending on the interpreter)
…ta table in fasta2bed refactor: change name of FindAmbigousOptions method to find_ambiguous_options
…rimers refactor: use named keyword arguments in calling this method instead of *args and **kwargs docs: improves the docstring for this find_or_read_primers() method
refactor: fix imports throughout the project to be static imports instead of relative imports refactor: move get_args and the argument parser to its own file (args.py) refactor: split index-checking code to their own respective methods instead of having everything in main() refactor: move the building of the primer index to its own method primer_df_to_primer_index() in an earlier stage of the call-order. This is no longer done on a per-process basis after the multiprocessing tasks to cut the reads have been dispatched refactor: improve the call order for the multiprocessing flow (use dispatchers and executors) refactor: move the methods for indexing the reads into class SequenceReads feat: add support for gzipped fastq output perf: use pgzip for multithreaded writing of gzip file refactor: move functionality for alignment matrix parsing to its own file (alignmentmatrix.py) fix: disable the progress bar when in debug mode (verbose) refactor: reduce complexity of most functions and improve call-order (except in cut_reads.py)
…mers to each other in the index for accurate removal Implemented in 5b16301 but commitmessage was missing this feature
…nt based search with parasail
…se the normal included re library
deps: update dependencies in setup.py deps: remove intel channel from conda recipe file
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…ad counts (will throw zerodivisionerror)
style: formatting with black&isort
…r as alignment-score in bedfile style: formatting with isort & black
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A few changes.