Steve Davis

I'm trying to update the version in the change log with this configuration: ``` [bumpversion:file:HISTORY.rst] search = in_progress_version replace = in_progress_version\n-------------------\ncoming soon\n\n{new_version} ``` How can I make bumpversion convert the...

What is the recommended workflow to produce a VCF file when starting with two unaligned bacterial whole-genome fasta files, each approximately 3 million nucleotides? Any particular aligner and file format...

Added developer instructions to setup rp2 in a conda environment.

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Very simple 1st pull request, mostly to test the process and make sure everything is setup properly. Added developer instructions to setup rp2 in a conda environment.

Question. How can install a pre-built binary version of pdftools 1.8 for Windows? I need the old version to match the behavior of the 1.8 version installed in our production...

Broken in 0.7.3 : date not detected with specific surrounding text

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These test cases pass with version 0.7.1 and fail with version 0.7.3 ``` line = "as of June 30, 2019. Management" assert list(find_dates(line)) == [datetime.datetime(2019, 6, 30)] line = "As...

Reproducible results

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Is there a way to generate identical results when running ttr with identical config files? I'm seeing different results in the seqs_sim.txt, sim.vcf, and var_site_matrix files.

Not sure if this is a bug or a misunderstanding on my part. Consider these example VCF records: ``` #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sample1 chrom...