toupper case bug fix in inputs

phac-nml / biohansel

Rapidly subtype microbial genomes using single-nucleotide variant (SNV) subtyping schemes

Apache License 2.0

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toupper case bug fix in inputs #70

Closed kbessonov1984 closed 5 years ago

kbessonov1984 commented 5 years ago

@peterk87 current version of biohansel does not work on fasta/q files with lower case as comparisons to tiles fail. In current patch all input sequences are converter to upper case on the fly without modification of original input files. The parsers.py was modified at lines 124 and 76. Please accept this change and update bioconda package to a newer version. Thank you.

peterk87 commented 5 years ago

Hi @kbessonov1984 can you reopen this PR to merge into development instead of master so I can include these changes in the patch update #65 ? Also, if it's not too much trouble can you add a unit test? Thanks

kbessonov1984 commented 5 years ago

@peterk87 OK, I will push new code to the development branch. Did not know about upcoming patch.