Anže Starič

sam_hdr_remove_lines is inefficient if original header contains a lot of lines

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**Steps to reproduce** 1. Create an input.bam file with ~1.5M `@RG` header lines. it can contain a single read, it does not really matter 2. Create a filter.txt file with...

When a large file was passed to the -H parameter, bwa-mem2 spent more than 10 minutes just reading the lines from the file (I experienced this on a 70MB file...

Learners should not hold references to widgets

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When learners are used with Tests & Score widget, they get deep_copied, which is implemented in python as pickling and unpickling. If a learner holds a reference to a widget,...

As suggested in https://github.com/biolab/orange3/issues/2793#issuecomment-346713946 http://orange-development.readthedocs.io/widget.html#input-output-signal-definitions

conda_env: add optional dependencies

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### Description Prototype for optional dependencies in environment.yml file as requested in https://github.com/conda/conda/issues/12098. Adds additional `optional_dependencies` section to environment.yml. Once can list several groups of dependencies there which do not...

Example workflow for cluster analysis

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Include cluster analysis, differential expression, and Go ontology