Chris Wright

Behaviour of `.collect()` and `.toList()`

11

## Bug report The semantics of these two operators are poorly documented and counter intuitive. From the documentation its not clear what the different between `.collect()` and `.toList()`, as the...

Inconsistent behaviour for glob process outputs

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## Bug report ### Expected behavior and actual behavior According to, https://www.nextflow.io/docs/latest/process.html#multiple-output-files, a glob pattern can be used to emit a list of multiple items from a process into an...

Command-line parameter type casting can have unintended consequences

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## Bug report (Please follow this template replacing the text between parentheses with the requested information) ### Expected behavior and actual behavior When running with AWS batch some container image...

High memory use when using Python and threads

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The program [align.py](https://github.com/lh3/minimap2/files/7816510/align.py.txt) uses mappy to align reads in Python using multiple worker threads. After loading the index the memory usage jumps up quickly to >20Gb and then continues to...

Parallelization across regions

1

Thank you. Would you consider adding that as a feature to have it detect a set number of regions or chromosomes and parallelize itself? Also it does not seem like...

BED spec doesn't handle give an opinion on NaN in numeric fields

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Section 3.3 of the specification has:  and links to "IEEE Standard for Binary Floating-Point Arithmetic. IEEE 754–1985, 1985". This IEEE specification does not specify how NaNs should be represented...

The example here: https://echarts.apache.org/examples/en/editor.html?c=data-transform-filter uses `datasetId` to reference datasets from series' definitions rather that `datasetIndex`, this does not appear in the documentation.

PyPI package does not install

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Under Python 3.8, Linux x86 the source package is fetched (there's only a Python 3.7 wheel) but fails to install. ```$ pip install pyabpoa Collecting pyabpoa Using cached pyabpoa-1.4.0.tar.gz (738...

I'm starting to investigate various memory errors we have seen with clair3 code. This commit is a small one have getting acquianted with the bits full alignment feature code (the...

https://github.com/yangao07/abPOA/pull/62 went most of the way to setting up building and pushing wheels to PyPI. There currently are no wheels on PyPI. The GitHub project needs to be given credentials...