pyBigWig

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Cannot add entries of value type int, but only float

2

pybigwig version: `0.3.18` When I tried adding entries of int type like ``` import pyBigWig import numpy as np hg19_chr1_len = 249250621 with pyBigWig.open("/path/to/a/bigwig", "w") as bw: bw.addHeader([("chr1", hg19_chr1_len)]) bw.addEntries("chr1",...

XikunZhang

Document performance considerations?

4

I'd like to use pyBigWig to collect values at many intervals from many bigwigs, and I'd love to know what's performant. 1. is there overhead to opening a bigwig with...

alexlenail

Suppress logging/error messages

2

Is it possible to suppress the logging and error messages? Using this as a library I would rather catch errors by exception than seeing a message. Handling known error cases...

EricR86

BigBed interval problem

7

I am creating a list of histograms, one for each file using below code: ### Imports ### import numpy as np import pyBigWig as bw import matplotlib.pyplot as plt import...

jtd032

get the list of all possible stats

2

Hi, I am wondering if there is a way to get the list of all possible stats described here: https://github.com/deeptools/pyBigWig/blob/705b07495ea78740eb7ea94fb0082e23661d9929/libBigWig/bigWig.h#L99-L107 For example, ``` import pyBigWig possible_stats = pyBigWig.stats_cases possible_stats ['mean',...

lldelisle

Implement #133

2

Try enabling a numpy feature that will actually pull in numpy as a dependency.

dpryan79

Can't enforce numpy features when pyBigWig is used as a dependency in downstream package

1

There's an issue when `numpy` features are necessary for downstream packages of `pyBigWig`. The current `setup.py` checks that `numpy` is currently in the python path to build the necessary extension....

EricR86

Writing a nan value should leave a gap

7

Hi, Not sure whether to consider this a bug, but given that `bw.values("chr1", start, end)` produces `nan` values for missing values, it seems that `bw.addEntry()` with `nan` values should produce...

rcasero

On FreeBSD 14, and possibly other platforms, roundup() is defined as a macro in sys/param.h. The patch below resolves compile issues: ``` --- libBigWig/bwValues.c.orig 2023-12-16 13:51:54 UTC +++ libBigWig/bwValues.c @@...

outpaddling

Support for python >=3.11

1

Hi there, Are you planning on updating the package to support python 3.11? In the pip definition, only python >= 3.7 is required, but the bioconda version limits python to...

CodingKaiser