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I did a fresh install of flye with micromamba. Python is 3.9.
I get a core dump on the minimap2 step. Any suggestions?
Thanks!
less /Spawn/Isolates/LT001001/results_flye_correct/10-consensu…
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Hello,
Our team has been using Minimac4 to do imputation work. We have found that this program utilizes the `InputFile` from libStatGen to do BGZF I/O.
It seems that libStatGen would benefit fr…
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There appears to be an issue in the ``.read()`` and/or ``.readline()`` methods as per these issues using ``Bio/bgzf.py`` within ``pyfaidx``:
https://github.com/mdshw5/pyfaidx/issues/125
https://gi…
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Dear Giulio,
When I run this command from the Mocha page on my data:
```
bcftools isec --no-version -Ou --complement --exclude "N_ALT>1" --write 1 $dir/$pfx.unphased.bcf $dir/$pfx.xcl.bcf | \
…
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Howdy,
I am running the following command to genotype a short read to a reference and I get the "invalid BGZF file: does not end in proper EOF marker" error. I haven't edited any of the files since…
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I had to turn off multithreaded GAM read because this would break on Mac:
```
vg construct -r test/1mb1kgp/z.fa -v test/1mb1kgp/z.vcf.gz > z.vg
vg sim -n 10000 -s 23 -a -x z.vg > sim.gam
# This fails
…
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bgzf_getline strips line delimiters.
Here is test to verify this:
```
import pytest
import pysam
import tempfile
@pytest.fixture(params=[
"A\nB\nC\n",
"\nAAA\t",
"AAA",
…
K377U updated
6 years ago
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I noticed that the index written during compression by `bgzip` (`-i`) is missing the final block offset, while if re-written (`-r`) it is present. This is specifically noted in the source for bgzf.c a…
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I use the commad ""/usr/bin/basevar" -h",but it dosnt work !
return me "undefined symbol: hts_utell"
whole waring:
Traceback (most recent call last):
File "/usr/bin/basevar", line 9, in
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