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Hello!
My program meets some problems.
I checked the log file, and found this.
The first time I ran my code, I got this error.
[E::bgzf_uncompress] Inflate operation failed: 3
[E::bgzf_read] Re…
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Hello.
When I ran `mosdepth` on our bam file I've got error which origin is from `hts-nim` - that's why I've created issue here.
Here is my error:
```
root@b79bb970b062:/outputs# mosdepth -t 20 . …
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I think gcc 13.2 and later are more strict about needing to have headers included in a file if you are using functions there.
g++ -O3 -Wall -std=c++17 -DWITH_HTSLIB -o bgz_writer.o -c bgz_writer.cp…
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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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Hello!
I've successfully gotten the .gamp file of the transcriptome file with `vg mpmap` and he seems to have no problem. But when I run rpvg, he has the following error:
Random number generator …
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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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As discussed in https://github.com/marcelm/cutadapt/issues/757 adding BAM support to dnaio would have several advantages for cutadapt. The alternative is to defer to pysam instead, and keep dnaio at i…
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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…