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I'm not sure if this is intentional... `samtools view` accepts any strings as argument to `-q/--min-MQ` without complaining:
```
samtools view -c -q foo ds051.actb.bam
15098
echo $?
0
```
…
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```bash
$ samtools --version
samtools 1.13
Using htslib 1.13
$ uname -sr
Linux 5.4.0-1052-gcp
$ uname -m
x86_64
$ gcc --version
gcc (Ubuntu 7.5.0-3ubuntu1~18.04) 7.5.0
Copyright (C) 20…
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#1 upgraded foca to 0.12.0 but relied on an ugly hack to do so (see below). Removing this hack is not difficult, but requires replacing `config['FOCA']` everywhere by `config.foca`.
https://github.…
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Hello. I need to read those dicom files from the gcp cloud storage bucket. Is there any way I can pass the gs link to the WsiDicom.open() method?
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The following request
```
https://htsget.demo.umccr.org/reads/org.umccr.demo.htsget-rs-data/cram/mt.sorted_cram?class=header&format=bam
```
results in the following response
```
{
"htsg…
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Hi @ChristofferFlensburg,
We are facing some errors in SuperFreq trying to infer CNAs on RNA data.
The first error was related to the issue #100 (R 4.3.1 and SuperFreq 1.4.4):
> [E::bcf_hdr_p…
gbss2 updated
10 months ago
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**Describe the bug**
A clear and concise description of what the bug is.
**To Reproduce**
Steps to reproduce the behavior:
```
crypt4gh encrypt -f test -p user2.pub.pem -s user1.sec.pem
panic…
-
####
samtools 1.17
Using htslib 1.17
Features: build=configure libcurl=yes S3=yes GCS=yes libdeflate=no lzma=yes bzip2=yes plugins=no htscodecs=1.4.0
CC: gcc
CPPFLA…
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Hi, I'm trying to run TBprofiler and facing some error, but I can't figure out whats the problem to fix it. I have confirmed (I hope) that I have all the input files and as I am facing this error, I w…
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In cases where se several encryption keys are used, no error message is returned if one of the keys is missing.
Example. Command:
crypt4gh encrypt --recipient_pk key1.pub --recipient_pk key2.pub…