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Hi!
I am using sawfish v.0.12.6 to identify SVs in my PacBio Hifi data that I have aligned to a reference genome using pbmm2.
However, I get the following error message for each of my 10 samples:
…
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Minutes from yesterday's meeting:
@glennhickey is currently working with Peter on a mapping experiment comparing mapping to vg vs mapping to the linear reference augmented with alts.
We can use …
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**Description**
At my debugger I try to determine subroutine name for tracing purpose.
```perl
use B qw/ svref_2object /;
sub sub_name {
my $r = shift;
return $r unless ref $r;
re…
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Hello, Thank you for the great pipeline!
Now, I try to run the pipeline to call SV. I get an error when trying to run sv_pipeline.cwl, the error as below:
```Shell
cwltool /home/liuhui/ctDNA-pipeli…
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This is similar to issue #290
PVFM are not saved
``` perl
> cat test.pl
format STDERR =
.
my $stdout = *STDOUT{IO};
my $stderr = *STDERR{FORMAT};
print ref($stdout).' || '.ref($stde…
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Hello,
I am a bit confused with a merged SV having a position -1.
```
chr17_KI270729v1_random -1 chr17_KI270729v1_random_395 C . PASS SUPP=26;SUPP_VEC=111111…
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Hi,
I was playing around with the pyvips image loaders new_from_file and openslideload. I noticed that when you write an image using pyvips and then load it using openslideload, then openslideload …
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### Operating system
ubuntu 20.04
### Platform
64bit x86
### OpenSlide Python version
openslide.__version__
### OpenSlide version
4.0.0
### Slide format
svs
### Issue det…
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In .Net 3.1 and 5 the logging was grouped into one message. Now each line is an info message from VueCliMiddleWare, it's not good for debugging.
![image](https://user-images.githubusercontent.com/126…
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Hi,
I used duphold on some VCFs containing SVs called with Sniffles where the alignment was done using minimap2. The data used is all nanopore longread data. I was wondering if duphold is supposed …