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relevant issue: https://github.com/LieberInstitute/megadepth/issues/6
I am trying to build megadepth on alpine container in order to have a "slimmer" image in the end.
I get various issues from co…
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I'm trying to convert a 19gb .sam file to .bam format using the samtools view command. I've seen a related [issue thread](https://github.com/samtools/samtools/issues/67) on this site where it was sta…
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lumpy-sv-0.3.1 gaom4$ make
cd lib/htslib && \
./configure --disable-bz2 --disable-lzma --enable-libcurl
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compile…
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```
$ 13amp /bam -S /cram
$ ls -l /bam
```
So far the 13amp process has consumed 82m of CPU time (at 100%+ utillisation) but it has not returned anything for the directory listing yet.
13amp is run…
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Use tools from spacegraphcats to do the indexing https://github.com/spacegraphcats/spacegraphcats/issues/273
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Hi! Li Pan,
I tried to build PsBL according to the steps in readme.
I am working in a linux system. Initially `call_interaction.cpp` cannot find `htslib/bgzf.h` despite `htslib` is in my `$PATH`. I …
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Some of these look legit, some may arguably be false positives.
I also see some assignments inside of `assert()` calls in the diagnostics (there may be more in the code), which is generally conside…
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Hello,
I have simulated some of my own reference panels in `vcf` format that I'd like to use as reference panels. I wish to test it on Minimac4, which means I need it to be in `m3vcf` format. I can…
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### case: a file only with header lines
```
##fileformat=VCFv4.2
##nanopolish_window=MN908947.3:1-29902
##INFO=
##INFO=
##INFO=
##INFO=
##INFO=
##INFO=
##INFO=
##INFO=
##INFO=
##INFO=
…
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I have an Ubuntu 20.04 and followed the package install instructions at https://github.com/Gaius-Augustus/Augustus/blob/master/docs/INSTALL.md#HTSlib
bam2wig fails to compile. (Not a problem for me …