Alex Leonard

feat: Allow "temp" files to be conditionally removed by user-set parameter (extending --nt)

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### Description This PR changes the handling of temp files and the `--nt` parameter. It isn't directly related to #1602, but I believe it may be able to solve it....

True on v7.8.2, but from peeking at the code, there is no mention of wildcard constraints near the `glob_wildcards` definition. So code like this "fails" because it pulls in the...

Accessing translation table from giraffe autoindex workflow

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This is a bit of a winding journey to try and solve #3126 , so hopefully haven't missed out too many details. I'm using a minigraph GFA as input (so...

Hi, The segfault is caused for example [by this line](https://github.com/fritzsedlazeck/Sniffles/blob/c02731ad288b32949c583cca2252164b235e5cb6/src/sniffles/sniffles#L192), where pysam tries to open a file path that doesn't exist (i.e. `--vcf directory_not_yet_created/sample.vcf`). Totally valid choice to not allow...

extend splitHaplotype with fastq output option

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Fairly straightforward changes to allow splitHaplotype to take a `-fastq` flag to print out triobinned fastq reads. Canu may not use the quality values in assembly, but as the primary...

Unitigging memory requirements potentially overestimated for hifi reads

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Hello, I've been using (Hi)canu to assemble hifi reads, with some good success. I had a question regarding the bat-unitigging stage. ### command The overall command I'm running is `canu...

I know there is not a lot of support for minigraph P-lines (#27) and it would break if a user added any new assemblies, but tools like `vg deconstruct` appear...

Hi I was having issues compiling agc using `make -f makefile.release agc` (to avoid the python binding), and ran into several errors about a missing reference to a clcok like...

Hi Anton, This seems to be related to #141, but downloading the latest snapshot from 3657d9a seems to still have "path hits" after blasting in the GUI. The issue for...

Fixes a typo that gave a somewhat cryptic error when installing via `pip install .` ``` Getting requirements to build editable ... error error: subprocess-exited-with-error × Getting requirements to build...