Martin Vickers

Reading BAM Records into a FragmentStore in batches

8

How do I go about reading BAM Records into a FragmentStore in batches? I'm trying to work with the reads at specific bases within the TAIR10 genome. So first I...

Maintaining binaries for older OSs

18

Not an issue, just a question. Since the update of SeqAn that now requires GLIBC 2.14 the binaries I have created no longer run on many of the production HPC...

bwamem2 as a library and linking to own project

6

Hi, I was wondering how one might go about using bwa-mem2 as a library in the same way you can in the original bwa; https://github.com/lh3/bwa/blob/master/example.c or is there now another...

I've been trying to run progressiveCactus but I have the following error message; [martin@login progressiveCactus]$ source environment (python)[mjv08@bert progressiveCactus]$ ./bin/runProgressiveCactus.sh --help Traceback (most recent call last): File "./bin/../src/progressiveCactus.py", line 37,...

AttributeError: 'str' object has no attribute 'write'

1

Hi, I'm struggling to get liftoff to run, I'm getting the following ``` $ singularity exec ~/bin/liftoff.img liftoff -g Pisum_sativum_v1a_genes.gff3 assembly.fasta Pisum_sativum_v1a.fa extracting features 2022-01-28 11:37:47,988 - INFO - Populating...

Great name :-)

2

Not an issue.