Baraa Orabi /baraːʔ ʕraːbi/

Multi-threading

4

**Is your feature request related to a problem? Please describe.** The simulator is very slow when it comes to - Adjusting the lengths of reference contigs. This might be not...

When stddev is zero, mean is not cast to an integer, raising an error for `return junk_frag[:fragment_length]`

What happens when I use a mean fragment length bigger than the largest contig, with zero std.dev?

Getting multiple consensus paths

5

Is there a way to generate multiple consensus paths and not just only the best/heaviest path?

Output is not reproducible

1

In line 1505 of the `simulator.py` script: https://github.com/bcgsc/NanoSim/blob/23911b67ce4733f0468ac26296e25348e3b73b4b/src/simulator.py#L1504-L1506 The seed is reset before each process/thread is started. This overrides the setting of the random seed in here: https://github.com/bcgsc/NanoSim/blob/23911b67ce4733f0468ac26296e25348e3b73b4b/src/simulator.py#L2180-L2181 It also...

Why is there only one CIGAR reported when there are multiple alignment locations being found? Which of these locations does the CIGAR belong to? Is there a way of getting...

Order of operations in CIGAR

4

I found that Minimap2 sometimes generates an unusual order of CIGAR opertations; with some `N`s, followed by some `I`s then followed by more `N`s instead of the more expected order...

Single base exon in splice alignment

1

I have a long read (ONT) that I am aligning to the reference genome using Minimap2 `-x splice` mode. Minimap2 is generating a 1bp exon as part of the alignment...