error when visuzlization about alignoth HOT 3 CLOSED

Hi there,

the corresponding line in the code is

let tid = bam.header().tid(region.target.as_bytes()).unwrap() as i32;

This suggests the given target (e.g. chr1) is not present in your bam header or probably even file in general. The error message could be improved quite heavily on our side here. I'll try to fix that asap so please keep this issue open until then.

Hope this helps,
Felix

from alignoth.

Hello Felix,

I am visualization a bam file from a bacterial genome (not human genome) and it is fragmented. There is not chr1 or something, each fragment is like bacterial name_1 or something. I was using bwa mem to mapping not Bowtie2.

Thanks,

Jianshu

from alignoth.

@jianshu93 sure, the chr1 was just an example. Could be any other contig name that causes the failure here. I've just released version 0.6.1, which will provide a better error message that hopefully solves your problem by telling you what is wrong with your input. In case there is still an issue with 0.6.1, please feel free to reopen this issue or open a new one. Thanks!

from alignoth.