Valeriu Ohan

@wm75 thank you for the data! We would have struggled long and hard to reproduce the issue without it. First, when you specify a mpileup window (with **-r**), reads that...

I haven't looked at your data yet, but it looks similar to #986.

After looking at the data, it appears not be related to #986. In fact, it works as ~~expected~~ intended. Two of the 5 read pairs overlapping position 5064 are: ```...

[sam.c:4310](https://github.com/samtools/htslib/blob/3f140ad0bd64beeed2884b818e7b7a08ef06721d/sam.c#L4310) ```c if ( a_iref+a->core.pos != b_iref+b->core.pos ) continue; // only CMATCH positions, don't know what to do with indels ``` Also, `cigar_iref2iseq_next` only returns `BAM_CMATCH` (0) or an error...

Similar to https://github.com/samtools/samtools/issues/1118 If you don't want to try the develop branches of HTSlib and samtools, which now offer more details on this kind of errors, you can try running...

What does the kernel log show you? Run `cat /var/log/kern.log`, if you have permission, or `dmesg -k` just after `bcftools` is killed.

Yes, the BED file is used as a post-processing filter, while the index is required when target regions are explicitly provided as command line arguments. For `samtools view`, there is...

I had a similar need and found the solution in [Libz.jl](https://github.com/BioJulia/Libz.jl/blob/master/src/checksums.jl). On the other hand, although these days I mostly write C code, I tend to disagree with the use...

No, `tabix` doesn't burn its version into the output index. How would that information help you? Also, bear in mind that the latest released and maintained version of `tabix` is...

If you just want the version of `tabix` you are currently using, you can obtain that with the command: `tabix --version`