daviesrob

I can see that this would make downstream processing quicker, although it probably wouldn't change the speed of `samtools depth` too much apart from having to write less output. But...

@colindaven It's not quite the same. #423 inverts the filter test but leaves the region list unchanged - so flags and BED files (which act as a filter) get inverted....

The message you saw was removed in commit 6435bcca21 (look in bam_import.c) which was between releases 0.1.19 and 0.2.0. You may not be running the copy of samtools you expect...

Sadly there isn't a good solution for BAM at the moment. For now, the workarounds are: 1. Break your large chromosome at some convenient point(s) so no part is longer...

No, it's not expected. What version of samtools are you using, and would it be possible for you to make a minimal file that reproduces the problem?

Having looked at this a bit more closely, I've noticed that the FLAGs on your output file example is 272, which means `REVERSE,SECONDARY`. So it's possible that whatever produced the...

The EBI also have documentation on how to use squid to cache the references: https://ena-docs.readthedocs.io/en/latest/retrieval/programmatic-access/cram-reference-cache.html

`faidx` is supposed to support long chromosomes, but the length seems to get capped at 2^32 bases. The problem is in [this line](https://github.com/samtools/htslib/blob/008eabd3/faidx.c#L734), which originally prevented an overflow when the...

samtools/htslib#1446 should have gone most of the way to fixing this. I'm leaving this issue open for the moment though as I notice that there are a few other improvements...

Getting access to your files would be useful. It worked on my test one, but I cheated a bit by making my sequences all "N" so they compressed down to...