James Bonfield

I'm not convinced this is ideal. While some commands do this, it's not without problem. Specifically on Windows it's not easy to distinguish between reading from stdin being a file...

Closing this as we don't have any plans to extend support for implicit stdin right now, but we may revisit this in the futue.

To test if this is a bottleneck, you may wish to add various [mbuffer](https://manpages.ubuntu.com/manpages/bionic/man1/mbuffer.1.html) parameter sets inbetween bwa and samtools to see if adding an additional memory buffer improves the...

Your BC tag is invalid. You have `BC:Z:1`, but the SAMtags specification states it must be sequence, possibly with `-` or `+` separating the multiple barcodes. I'm not sure why...

Agreed. We'll leave this issue open as we have other things that need fixing here clearly.

Thank you for responding. It's good to know at least someone is using it so our efforts aren't wasted. Heng does have a better alternative tag (cs I think), but...

There are essentially two different uses of FASTQ out there now. The original use was for old Sanger-style technology input data or for consensus sequences from assemblies. Line wrapping was...

I think I'd be in favour of `-n 0` just being a synonym for no wrapping, but we could add an explicit `--single-line` option too as it's trivial. Either way...

To be clear, I'm only *assuming* the original intent for fqidx given the name and extreme similarity to faidx, along with its use on references instead of individual read sequences....

> I suppose my one other plea would be consistency -- samtools fastq outputs 4 line records. Of course, that's opening up a new can of worms as samtools fasta...