Looks good thanks, especially removing the code duplication. I've taken the liberty of pushing a commit to add the option into the man page, hopefully that looks alright. If it is, I'll squash everything together and merge it.

Do let us know if you think you have anything else that might be useful. There's no hard-and-fast rules about what gets included - I would guess the criteria is how much work there is in porting it into the samtools framework plus ongoing maintenance compared to how many people are likely to want to use it.

Thanks for the prompt response. It's now rebased into a single commit. Let me know if there's anything else needed for this PR.

Nothing else needed, and now merged.

Thanks.

Could this be extended to exclude readnames too? I use both sets of logic in different contexts. Perhaps adding a ^ to the front of the FILE could indicate exclusion as used in bcftools.

You can invert the filter at the moment, albeit not completely efficiently, using the -U option ("output reads not selected by filters to FILE"). So just use -U to output the data you want and -o /dev/null to throw away the rest. E.g.:

samtools view -N names -b -o /dev/null -U keep.bam in.bam

You can also use -U - to send the data to stdout.

Ha! Never would have though to try that. Thanks.

Hi, I would like to ask how is the speed of this function? Is it random access? or traverse the input file