On finswimmer's answer to “samtools mpileup skipping read” there was previously a discussion in the comments re the (now corrected) overly wide claim that samtools mpileup was deprecated.

There was a very small amount of to and fro (between terdon and me) as understanding was reached, which would have been deleted by its respective authors in due course.

Instead, it appears that terdon has deleted the entire conversation while editing the answer to reduce the scope of the deprecation claim.

This is unfortunate, as I had carefully composed my initial comment to explain why VCF/BCF mpileup has been moved from samtools to bcftools and thus confirm that there are no plans for any further mpileup moves — which is information that has now been lost.

It would be appreciated if moderators would use a more considered approach when deleting other people's work.

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    $\begingroup$ Thank you for bringing this here and in such a calm, constructive manner. That is very much appreciated! $\endgroup$ – terdon Aug 23 at 8:20

I'm afraid this is standard operating procedure on Stack Exchange sites. Comments are ephemeral, expressly designed to be deleted without warning. The idea is that comments should be used to ask for clarification, and then once consensus has been reached, they should be edited into the question or answer instead.

That's precisely what happened here. The claim that samtools mpileup is deprecated was incorrect, finswimmer meant that it was only deprecated when generating VCF files. Since finswimmer (not I) edited the answer to remove that claim, the comments were no longer relevant and since the entire comment thread was based on a misunderstanding, there was no reason to keep it around. It wasn't providing anything relevant to the actual question asked, so I deleted it. Here is a screenshot of the thread:

comment screenshot

This is something that is often surprising for folks who come to SE from other online resources. But this really is how comments are supposed to work, and is explained in the relevant help page, parts of which I quote below::

Comments are temporary "Post-It" notes left on a question or answer. They can be upvoted (but not downvoted) and flagged, but do not generate reputation. There's no revision history, and when they are deleted they're gone for good.


When should I comment?

You should submit a comment if you want to:

  • Request clarification from the author;
  • Leave constructive criticism that guides the author in improving the post;
  • Add relevant but minor or transient information to a post (e.g. a link to a related question, or an alert to the author that the question has been updated).

When shouldn't I comment?

Comments are not recommended for any of the following:


  • Secondary discussion or debating a controversial point; please use chat instead;

So, as a general rule, if you want something to stay with a post, make it an edit and not a comment. This is a collaborative site, so editing to improve a post or add extra information is absolutely encouraged. Comments, however, are ephemeral.

  • $\begingroup$ Mate, I've been answering questions on SE sites for 10 years. This was not an invitation for you to explain what you see as the rules; it was an invitation for you to take a more nuanced approach and a notification/request that someone could usefully wield the undelete button here. For reference, here and here are examples of useful years-long context provided by comment threads, and here is an example of undeleted noise on bioinf.SE. $\endgroup$ – John Marshall Aug 23 at 8:59
  • $\begingroup$ “the comments were no longer relevant […] It wasn't providing anything relevant to the actual question asked” Please reread my comment (“Indeed, mpileup has been split […]”) and explain why you think it provides no useful context to the as-now-edited “BTW” paragraph of the answer. (I have already spent time composing that text once, so your suggestion of spending more time recomposing it from scratch again to edit the answer is not very appealing.) $\endgroup$ – John Marshall Aug 23 at 9:09
  • $\begingroup$ @JohnMarshall I was answering with an eye to having a reference for other users about comments as well. Sorry if that came across as condescending, that was not my intent. I honestly don't see how the comments provide anything useful after the edit. What would be the point of keeping a now obsolete comment thread whose conclusion is already included in the answer? Mpileup is not deprecated, so why explain why it is not deprecated? The logic of the tool's devs isn't really relevant to the question. And thanks for pointing out that other noise, you're quite right and I've now deleted them. $\endgroup$ – terdon Aug 23 at 9:13
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    $\begingroup$ @JohnMarshall I asked one of the other mods to have a look as well since I was directly involved in this and so I might not be looking at it objectively. $\endgroup$ – terdon Aug 23 at 9:33
  • $\begingroup$ You are failing to distinguish between “comment thread” (which I agree is obsolete — see ¶2 of my initial question above) and “one particular comment” (which I am claiming is individually valuable). As you have been kind enough to provide a screenshot of the deleted text, I have now rectified the situation in question. But the general point remains. $\endgroup$ – John Marshall Aug 23 at 9:37
  • $\begingroup$ @JohnMarshall yes, I was referring to that specific comment, the one where you explain the rationale behind why the samtools devs decided to deprecate samtools mpileup when used for vcf output. I don't see why that is useful, relevant or in any way worth keeping. That's why I deleted it. Since you put it back, I won't antagonize you by deleting again, but you have yet to give your rationale for why you feel it was worth all this effort. It seems like an off topic aside that clutters up the answer to me. $\endgroup$ – terdon Aug 23 at 9:48
  • $\begingroup$ If you think that, then your consistent position would be to delete the entire “<strike>BTW samtools mpileup is deprecated</strike>” paragraph from the answer. $\endgroup$ – John Marshall Aug 23 at 9:59
  • $\begingroup$ @JohnMarshall yes indeed, that would be my preference but since finswimmer chose to cross it out instead, I let that be. I'm actually trying not to be too heavy handed, this meta discussion notwithstanding. $\endgroup$ – terdon Aug 23 at 10:02
  • $\begingroup$ “you have yet to give your rationale”— The rationale is (1) inherent in the fact that someone took the time and effort to contribute related information to this website, and (2) already provided as ¶4 of my initial question above. $\endgroup$ – John Marshall Aug 23 at 13:20
  • $\begingroup$ @JohnMarshall yes, but why is that information helpful in the context of that specific Q&A? It only came up at all because the answer made an incorrect claim. The claim was then removed, so the comments were no longer relevant. $\endgroup$ – terdon Aug 23 at 13:41
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    $\begingroup$ The claim has not been removed, merely partially overstruck. I refer you to my previous comment, with which you expressed agreement, noting that a consistent position would be to also delete the “BTW” paragraph. $\endgroup$ – John Marshall Aug 23 at 13:48

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