--MD doesn't work with splice alignment because I don't know how to encode introns in MD.

Thank you, just another question....
Does the "samtools calmd " command consider introns as indels?

I don't know. Although I implemented the initial calmd, I have forgotten the details and the samtools team may have made significant improvements to it. You have to ask the samtools team unfortunately.

Thank you for your quick answer, I'll ask them!

I have seen your question at samtools/samtools#809. Do you prefer MD to include introns or not to include introns? What's the use case in your mind? Thank you.

@lh3 With --MD tag not working with splice alignment, we should expect --cs tag not to work too? As you are constructing --cs out of --MD/cigar and the query/ref sequences. Am I right?

I see no error when I use --cs with splice alignment, but the output sam files do not contain cs tags. It would be great if you can produce a warning to let users know about it.

I get the same error with the --MD flag, which is now clear of course. But on the comment above by @SaberHQ: I do get the cs tags in the SAM output when running a spliced alignment with --cs

@SaberHQ --cs has been working for a long time. If it doesn't, please send me an example.

3a119d6 enables --MD to work with spliced alignment. I am closing this issue. If the new code has bugs, please create a new issue.