Incompatability with latest bwa due to tabs in @RG

[EugeneBragin]

snippy/bin/snippy

Line 214 in 848a62e

$bwaopt .= qq{ -v 2 -M -R '\@RG\tID:$rgid\tSM:$rgid'};

line 214:
https://github.com/tseemann/snippy/blob/v3.1/bin/snippy#L214

This is double quoted string, which interpolates \t into actual tab, however latest bwa dies if it sees tabs there:
https://github.com/lh3/bwa/blob/master/bwa.c#L428

which could be clearly seen in the error log, among other warnings and messages:
[E::bwa_set_rg] the read group line contained literal characters -- replace with escaped tabs: \t

however this scenario is not handled and it keeps going further.

A simple double-escape of tab: $bwaopt .= qq{ -v 2 -M -R '\@rg\\tID:$rgid\\tSM:$rgid'};
solves the problem

[tseemann]

This was already fixed 11 days ago 34fab55
but I have not made a new release yet.

In fact I did exactly the same thing as you suggested:
+$bwaopt .= qq{ -v 2 -M -R '\@RG\\tID:$rgid\\tSM:$rgid'};
Great minds think alike!

Thanks for the report, it reminds me I need to make a new release.

[EugeneBragin]

Thanks @tseemann
really good set of tools btw

[tseemann]

It will appear in official 3.2 release.

[sachalau]

@tseemann I'm running into the same problem using the bioconda version which is still 3.1. I was starting to update the bioconda recipe to upload the new release... before realizing I was a bit early :')
Do you have an idea regarding when you'll be able to release this new version ?
Thanks a lot for all the good work !
(pinging you because I don't know whether you receive notifs on closed issues, sorry)