does Deacon check order of read-pairs is correct?

[handibles]

Thanks for the great tool (and Hostile before it).

Just wondering whether Deacon checks that the R1 and R2 are paired correctly for paired input (R1.fastq, R2.fastq)?

If it does check, does it fix incorrect read-pairings prior to decontam / in the output files (can outputs be assumed to be correctly paired)? Have had a quick look through the code but am a scullion cur so insight is limited.

[bede]

Hi and thanks!
Deacon currently only cares if read counts do not match between paired inputs – there is currently no header-level pair name validation, which would slow things down. Deacon uses paraseq for the last few versions, and there has been some discussion about an optional pair validation mode here noamteyssier/paraseq#60 (PR open) and here noamteyssier/paraseq#47 (cc @nrminor).