Error in RG argument does not stop minimap2

[dariober]

If an invalid RG line is passed to option -R, minimap detects the error but keeps going without adding RG tags. Maybe better to make it quit? E.g:

minimap2 -V
2.17-r941

minimap2 -R 'foobar' -a some.fasta some.fastq > /dev/null

[M::mm_idx_gen::2.132*1.00] collected minimizers
[M::mm_idx_gen::2.469*1.25] sorted minimizers
[ERROR] the read group line is not started with @RG             <============
[M::main::2.469*1.25] loaded/built the index for 36 target sequence(s)
[M::mm_mapopt_update::2.633*1.24] mid_occ = 32
[M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 36
[M::mm_idx_stat::2.762*1.23] distinct minimizers: 5072250 (89.73% are singletons); average occurrences: 1.216; average spacing: 5.327
[M::worker_pipeline::8.651*2.27] mapped 4000 sequences
[M::main] Version: 2.17-r941
[M::main] CMD: minimap2 -R foobar -a ref/TriTrypDB-45_LmajorFriedlin_Genome.fasta /export/projects/III-data/wcmp_bioinformatics/db291g/data/20190906_catarina_nanopore/20190902_1335_MN23371_FAK87904_27b810d7/fastq_pass/FAK87904_a513394c0ef96eff721553a5edf39959f27553c9_44.fastq.gz
[M::main] Real time: 8.718 sec; CPU: 19.723 sec; Peak RSS: 0.641 GB

[lh3]

Maybe better to make it quit?

Fair enough. I will consider this in the next release.