minimap2 doesn't croak when unequal numbers of reads are in fwd and rev files #58
Description
~/git/coverm/tests/data$ coverm genome --single-genome -c bad_read.1.fa <(randomFasta.pl 100 5) bad_read.2.fa bad_read.2.fa -r 7seqs.fna --min-covered-fraction 0
relevant minimap2 output
[2021-02-02T06:41:27Z DEBUG coverm::bam_generator] The STDERR for the MINIMAP2_SR part was: [M::main::0.002*1.27] loaded/built the index for 7 target sequence(s)
[M::mm_mapopt_update::0.002*1.27] mid_occ = 1000
[M::mm_idx_stat] kmer size: 21; skip: 11; is_hpc: 0; #seq: 7
[M::mm_idx_stat::0.003*1.24] distinct minimizers: 9434 (100.00% are singletons); average occurrences: 1.000; average spacing: 6.044
[W::mm_bseq_read_frag2] query files have different number of records; extra records skipped.
[M::worker_pipeline::0.003*1.18] mapped 10 sequences
[W::mm_bseq_read_frag2] query files have different number of records; extra records skipped.
[W::mm_bseq_read_frag2] query files have different number of records; extra records skipped.
[W::mm_bseq_read_frag2] query files have different number of records; extra records skipped.
[M::main] Version: 2.17-r941
[M::main] CMD: minimap2 --split-prefix /tmp/.tmpnOkBsU -a -x sr -t 1 /tmp/coverm-mapping-index.FY2fg0iAmiL8/7seqs.fna bad_read.1.fa /dev/fd/63
[M::main] Real time: 0.005 sec; CPU: 0.005 sec; Peak RSS: 0.006 GB
Only fix is to grep the stderr for 'different number of records' I guess. Gah.