When multiple inputs specified, BCALM silently loses data

[karel-brinda]

Minimal example

$ printf '>seq1\nAAAAAAAAAAA' > 1.fa
$ printf '>seq1\nCCCCCCCCCCC' > 2.fa
$ bcalm -kmer-size 11 -abundance-min 1 -in 1.fa -in 2.fa -out output
$ cat output.unitigs.fa 
>0 LN:i:11 KC:i:1 km:f:1.0   L:-:0:-  L:+:0:+ 
AAAAAAAAAAA

FOF

This works ok:

$ printf '1.fa\n2.fa' > list.txt
$ bcalm -kmer-size 11 -abundance-min 1 -in list.txt -out output2
$ cat output2.unitigs.fa 
>0 LN:i:11 KC:i:1 km:f:1.0   L:-:0:-  L:+:0:+ 
AAAAAAAAAAA
>1 LN:i:11 KC:i:1 km:f:1.0   L:-:1:-  L:+:1:+ 
CCCCCCCCCCC

cc @OndrejSladky @PavelVesely (kudos @jermp for pointing out an inconsistently low number of k-mers in one of our experiments)