fasterq-dump "--only-aligned" and "--only-unaligned" ignored when combined with "--fasta"

[jgans]

It appears that requests to output a subset of reads (using either the --only-aligned or the --only-unaligned flags) are ignored by fasterq-dump (version 3.0.0) when fasta output has been specified with the --fasta flag:

For example, when extracting reads from ERR1138826, the number of reads written does not change when the --only-unaligned flag is used in conjunction with --fasta:

$ fasterq-dump ERR1138826 --fasta --only-unaligned
spots read      : 4,227,697
reads read      : 8,455,394
reads written   : 8,455,394 <-- Output includes aligned and unaligned (unexpected behavior!)

$ fasterq-dump ERR1138826 --fasta
spots read      : 4,227,697
reads read      : 8,455,394
reads written   : 8,455,394

The same unexpected behavior is encountered when combining --fasta and --only-aligned. However, the expected output is obtained when --fasta-unsorted is used instead of --fasta, i.e.:

$ fasterq-dump ERR1138826 --fasta-unsorted --only-unaligned
spots read      : 4,227,697
reads read      : 1,662,845
reads written   : 1,662,845 <-- Output only includes unaligned reads (as expected)

$ fasterq-dump ERR1138826 --fasta-unsorted
spots read      : 4,227,697
reads read      : 8,455,394
reads written   : 8,455,394