Odd adapter parsing about ea-utils HOT 10 CLOSED

Adapter input is "fasta" format.... so

>name
ad1
>name
ad2

Also, it only reports the adapters found.   So if you pass 20 of them, it will 
only report the 3 or 4 it finds.

[deleted comment]

In my opinion this issue should be re-open as "valid" and addressed.  One of 
the adapter in my example is actually a real illumina adapter and fastq-mcf had 
failed to recognize it.  The abitrariness of your "filtering" is worrisome.

If you can give me an example of where an adapter should be clipped, that would 
be OK.   I believe the adapter was "real"... it's filtered  if it's not found 
in the fastq file in significant numbers.

[deleted comment]

I'm going to close this issue, only because it's old, and I can't reproduce it 
reliably.  I did greatly increase the sampling window to fix a number of issues 
people have seen where they were concerned with undetected adapters, however at 
some point, the benefits outweigh the risks of false-positive clipping.