--max-ns 0 does not seem to work, still getting reads with Ns

[GoogleCodeExporter]

What steps will reproduce the problem?
1. fastq-mcf --max-ns 0 -o test1 -o test2 -R adapters.fa test1.fq.gz test2.fq.gz

What is the expected output? What do you see instead?

Expected to see reads with Ns discarded. Saw reads with Ns.

    cat test1 test2 | awk '(NR+2)%4==0' | grep -c N
    73

What version of the product are you using? On what operating system?

ea-utils.1.1.2-537.tar.gz on linux x86_64

Please provide any additional information below.

Original issue reported on code.google.com by sujaiku...@gmail.com on 2 Oct 2013 at 3:32

Attachments:

• test1.fq.gz
• test2.fq.gz

[GoogleCodeExporter]

right! i only ever tested with 1 & 2....   i will fix today.  thanks

Original comment by earone...@gmail.com on 2 Oct 2013 at 3:35

[GoogleCodeExporter]

Thanks for looking into this! And for the terrific tool 
(fast/efficient/flexible with pipeable output)

Do use the attached files instead. The ones above have no Ns post filtering in 
test1

Also, I should have said, I tried all combinations of one or both of: --max-ns 
0 and --mate-max-ns 0, but got the same results in all cases:

fastq-mcf --max-ns 0 --mate-max-ns 0 -o test1 -o test2 -R adapters.fa 
test1.fq.gz test2.fq.gz

awk '(NR+2)%4==0' test1 | grep -c N
4
awk '(NR+2)%4==0' test2 | grep -c N
41

----

as you said --max-ns or --mate-max-ns 1 or 2 seem to work fine.

Original comment by sujaiku...@gmail.com on 2 Oct 2013 at 4:04

Attachments:

• test1.fq.gz
• test2.fq.gz

[GoogleCodeExporter]

I just tried changing line number 1286 in fastq-mcf.c (in 
ea-utils.1.1.2-537.tar.gz) to:

    if (t_max_ns >= 0) {

and it seemed to do the trick.

Original comment by sujaiku...@gmail.com on 3 Oct 2013 at 1:08

[GoogleCodeExporter]

yep, that's the same change i just made (and checked in)

Original comment by earone...@gmail.com on 3 Oct 2013 at 1:09

[GoogleCodeExporter]

Thanks so much!

Original comment by sujaiku...@gmail.com on 3 Oct 2013 at 1:10

[GoogleCodeExporter]

Original comment by earone...@gmail.com on 3 Oct 2013 at 1:51

• Changed state: Fixed