dstreett / Super-Deduper

An application to remove PCR duplicates from high throughput sequencing runs.
11 stars 4 forks source link

Functional Testing #21

Closed dstreett closed 8 years ago

dstreett commented 8 years ago

Hey @bioSandMan,

I just merge your test into develop ran it. A little later I realized I was zeroing out the ID key to find duplicates so everything was considered a duplicate.

The 'make test' was OK in both. cases.

Example: Building with correct source code. R1 and R2 looks as follows.


@NODUP
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+
BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
@NODUP
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
+
BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB

Output of Super-Deduper

NODUP
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
+
BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
@NODUP
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+
BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB

Totally expected to pass test and it does.

if [ ! -d "superTests" ]; then mkdir superTests; fi;
python testSD.py 
.
----------------------------------------------------------------------
Ran 1 test in 0.001s

OK

However, under the bug version. . .

The output with the same input is.


@NODUP
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+
BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB

The other NODUP header doesn't show up.

The 'make test' shows this though.

if [ ! -d "superTests" ]; then mkdir superTests; fi;
python testSD.py 
.
----------------------------------------------------------------------
Ran 1 test in 0.001s

OK

Make test should fail under these conditions, but they don't seem to be. Let me know if you have any questions and when you would like me to test it again.

bioSandMan commented 8 years ago

At the moment everything will pass since I've been rebasing the tests on assertions. I should have this figured out shortly.

dstreett commented 8 years ago

Fixed with #23 PR.