Breakdancer Output : What'S Wrong With This Query ??

Question

[madkitty]

I ran Breakdancer on a sample dispatched into 4 bam files. Where options -g -h are set an error message shows up :

perl bam2cfg.pl  -g -h 1.bam 2.bam 3.bam 4.bam > sample1.cfg
Use of uninitialized value in printf at bam2cfg.pl line 222.
Use of uninitialized value in printf at bam2cfg.pl line 222.
Use of uninitialized value in printf at bam2cfg.pl line 222.
Use of uninitialized value in printf at bam2cfg.pl line 222.

So I ran Breakdancer with no option on it with the following query :

perl bam2cfg.pl  1.bam 2.bam 3.bam 4.bam > sample1.cfg
breakdancer_max sample1.cfg > sample1.txt

No error message shows up but the output files shows big overlapping sections and long Copy Number segment, you can see it here :

http://tinypic.com/r/iwjdar/6

http://i46.tinypic.com/iwjdar.jpg

(output histograms show an insert size of 160bp)

[Michael]

I don't know breakdancer but this is only a warning, trying to print an undefined variable. Ofc, that is a sign of bad perl hacking or lack of testing, maybe both. It might still give you output which you can use the question is do you still trust the skills of the programmer, or would you try to debug it yourself (look at line 222), or send a report to the author? Normally, if I see such warnings I assume the code is just bad and don't use it, unless it's my own code of course

[madkitty]

funny thing, I had the same thought after all and decided to run the cfg file with -g -h no matter what. When I checked the code line 222 was empty only one bracket '}' was there.. so maybe the program was expected some print stdout function or smth.. anyway, let's see tomorrow morning the output of Breakdancer. Thanks :)

Answer 1

[madkitty]

question answered with previous comment