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Old 09-06-2010, 01:32 PM   #1
cliff
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Default how to make BreakDancer's bam2cfg.pl work?

Dear All,

I hope someone here can help me figure out how to make BreakDancer's bam2cfg.pl work. I just downloaded the latest version of BreakDancer from http://breakdancer.sourceforge.net/index.html

From this page http://breakdancer.sourceforge.net/moreperl.html, it looks like we need download two perl modules. So, I downloaded them and put them into a library directory and added

Code:
use lib 'myDirectory/lib/';
at the beginning of bam2cfg.pl.

But after I ran bam2cfg.pl, I still got this error

Code:
Use of uninitialized value in printf at /myDirectory/bam2cfg.pl line 223.
Can anyone share your experience of doing this?

All your help will be greatly appreciated.

-c
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Old 09-07-2010, 12:09 AM   #2
KevinLam
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Default

actually on my CentOS system i found that i needed 3 modules

this are my own notes
#Perl version requires below install using cpan as root
cpan
install Statistics:escriptive;
install Math::CDF;

install GD::Graph::histogram

if you have root access and install using CPAN you do not need to fuss with the use lib option.


but your error seems like it has another reason. can you print the line 223 here?

for my version i only see
Quote:
}

Last edited by KevinLam; 09-07-2010 at 12:19 AM.
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Old 09-07-2010, 12:39 AM   #3
natstreet
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I downloaded breakdancer a minute ago and tried running bam2cfg.pl and get the error message

Code:
Use of uninitialized value in printf at perl/bam2cfg.pl line 222
This is line 222

Code:
      printf "%d",$flagHgram{$rg}{all};
I installed the three libraries required using CPAN.
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Old 09-07-2010, 03:35 AM   #4
KevinLam
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Hmmm I am using version
breakdancer-1.0_2010_06_24

but I see the same code.
will upgrade and try tomorrow.
$rg is the readgroup. perhaps the read group wasn't defined?
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Old 09-07-2010, 06:32 AM   #5
cliff
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Quote:
Originally Posted by natstreet View Post
I downloaded breakdancer a minute ago and tried running bam2cfg.pl and get the error message

Code:
Use of uninitialized value in printf at perl/bam2cfg.pl line 222
This is line 222

Code:
      printf "%d",$flagHgram{$rg}{all};
I installed the three libraries required using CPAN.

my error is the same. I added

Quote:
use lib 'myDirectory/lib';
at the beginning of bam2cfg.pl so my line 223 is your line 222.

Have you changed line 61 or 60 to


Quote:
open(BAM,"yourDirectory/samtools view -h $fbam |") || die "unable to open $fbam\n";
I installed three modules and changed line 61 but still got the same error...
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Old 09-07-2010, 09:15 AM   #6
Xian
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The error message is probably due to that the readgroup hasn't shown up as the key for flagHgram. Please change line 222 to

if(defined $flagHgram{$rg} && defined $flagHgram{$rg}{all}){
printf "%d", $flagHgram{$rg}{all};
}

Basically just adding a condition to print out the histogram number.

If the same error still appears after adding the condition, please try not using the option -g.
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