SAM4WebLogo bug? Some output sequence lengths are short by 1 character

[ashipde]

I am using the latest master version of jvarkit with Java 1.8 on CentOS with a command like:

java -jar sam4weblogo.jar -r X:129920493-129920543 myData.bam 2> /dev/null | awk 'NR%2==0' > myMsa.txt

While all output sequences are expected to be 51-characters long, same as the region size, I see some that are shorter by one character. Is this a bug?

AGCCCTAAAAGAGTTTGAGCAGCTGTGGAAGGTTAATCCAGCTGCAGCACT
AGCCCTAAAAGAGTTTGAGCAGCTGTGGAAGGTTAATCCAGCTGCAGCACT
-----TAAAAGAGTTTGAGCAGCTGTGGAAGGTTAATCCAGCTGCAGCACT
---------AGAGTTTGAGCAGCTGTGGAAGGTTAATCCAGCTGCAGCACT
AGCCCTAAAAGAGTTTGAGCAGCTGTGGAAGGTTAATCCAGCTGC-----
AGCCCTAAAAGAGTTTGAGCAGCTGTGGAAGGTTAATCCAGCTGCA----
AGCCCTAAAAGAGTTTGAGCAGCTGTGGAAGGTTAATCCAGCTGCAG---

[lindenb]

You're right thanks, I've recently changed the code but I didnt' test it. I've updated the sources, can you tell me if it works now ?

Thanks

P.