Error conversion mpileup to sync

GoogleCodeExporter commented 9 years ago

Hi,
A problem occured sometimes when converting mpileup to sync format of 
popoolation:
perl mpileup2sync.pl --input Input.mpileup --output Output.sync --fastq-type 
'sanger'

The error given is:
Fucked entry gnl|unk|Bti_11c 1  T   0 blablabal...  >>=8>>> at 
/home/a/abran_02/popoolation2/Modules/Pileup.pm line 50, <$ifh> line 1.

The problem occurs when some samples in the mpileup are uncovered at this 
position thereby leaving empty columns in the mpileup.
I corrected the issue by using a simple sed command in the pileup that replaces 
the empty columns by a "ghost read" of 0 quality in Sanger encoding:
sed 's/\t\t/\t!\t!/g' Input.Mpileup > Output.Mpileup
Then the same command using the new Output.Mpileup works fine.
But I guess it would better to modify the original script :)
Cheers

Antoine

Original issue reported on code.google.com by Ant1Br...@gmail.com on 25 Apr 2012 at 9:21

GoogleCodeExporter commented 9 years ago

Thanks for your comment. Seems like a creative solution :)

Original comment by RoKof...@gmail.com on 2 May 2012 at 11:17

GoogleCodeExporter commented 9 years ago

Hello,

I notice the same problem but in the .sam file, there is em pty column tagged 
as XA:Z:, but for me it make fail the conversion into .bam file telling me that 
there is missing column in auxiliary data (I am not sure what it suppose to 
mean :p ). Anyway I solved the problem in an other way by removing the empty 
column XA:Z with a small python script but it time consuming on bigger sample. 
Any idea why there is this extra column XA:Z: ? is it an important one? Anyway 
to solve that without removing/adding a column?

Original comment by braud.ma...@gmail.com on 3 May 2013 at 5:34

niuhuifei / popoolation2

Error conversion mpileup to sync #5