#7 results are 0 snp and 'na' for measure

[Anonymous]

Originally created by: sujan.ma... (code.google.com)@gmail.com

What steps will reproduce the problem?
1. params used
perl Variance-sliding.pl --input example.pileup --output example.pi.txt --snp-output example.snps.txt --measure pi --pool-size 25 --fastq-type illumina --min-count 2 --min-coverage 6 --max-coverage 100000 --min-covered-fraction 0.01 --min-qual 25 --window-size 100000 --step-size 10000

2. regular pileup file with 6 columns

Chr01    205577    A    142    .$.$.$,$,,,...$...,,,.,,,..,.,.,..,..,...,,,.C,..,.,,,.,.,..,,,..,,,...,.,....,.,,,.,.,,,,..,.,,.,,..,.,,...,...,,,.,..,......,,,...,,,,...,,..,,^].^].    <22@DD@A4#?@8FFF8FCH8?G<F(E?DH?<G>B4HGED)BDBE??@6@DDBDBB@9HG?@CHDJ5I;J;=JBC>GEG7F55<<JE5J6DA>;JHE<50BFH0FII0<:FAG=)FHHHFH95.FFF55.?FHF@>CE<9@?

Chr01    205578    A    142    ,,,...$..,,,.,,,..,.,.,..,..,.C.,,,..,..,.g,,.,.,..,,,..,,,...c.,....,.,,,.,.,,,,..,.c,.,,..,.,,...,...,,,.,..,......,,,...,,,,...,,..,,..^].^],^],^],^],    BD@<;#B?DD@A@:DA<A8C8F8DF6<G=(CG@3D;5DB;B(;3=9C:DG>?,FF9;AHEF&H9JCCI?F-?7B)G<)95JH)J&2E5&JC6H;)@/G&?JJ501H2IF)GJHHDH0,*HHH0&60FHF9+@F50C@C####

What is the expected output? What do you see instead?

Chr01    50000    0    0.000    na
Chr01    60000    0    0.000    na
Chr01    70000    0    0.000    na
Chr01    80000    0    0.000    na

Both window size and measure are issues

What version of the product are you using? On what operating system?
Popoolation 1.2.2 on Ubuntu 12.10

Please provide any additional information below.

[Anonymous]

Originally posted by: RoKof... (code.google.com)@gmail.com

your quality encoding is sanger not illumina
best ro

[Anonymous]

Originally posted by: jjjscu... (code.google.com)@gmail.com

I also have the same problem.

The command I use is:

perl Variance-sliding.pl --measure pi --input Comp.pileup --min-count 2 --min-qual 20 --min-coverage 4 --max-coverage 70 --pool-size 25 --window-size 3000 --step-size 1000 --output Comp.varslid.pi

the header line on my file is:

p5_sc00201      5283    A       3       AA^KA   gf_
p5_sc00201      5284    G       3       CCC     ei_

Can you give me some suggestions?