Outputs are all zero

[HungerNature]

I have download your update pileup2baseindel.pl scripts, it works fine for example. But to my own data, most of the outputs are zero which should not be expected.
My perl version:
This is perl 5, version 18, subversion 2 (v5.18.2)

Linux system:
CentOS 6.5

Command line : perl /path/to/pileup2baseindel.pl -i my_input.mpileup

Input file: my_input.mpileup (head lines):
chr1 26791 g 19 ,.,......,,....,.,, HA@/E?DIGCDGEEEDGBD
chr1 26792 g 22 ,...,......,,,....,.,, F55A0?<?EDGACCEGHEDH>B
chr1 26793 c 21 ,.........,,,....,.,, G1;CB?;FEI9FFGGGFDGDB
chr1 26794 c 22 ,...,......,,,....,.,, G3;>0ABBDFG5DFGIIGDHB<
chr1 26795 g 21 ,..,......,,,....,.,, F;;D>BCCFG:BHBGJGBIBD
chr1 26796 g 22 ,...,......,,,....,.,, FB=8E>DB>D=5AEHJGDBJ@D
chr1 26797 g 22 ,...,......,,,....,.,, F8B?G;=C@DA8@EI<GBDIBB
chr1 26798 c 21 ,..,......,,,....,.,, F<BCB6CB6D;@HIDHFDJDB
chr1 26799 g 22 ,...,......,,,....,.,, F59BB?A6@HJHIHDGDB
chr1 26800 c 21 ,...,......,,....,.,, C5>B<>>BC@@@HJHIECIDD

Output file: sample1.txt (head lines):
chr loc ref A T C G a t c g Insertion Deletion
chr1 26791 g 0 0 0 0 0 0 0 0 NA NA
chr1 26792 g 0 0 0 0 0 0 0 0 NA NA
chr1 26793 c 0 0 0 0 0 0 0 0 NA NA
chr1 26794 c 0 0 0 0 0 0 0 0 NA NA
chr1 26795 g 0 0 0 0 0 0 0 0 NA NA
chr1 26796 g 0 0 0 0 0 0 0 0 NA NA
chr1 26797 g 0 0 0 0 0 0 0 0 NA NA
chr1 26798 c 0 0 0 0 0 0 0 0 NA NA
chr1 26799 g 0 0 0 0 0 0 0 0 NA NA

[HungerNature]

I know what happen to my data. Cause the ref column of my input file are all lowercase. The basepileupindel perl scripts can't recognize it.

[riverlee]

Glad you figured it out yourself.

[mfoll]

In case someone needs it, a very small change in the code can fix it and we opened a PR a few months ago #5 fixing this issue

[LianaKafetzopoulou]

Same issue here, doesn't seem to be fixed when using the code in the link and also seems the code there is a different version to what is there now. Any chance there is a fix for this? Shame to not be able to use due to this!

[mfoll]

We use this script in one of our pipeline with a few changes and it works well: https://github.com/IARCbioinfo/needlestack/blob/master/bin/pileup2baseindel.pl
We also have a similar and faster C++ version here: https://github.com/IARCbioinfo/mpileup2readcounts

[LianaKafetzopoulou]

Awesome :) Thanks! Will try it out now!