Outputs are all zero #6
Description
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