Pindel Segmentation fault with -Q
 

I got Segmentation fault when using -Q. Have any idea about this?
Everything works fine if not using -Q.

there is what I got:


pindel -f $REF -i config_foo.txt -c chr8 -o pdel.out.chr8 -b foo.bkd -Q confirmed.chr8

Pindel version 0.2.4t, August 13 2012.
BreakDancer events: 22908
Processing chromosome: chr1
Skipping chromosome: chr1
Processing chromosome: chr2
Skipping chromosome: chr2
Processing chromosome: chr3
Skipping chromosome: chr3
Processing chromosome: chr4
Skipping chromosome: chr4
Processing chromosome: chr5
Skipping chromosome: chr5
Processing chromosome: chr6
Skipping chromosome: chr6
Processing chromosome: chr7
Skipping chromosome: chr7
Processing chromosome: chr8
Chromosome Size: 175793759
NumBoxes: 60005 BoxSize: 6526

Looking at chromosome chr8 bases 0 to 10000000.
Possible translocation from chromosome chr8 to chromosome chr1
…
…

getReads chr8 195793759
Insertsize in bamreads: 295
Number of reads in current window: 127044, + 63457 - 63587
Number of reads where the close end could be mapped: 33926, + 16994 - 16918
Percentage of reads which could be mapped: + 26.78% - 26.61%

BAM file index 0 33926
There are 33926 reads for this chromosome region.
Far end searching completed for this window.
Reads already used: 0
Far ends already mapped 22423
Checksum of far ends: 76402982
Searching some type of variant, replace this with the correct name in child class ...
Total: 6336 +3243 -3093
Sorting and outputing deletions ...
Segmentation fault

An internal data structure was notified but not all modules have been updated for it. sorry for the inconvenience. We are working on this.

Kai