We need to output a bam file for varaitions

[vezzi]

There must be a view to run the program in order to output the reads occurring in one SV. I other words after I run the typical FindTranslocation command I want to be able to pick up one of the Translocations and save all reads involved in that translocations.

i.e.

FindTranslocations --bam FILE.BAM --out test
cat   test_intra.bed
CHRA 123  456 CHRB 123 456 
FindTranslocation --extract  CHRA 123  456 CHRB 123 456 

and the last command will store in a bam file all reads that align between 123 and 456 in CHRA and in CHRB