Known limitation: BAM PNEXT field is not always correct

[janinl]

PNEXT becomes incorrect if some VCF insertions of deletions are present between the 2 ends of a read cluster.

We could set PNEXT to 0, a valid value showing that the information is unavailable, but we decided to stick with the incorrect value as it is still informative when browsing the BAM file manually.

See

EAGLE/src/c++/lib/genome/BamMetadata.cpp

Line 177 in edb2c08

unsigned long PNEXT = (directionIsForward?startPos2:startPos1) + globalPosShift; // TODO: This PNEXT is incorrect if there are some vcf indels between the 2 ends of the cluster