Current digest map insufficient if overhanging digest ends were filled in

[hansenp]

For the original Hi-C protocol, the overhanging digest ends are filled in.

For the truncation step, Diachromatic takes this into account but not for the align step. Consider the following illustration.

With the current implementation of the digest map both reads are assigned to the digest D3.

[pnrobinson]

@hansenp is this issue still open?

[hansenp]

I don't know.

[hansenp]

That's a long time ago. I assume it's still open.

[hansenp]

This should only affect a very small number of reads and therefore only have a minor impact. Reopen if necessary.