<INV> format

[awgymer]

We are facing some issues with the formatting for rows of type INV.

Based on the 4.2 spec (see section 5.4.7) it seems that if an INV is represented by a single row it should have an END value. However there is no such value provided in the output of Severus.

It may be as simple as adding the SVLEN value to the POS?

[aysegokce]

Hello @awgymer,
Thank you for pointing this out. We will add the END field to the INFO column. But in the meantime, END is POS+SVLEN. Is this issue only related to INVs, or does it also affect DUPs/DELs?

Best
Ayse

[awgymer]

I have only noticed this as an issue on the INV format rows. DUP and DEL appear to have the correct END.

[aysegokce]

Hello @awgymer,
In v1.2, we added the END field to INV entries. Regarding inversions, we now only report reciprocal inversions as INV and all other inverted junctions as BND.

Best,
Ayse