Inconsistent position IMGT 21 in kappa chain

[prihoda]

With the newest version of ANARCI, I'm getting weird behavior in the kappa chain (IGKV2-30*01).

Submitting without J region gives correct numbering:

anarci --scheme imgt -i DVVMTQSPLSLPVTLGQPASISCRSSQSLVYSDGNTYLNWFQQRPGQSPRRLIYKVSNRDSGVPDRFSGSGSGTDFTLKISRVEAEDVGVYYCMQGT
L 1       D
L 2       V
L 3       V
...
L 19      A
L 20      S
L 21      I   <----
L 22      S
L 23      C
...

Submitting with J region produces a gap at position 21:

anarci --scheme imgt -i DVVMTQSPLSLPVTLGQPASISCRSSQSLVYSDGNTYLNWFQQRPGQSPRRLIYKVSNRDSGVPDRFSGSGSGTDFTLKISRVEAEDVGVYYCMQGTFGQGTKVEIK
L 1       D
L 2       V
L 3       V
...
L 19      A
L 20      S
L 21      -   <----
L 22      I
L 23      S
L 24      C
...

Which shifts the whole remainder of the chain after position 21 by one position number.

[prihoda]

This gap at IMGT position 21 is created by latest ANARCI version in all the following germlines:

• IGKV1: IGKV1-12*01, IGKV1-12*02, IGKV1-13*01, IGKV1-13*02, IGKV1-16*01, IGKV1-16*02, IGKV1-17*01, IGKV1-17*02, IGKV1-17*03, IGKV1-27*01, IGKV1-33*01, IGKV1-37*01, IGKV1-39*01, IGKV1-39*02, IGKV1-5*01, IGKV1-5*02, IGKV1-5*03, IGKV1-6*01, IGKV1-6*02, IGKV1-9*01, IGKV1-NL1*01, IGKV1/OR-2*01, IGKV1/OR-3*01, IGKV1/OR-4*01, IGKV1/OR1-1*01, IGKV1/OR10-1*01, IGKV1/OR15-118*01, IGKV1/OR2-0*01, IGKV1/OR2-1*01, IGKV1/OR2-108*01, IGKV1/OR2-118*01, IGKV1/OR2-2*01, IGKV1/OR22-5*01, IGKV1/OR22-5*02, IGKV1/OR9-1*01, IGKV1/OR9-2*01, IGKV1/ORY-1*01, IGKV1D-12*01, IGKV1D-12*02, IGKV1D-13*01, IGKV1D-13*02, IGKV1D-16*01, IGKV1D-16*02, IGKV1D-33*01, IGKV1D-37*01, IGKV1D-39*01, IGKV1D-42*01, IGKV1D-42*02
• IGKV2: IGKV2-24*01, IGKV2-28*01, IGKV2-30*01, IGKV2/OR2-7D*01, IGKV2D-24*01, IGKV2D-26*01, IGKV2D-26*02, IGKV2D-26*03, IGKV2D-28*01, IGKV2D-30*01
• IGKV3: IGKV3-11*01, IGKV3-11*02, IGKV3-20*01, IGKV3-7*01, IGKV3-7*02, IGKV3-7*03, IGKV3-7*04, IGKV3/OR2-268*01, IGKV3/OR2-268*02, IGKV3D-11*01, IGKV3D-11*02, IGKV3D-11*03, IGKV3D-20*01, IGKV3D-20*02, IGKV3D-7*01, IGKV6D-41*01, IGKV7-3*01

With an older ANARCI version, it works as expected (commit 19d9de5)

The ANARCI webserver also seems to be unaffected, position 21 behaves as expected. Any thoughts @claire-marks?

[jochenater]

I'm experiencing the same problem. Downgrading to the py27 version works, but ideally I'd like to use the newer version.
Is anybody working on this?

[wjs20]

I've also discovered this issue. Did you find a fix.