NullPointerException in MergeMSFs.java

[dhuen]

When using IMGT/HLA 3.53.0, calling Kourami.jar to genotype an extracted bam will result in an NPE in MergeMSFs.java. This was traced to HLA*26:236 being present in hla_nom_g.txt but absent in alignments.

Might I suggest the following change in MergeMSFs.java?
Uncomment line 38.
Add after it:-
if (s==null) System.err.println("The following is may be present in hla_nom_g.txt but not in alignments: "+ g.getFirstAllele());

It will then report the ID so it can be deleted from hla_nom_g.txt. Deleting the spurious ID makes it possible to use IMGT/HLA 3.53.0.

Thank you for developing this software - it is pretty useful.