Bug in exportClones for mmu reference

[PoslavskySV]

Stack trace:

java.lang.NullPointerException
at com.milaboratory.mixcr.cli.ActionExportClones$CFilter.accept(ActionExportClones.java:108)
at com.milaboratory.mixcr.cli.ActionExportClones$CloneExportParameters$1.accept(ActionExportClones.java:192)
at com.milaboratory.mixcr.cli.ActionExportClones$CloneExportParameters$1.accept(ActionExportClones.java:187)
at com.milaboratory.mixcr.basictypes.CloneSet.transform(CloneSet.java:137)
at com.milaboratory.mixcr.cli.ActionExportClones.go0(ActionExportClones.java:62)
at com.milaboratory.mixcr.cli.ActionExport.go(ActionExport.java:52)
at com.milaboratory.cli.JCommanderBasedMain.main(JCommanderBasedMain.java:147)
at com.milaboratory.mixcr.cli.Main.main(Main.java:120)

note: Clone.getFeature(CDR3) gives not null, while Clone.getPartitionedTarget(0).getFeature(CDR3) gives null for some reason.

[dbolotin]

This seems to be connected with this code, which we've just deleted day ago. Stas, please confirm.

[PoslavskySV]

Test case:

@Test
public void name() throws Exception {
    VDJCGene gene = VDJCLibraryRegistry.getDefault().getGene(new VDJCGeneId(new VDJCLibraryId("default", 10090), "IGHV1-55*00"));
    GeneFeature intFeature = GeneFeature.parse("{CDR3Begin:VEnd}");
    Assert.assertNotNull(gene.getPartitioning().getRelativeRange(GeneFeature.parse("VRegion"), intFeature));
}