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TheJacksonLaboratory / vmvt

vmvt: variant-motif visualization tool
https://vmvt.readthedocs.io/en/latest/index.html
BSD 3-Clause "New" or "Revised" License
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Error when creating graphics for variant `chr3:10088407AG>A` #59

Closed ielis closed 4 years ago

ielis commented 4 years ago

When creating donor graphics for the variant chr3:10088407AG>A

@Test
public void someTest() {
    final String svg = vmvtGenerator.getDonorDistributionSvg("TTAgtaagt", "TTAtaagtg");
    System.out.println(svg);
}

the following error is thrown:

org.monarchinitiative.vmvt.core.except.VmvtRuntimeException: Bad data -- measured delta greater than max

  at org.monarchinitiative.vmvt.core.svg.delta.DeltaSvg.writeTicks(DeltaSvg.java:188)
  at org.monarchinitiative.vmvt.core.svg.delta.DeltaSvg.write(DeltaSvg.java:267)
  at org.monarchinitiative.vmvt.core.svg.delta.DeltaSvg.getSvg(DeltaSvg.java:238)
  at org.monarchinitiative.vmvt.core.VmvtGenerator.getDonorDistributionSvg(VmvtGenerator.java:96)
  at 
 ... 
 (shortened)

Apparently, events as extreme as this one (deletion of G from the GT dinucleotide) are possible, this variant is present in the Pfeiffer.vcf that is shipped with Exomiser.

pnrobinson commented 4 years ago

The issue seems to be that this is a multinucleotide change TTA[gt/ta]aagt and both changes reduce the score.

pnrobinson commented 4 years ago

I think the best thing is to write a red box around the Delta Ri in these cases image

The bug should be fixed now. Please update to version 0.9.1 @ielis