Opened 4 months ago

Closed 4 months ago

#1210 closed defect (fixed)

Variant calling fails if no variants are found

Reported by: Nicklas Nordborg Owned by: Nicklas Nordborg
Priority: minor Milestone: Reggie v4.25
Component: net.sf.basedb.reggie Keywords:
Cc:

Description

The first vcfanno step fails with an error message:

=============================================
vcfanno version 0.3.2 [built with go1.12.1]

see: https://github.com/brentp/vcfanno
=============================================
vcfanno.go:115: found 4 sources from 1 files
vcfanno.go:156: falling back to non-bgzip
panic: runtime error: invalid memory address or nil pointer dereference
[signal SIGSEGV: segmentation violation code=0x1 addr=0x14 pc=0x5602b5]

goroutine 5 [running]:
github.com/brentp/bix.tIndex.Skip(0x0, 0xc000024f00)
  /home/brentp/go/src/github.com/brentp/bix/csi.go:48 +0x5
github.com/brentp/bix.New(0xc000024980, 0x10, 0xc00009df78, 0x1, 0x1, 0x0, 0x0, 0x0)
  /home/brentp/go/src/github.com/brentp/bix/bix.go:152 +0x620
github.com/brentp/vcfanno/api.(*Annotator).Setup.func1(0xc0001ce730, 0x1, 0x1, 0xc0001fe3c0, 0x0, 0xc000024980, 0x10)
  /home/brentp/go/src/github.com/brentp/vcfanno/api/api.go:792 +0x235
created by github.com/brentp/vcfanno/api.(*Annotator).Setup
  /home/brentp/go/src/github.com/brentp/vcfanno/api/api.go:783 +0x15e

If there are no variants there is no need to run the annotation or filtering steps so we could simply bypass that and copy the raw file to the expected places. If we do that, the rest of the code should probably work as normal.

Change History (3)

comment:1 Changed 4 months ago by Nicklas Nordborg

In 5775:

References #1210: Variant calling fails if no variants are found

Added a test to the script after VarDict that checks the number of variants. If there are no variants in the VCF, the rest of the pipeline is skipped and the raw file is simply copied to the expected places.

comment:2 Changed 4 months ago by Nicklas Nordborg

In 5776:

References #1210: Variant calling fails if no variants are found

Updated the manual confirmation wizard so that 0 variants is not considered an error condition.

comment:3 Changed 4 months ago by Nicklas Nordborg

Resolution: fixed
Status: newclosed
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