mateclever does not run through

[Manuel Holtgrewe]

Apparently, there is a problem in mateclever. vcf-to-deletionlist writes out files that look as follows:

1 100145902 100146268 DEL
1 100212165 100212508 DEL
1 100471100 100472708 DEL
1 100768454 100768795 DEL
1 100782792 100783179 DEL
1 100860224 100860673 DEL
1 100956244 100956589 DEL

However, merge-putative-variations complains about a missing weight column:

Error: Error parsing variation list: weight column missing. Offending line: 1

I'm using the current master branch.

[Manuel Holtgrewe]

It appears to me that postprocess-predictions would have to write generate a weight column from all.clever.out (by the Wiki manual). This can then be used by vcf-to-deletionlist to write out a weight.

Would the expected_support column from all.clever.out be the correct one?

[Tobias Marschall]

Yes. Correct. Thanks for reporting this and providing a fix. I fixed some related little issues. The current master version (7482f5) should work.