Closed travc closed 2 years ago
@travc I'm starting to attack bugs. Can you provide the command line you used and I will see what I can do.
Any example with a long deletion should trigger the problem. It is using pairwise alignment to derive a reduced representation of the differences and this is quadratic in space.
On Thu, Mar 31, 2016, 23:52 Zev Kronenberg notifications@github.com wrote:
@travc https://github.com/travc I'm starting to attack bugs. Can you provide the command line you used and I will see what we can do to fix your issue.
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@ekg I could skip variants if the INFO line has abs(POS - END) > X? Or would that be a lousy hack?
Maybe we just set a maximum. Beyond 1000 even, I don't know if we should attempt to decompose. Shorter even might make sense. Like, 100.
On Fri, Apr 1, 2016, 00:15 Zev Kronenberg notifications@github.com wrote:
@ekg https://github.com/ekg I could skip variants if the INFO line has abs(POS - END) > X? Or would that be a lousy hack?
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We introduced wavefront as an aligner and this problem should be solved. Also the -L switch behaves properly on master.
This is an odd use case, so not really a bug per-se. However, it might crop up in other situations given how freebayes really likes to make long complex calls...
I'm running RNAseq data (tophat hacked to change CIGAR N's to D's), which seems to be working mostly ok. But I hit one rare snag:
vcfallelicprimitives
is hanging (or at least taking a ridiculously long time) on one particular variant line: I think the relevant part isTYPE=del,del
andLEN=19323,19332
Yeah, that is an intron which should be N, but I recoded to D so I could call with freebayes.A vcf containing just that line is: https://popi.ucdavis.edu/~travc/tmp/hangs_vcfallelicprimitives.vcf
... Additionally ... Can
vcffilter
handle those multi-value fields properly? The docs on it should probably be updated to clarify.