Cannot fetch on call_h_s.vcf. Is it sorted/indexed? about truvari HOT 4 CLOSED

Hello,

I'm unable to recreate this error.
However, when I re-run on your vcfs after running tabix -p vcf <VCF> on your two inputs, I do get an error saying:

  File "/home/english/truvari/truvari.py", line 931, in <module>
    run(sys.argv[1:])
  File "/home/english/truvari/truvari.py", line 811, in run
    seq_similarity = var_pctsim_lev(entryA, entryB)
  File "/home/english/truvari/truvari.py", line 145, in var_pctsim_lev
    if len(entryA.REF) < len(entryA.ALT[0]):
TypeError: object of type '_SV' has no len()

This has to do how these aren't sequence resolved calls (i.e. using <DEL> instead of presenting the full sequence in ALT). To get around this error, one simply needs to run truvari with --pctsim 0

Without any more information, I'm not sure what can be done. Are you certain you were pointing at the correct files and the tabix indexes were up to date?

from truvari.

Hello,

Thank you for your kind reply.

I have re-run the inputs with cmds like:

tabix -p vcf baseline.vcf.gz
tabix -p vcf call_h_s.vcf.gz
truvari.py -b baseline.vcf.gz -c call_h_s.vcf.gz -o out [--pctsim 0]

with or without the --pctsim 0 option, I got the same error saying:

File "/home/gst/sftw/SV-Call/truvari/truvari.py", line 926, in
run(sys.argv[1:])
File "/home/gst/sftw/SV-Call/truvari/truvari.py", line 661, in run
contig = vcfB.fetch(contig, 0, 1000)
File "/home/gst/sftw/anaconda2/lib/python2.7/site-packages/vcf/parser.py", line 599, in fetch
self.reader = self._tabix.fetch(chrom, start, end)
File "pysam/libctabix.pyx", line 447, in pysam.libctabix.TabixFile.fetch
ValueError: start out of range (1000)

It seems that something went wrong during the INPUT procedure. Any suggestions?

Thank you!

Best wishes,

Songtao Gui

from truvari.

The problem seems to be happening with pysam even though truvari is calling the function correctly.
The only instances of problems similar to this I can find are pysam-developers/pysam#41 and https://www.biostars.org/p/113309/ but neither of these seem particularly relevant to this error. You seem to be using python 2.7 instead of python3, and, like I said, we're not calling fetch weirdly.

Could you test the pysam directly and run something like:

import vcf
v = vcf.Reader(filename="call_h_s.vcf.gz")
for x in v.fetch("7", 0, 1000): 
    print x

from truvari.

Thanks！
It was the pysam problem, Truvari works fine as soon as I used python 3 instead.
Thank you again for your help.
Best wishes.

from truvari.