vapor script: local variable 'info' referenced before assignment

[ghost]

I received the following error while trying to run vapor on a vcf file:

Traceback (most recent call last):
  File "/root/.local/bin/vapor", line 4, in <module>
    __import__('pkg_resources').run_script('VaPoR==0.0.1', 'vapor')
  File "/usr/lib/python2.7/dist-packages/pkg_resources/__init__.py", line 698, in run_script
    self.require(requires)[0].run_script(script_name, ns)
  File "/usr/lib/python2.7/dist-packages/pkg_resources/__init__.py", line 1623, in run_script
    exec(script_code, namespace, namespace)
  File "/root/.local/lib/python2.7/site-packages/VaPoR-0.0.1-py2.7-linux-x86_64.egg/EGG-INFO/scripts/vapor", line 302, in <module>

  File "/root/.local/lib/python2.7/site-packages/VaPoR-0.0.1-py2.7-linux-x86_64.egg/EGG-INFO/scripts/vapor", line 287, in vcf_list_readin

UnboundLocalError: local variable 'info' referenced before assignment

Looking at line 287 of vapor, it appears the code does not account for if the "Other" field does not appear in the INFO column. The vcf file I'm using is the output of running Manta on a BAM file, which does not include this. The Manta output format is detailed here: https://github.com/Illumina/manta/blob/master/docs/userGuide/README.md#manta-vcf-reporting-format.

Also, can you please let me know if vapor supports multi-sample vcf files? The vcf I'm using consists of 3 samples created from 3 different BAM files, so should I use the "--pacbio-input" parameter 3 times, one with each bam file?

[xuefzhao]

so the 'other' option is only used if the svtype listed in vcf is beyond the scope of ' DEL','INV','INS',' DISDUP', 'TANDUP', and the couple complex format we defined. I would suggest you to transfer vcf to bed and work with those for now. I am also working on the vcf part, trying to make it as inclusive as possible.

[xuefzhao]

and vapor do not work with multi-sample vcf files, so to run multiple samples, you want them each in different vcf file then apply vapor