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Issues running svict #12

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shahmj opened this issue Apr 9, 2019 · 3 comments
Open

Issues running svict #12

shahmj opened this issue Apr 9, 2019 · 3 comments
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@yenyilin

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@shahmj
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shahmj commented Apr 9, 2019

Hi,

I'm trying to run this on a regular bwa mem bam file. I noticed 2 issues:

  1. svict expects "SO:coordinate" as the third column but in the bam that I'm providing it is the fourth. Could you make this more generic?
  2. svict then failed on the second to last decoy contigs, after going through most of the other supercontigs; right on or after NC_007605 and the last one is hs37d5. I didn't get any error messages. Is this a known issue?

Thanks,
Minita
@yenyilin
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yenyilin commented Apr 9, 2019

Hi, we will fix (1) shortly. For (2) did you use the latest commit already?

Thanks.

@yenyilin yenyilin self-assigned this Apr 9, 2019
@shahmj
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shahmj commented Apr 10, 2019

I did a conda install yesterday. I don't see the version in the usage though.

@jeffpbruce
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I am still having this issue, was it fixed?

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@shahmj @jeffpbruce @yenyilin