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robinandeer/puzzle
Incompatible usage of GeminiPlugin

Hello, issue is during execution of command gemini browser my.db --use puzzle there is problem with compatibility of interfaces: In line 267 of file gemini_browser.py there is usage of GeminiPlugin which ...
  • DamianSkrzypczak
  • Opened 
    on Oct 10, 2017
  • #231

robinandeer/puzzle
path

Hi everybody, I see in the requirements path.py is needed. I tried to install all of these, and downgraded cyvcf2 to version 0.2.8 I believe. A version for path.py is not stated in the requirements.txt ...
  • colindaven
  • 1
  • Opened 
    on Jan 24, 2017
  • #230

robinandeer/puzzle
Puzzle crashed while visualising large CNV

Puzzle crashed while visualising a large CNV. I got the following error-message; how can I fix this? Traceback (most recent call last): File /Users/johlun/miniconda2/envs/puzzle/bin/puzzle , line 11, ...
  • johsko
  • Opened 
    on Sep 29, 2016
  • #229

robinandeer/puzzle
gemini plugin

Hello, I recently installed puzzle and was hoping to view a gemini db with it. The install was fine ( I think). There are a couple of warning with the flask import and I am not sure if these are important? ...
  • ramaniak
  • 2
  • Opened 
    on Jun 22, 2016
  • #228

robinandeer/puzzle
File "cyvcf2/cyvcf2.pyx", line 155, in cyvcf2.cyvcf2.VCF.__init__ (cyvcf2/cyvcf2.c:7106) TypeError: Expected bytes, got path

Hello there! Recently I installed the latest version of puzzle, it was installed without any apparent error, however when I run the test example I get the following error: Traceback (most recent call ...
bug
  • J35P312
  • 6
  • Opened 
    on Jun 22, 2016
  • #227

robinandeer/puzzle
Create a proper test gemini database

We should have a gemini database with synthetic variants so we always know what to expect when writing tests
Easy
enhancement
GEMINI
  • moonso
  • 1
  • Opened 
    on Apr 29, 2016
  • #225

robinandeer/puzzle
Frequency filter stopped working?

Tested w/ Safari, VEP annotation, vcf-file, init,load view.
  • dnil
  • 8
  • Opened 
    on Apr 8, 2016
  • #217

robinandeer/puzzle
Enable uploading of regions in bed format

This would create a way to narrow the analysis to custom regions
enhancement
Intermediate
  • moonso
  • Opened 
    on Apr 8, 2016
  • #216

robinandeer/puzzle
Gene list searching appears to default to wildcard

this becomes cumbersome for genes with short names (like AR or T) or genes in gene-families where one may want see TMEM5 but not TMEM52.
  • dnil
  • 1
  • Opened 
    on Apr 8, 2016
  • #214

robinandeer/puzzle
Allow analysis on multiple individuals from different cases

  • moonso
  • 3
  • Opened 
    on Apr 8, 2016
  • #213
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