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Plots missing from summary.html file #580

@ethering

Description

@ethering

Describe the bug
Non-imbedded images are not being displayed in the snpEff summary.html file (see screenshot). Embedded tables are fine.
The following plots are missing:

  • Number of annotations and region counts
  • Quality
  • Insertions and deletions length
  • Allele frequency
  • Allele count
  • Hom/Het per sample (for all samples)
  • Variants by chromosome

For example:
Image

To Reproduce
snpEff version SnpEff 5.2f (build 2025-02-07 08:36)
Java JDk version: jdk-21.0.5

SnpEff full command line:
java -jar snpEff.jar mEreEur2.1 Hedgehogs_genotypes.vcf.gz > all_genotypes/Hedgehogs_genotypes_snpeff.vcf

Expected behaviour
Plots should appear in the summary.html file.

Additional context
This issue is similar to the closed but unresolved issue at #375 (comment)

The images that don't display are all embedded URLs, linked to http://chart.apis.google.com/
If I copy and paste one of the links into my web browser I get "The requested URL /chart was not found on this server."
An example of one of the links can be found HERE
According to this page: https://en.wikipedia.org/wiki/Google_Chart_API, the Google Chart API is deprecated, and the server was turned off on March 18, 2019.
In the SnpEff source file GoogleHistogram.java it states that the plots are made using 'A simple wrapper to google charts API (from charts4j)'.

Is it possible that the plots are using a deprecated server/service and that charts pointing to http://chart.apis.google.com do not now work?
This Google Groups thread, which states that the service is deprecated, suggests using QuickChart as an alternative.

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