Can we get rid of org.apache.logging.log4j? about gkl HOT 9 CLOSED

This is motivated by trying to keep the JAR size of fgbio as small as possible. fulcrumgenomics/fgbio#483. Another idea that could help is having the inflater/deflater parts of the code in a separate JAR than the SW/HMM portions, so we don't have to include the latter.

Examining the size of the dependencies included (using this gist) we see:

Total dependencies size:                           4.52 Mb

htsjdk-2.9.0.jar                               1,528.30 kb
log4j-core-2.5.jar                             1,080.17 kb
snappy-java-1.0.3-rc3.jar                        967.05 kb
commons-jexl-2.1.1.jar                           261.36 kb
commons-compress-1.4.1.jar                       235.71 kb
commons-io-2.4.jar                               180.80 kb
log4j-api-2.5.jar                                143.32 kb
xz-1.5.jar                                        97.22 kb
ngs-java-1.2.4.jar                                72.40 kb
commons-logging-1.1.1.jar                         59.26 kb
gatk-native-bindings-0.1.0-rc-1.jar                6.33 kb

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Could we not just use commons-logging, or the logging in htsjdk?

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Hi @nh13 - thanks for the input. We're reviewing this suggestion this week. I don't see any issue with logging elsewhere as you suggest. Which GKL components does fgbio use? The Deflater?

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@mepowers we are starting to use the inflater and deflater. This was also an issue in GATK and Picard (broadinstitute/picard#883). They solved it by adding a configuration file and muting the logging, but that means they also include the log4j transitive dependency, making the JAR they distribute larger.

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Log4j can be replaced with the log4j-over-slf4j bridge API and the redirected to the Java stock logging API using the slf4j-jdk14 adaptor. See for details here.

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@pdtommaso thank-you! I did see that but I am trying to reduce the number of dependencies so I am not thrilled to include a few more to bridge the logging frameworks. I’ll look how much size they add.

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@nh13 - we discussed this internally as a team today and unfortunately updating the logging isn't a priority right now. We do not have plans to change this.

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Would you accept a PR to remove logging?

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@nh13 - we wouldn't. We're only requesting PRs for bug fixes.

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