japsa
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mdcao
Just Another JAva Package for Sequence Analysis
Bumps [htsjdk](https://github.com/samtools/htsjdk) from 2.18.2 to 3.0.1. Release notes Sourced from htsjdk's releases. 3.0.1 Fix for a long standing vulnerability around temporary directory creation which could expose data to malicious users...
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Bumps [gson](https://github.com/google/gson) from 2.3 to 2.8.9. Release notes Sourced from gson's releases. Gson 2.8.9 Make OSGi bundle's dependency on sun.misc optional (#1993). Deprecate Gson.excluder() exposing internal Excluder class (#1986). Prevent...
To avoid this when playing around with development in Japsa, ensure new argument names are completely different from existing argument names. eg. '--read' conflicts with '--readList' as the CommandLine module...
Bumps commons-io from 2.5 to 2.7. [](https://docs.github.com/en/github/managing-security-vulnerabilities/about-dependabot-security-updates#about-compatibility-scores) Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a...
Hi, I'm having an issue running the resistance gene identifier when running it on pre-basecalled reads. Without making the tmp directory in advance, I get a FileNotFoundException for tmp/resFind_JSA_4_2_ai.fasta But...
Bumps [junit](https://github.com/junit-team/junit4) from 4.8.1 to 4.13.1. Release notes Sourced from junit's releases. JUnit 4.13.1 Please refer to the release notes for details. JUnit 4.13 Please refer to the release notes...
XM fails to compress large files (3GB) with the following message: Exception in thread "main" java.lang.OutOfMemoryError: Requested array size exceeds VM limit at java.util.Arrays.copyOf(Arrays.java:3236) at japsa.seq.FastaReader.nextSequence(FastaReader.java:159) at japsa.tools.bio.xm.ExpertModelCmd.main(ExpertModelCmd.java:130)
I'm trying to compress a DNA sequence file and it throws a nullpointer. Any ideas why? ``` java -version openjdk version "1.8.0_242" OpenJDK Runtime Environment (build 1.8.0_242-b08) OpenJDK 64-Bit Server...
We are using japsa tool to evaluate the accuracy of the basecallers. We would like to know why identity rate in japsa is defined as 1 - (mismatch + insertion)?...
