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v2.3.8

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@YuSugihara YuSugihara released this 18 Oct 02:49
· 7 commits to master since this release
v2.3.8
2c8db6c

What's new in this version:

  • Colorblind-friendly plot colors: The default colors used in the generated plots have been updated to be more accessible for individuals with color vision deficiencies, ensuring better readability for everyone.

  • Improved logging format: We have enhanced the log formatting during the execution of MutMap and MutPlot, providing clearer and more consistent output, making it easier to track the progress of the analysis.

  • Automatic handling of large genome BAM indexing and VCF tabix errors: For large genomes like wheat, we’ve added automatic handling for errors during BAM indexing and VCF tabix creation. If samtools index fails, the script will automatically retry with samtools index -c. Similarly, if tabix fails, it will automatically retry with tabix -C.

  • Extended BAM support: The script has been updated to ensure that when starting with BAM files, essential operations such as BAM filtering, fixmate, and markdup are performed automatically, ensuring consistency with workflows starting from FASTQ files.

  • Updated environment variable settings: To prevent errors related to numpy imports and multithreading issues, we have adjusted the placement of environment variables like OMP_NUM_THREADS and USE_SIMPLE_THREADED_LEVEL3, providing a more stable runtime environment.

  • New documentation files: We’ve added two new markdown files to the doc directory:

    • 01_MutMap_Commands_Breakdown.md: This file provides a detailed breakdown of the commands used in MutMap, helping users understand and utilize the tool more effectively.
    • 02_Guide_to_Build_SnpEff_DB.md: A guide to assist users in building a SnpEff database, offering step-by-step instructions for integrating SnpEff into their MutMap analysis.
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