JBrowse 1.16.10 maintenance release
Hello all,
This release contains changes that help people rendering SNPs from reads with multiple CIGAR skips, e.g. Iso-Seq. It also includes a modest speedup for long reads and automatic generation of MD tags for BAM, and more. Please see the changelog below!
- JBrowse-1.16.10.zip - minified release
- JBrowse-1.16.10-dev.zip - use this if you modify jbrowse source code or use plugins
- JBrowse-1.16.10-desktop-win32-x64.zip
- JBrowse-1.16.10-desktop-linux-x64.zip
- JBrowse-1.16.10-desktop-darwin-x64.zip
Minor improvements
Added an optimization for BAM that helps for long reads especially (@cmdcolin)
Added generation of the MD tag if none is specified in BAM (issue #1022, @cmdcolin)
Added
customRefRenameandreplaceRefRenameglobal configs for extending and replacing ref renaming functionality respectively. Ref renaming helps things like chrM and chrMT to be loaded onto the same chromosome in jbrowse (@cmdcolin, issue #1506)Added support for a -f option for setup.sh. This option causes setup to skip installing perl prerequisites and setting up sample data. It is primarily intended to support faster builds in a Docker context. (@scottcain)
Bug fixes
Fix the display of mismatches from hard clipped BAM sequences (issue #1513)
Fix ability to use tracks from Open track dialog in combination tracks. Thanks to Sonny Arora for the repo (issue #1536)
Fix mismatch/SNP calculation for reads with multiple skips, e.g. Iso-Seq (@cmdcolin)