What's new in Artemis 18.2.0
Mar 14, 2022
- Upgrade log4j to latest version 2.17.2 (Issue #326).
- Upgrade Picard jar to latest version 2.26.11 and fix indexed file related bug introduced in PR #304.
- Remove redundant Evosuite tests.
- Fix Travis build.
- Other minor updates.
New in Artemis 18.1.0 (Dec 4, 2019)
- Performance improvements around GFF loading/saving
- Reorganised test data and added more unit tests
- Added fixes for exceptions generated when handling indexed GFF files
- Enabled command line help flag on writedb_entry script
- Added additional file suffixes, recognised by Artemis
- Added low_complexity_region and tandem_repeat feature keys
- Added fix to prevent validation aborting
- Scripts now return an exit code of zero, when run with -h
New in Artemis 18.0.3 (Nov 22, 2019)
- Fix for GitHub Issue #293 - Java version error for Mac OS X Mojave.
- RT ticket 621414 - addition of source field to Gene Builder GO term panel
- Various build and documentation updates.
- Addition of Docker file.
New in Artemis 18.0.2 (Nov 22, 2019)
- RT Ticket 648115 - display blast file hits correctly in Artemis to avoid having to do manual column re-ordering in the file.
- RT Ticket 649125 - fix for broken plot window popup menu on Windows.
New in Artemis 18.0.1 (Nov 22, 2019)
- Removal of references to old genedb Chado database.
- Addition of command line scripts to Mac apps.
New in Artemis 18.0.0 (Nov 22, 2019)
- Upgrade to Java 9+. Java 8 is no longer supported.
- Introduction of Maven to replace ant and make
- A number of bug fixes and new features
New in Artemis 13.2.0 (Dec 22, 2011)
- Added option to provide overview of the variation sites
- Change BamView filter to enable filtering in and out based on reads flag
- Add read count and RPKM calculations to BamView
- Add option in BamView to clone the alignment panel
- Create features option for VCF records
- Unit tests added for writing VCF/BCF sequences
- Add new Coverage view to BamView. It automatically switches to this view on zooming out
- Add options to write out or view FASTA sequences from VCF/BVF variation data
New in Artemis 13.0 (Dec 22, 2011)
- Add support for reading in indexed BCF (Binary VCF) files.
- Memory optimisation of codon caching, reducing the memory footprint.
- It is now possible to add BAM, VCF and BCF files from the command line using the JVM bam option, e.g. art -Dbam=/pathToFile/file.bam and for multiple BAM's/VCF's this is comma separated art -Dbam='/pathToFile/file1.bam,/pathToFile/file2.bam', it can also read the BAM's from URL's.
- Added option to display orientation of reads in BamView.
- In Bamview, display reads that are split over introns so that the exon boundaries can be identified by colouring the line between the aligned blocks grey.
- Add VCF panel to ACT.
- Support added to read indexed fasta sequence files. An index file is created using SAMtools.
- Add support for VCF v3.3 and v4.0.
- Add option to show combined coverage plots for multiple BAMs.
- Add show_forward_lines and show_reverse_lines as options for switching
- frame lines on and off.
- Add an option to delete qualifiers in the Find/Replace tool.
- Artemis can read in a set of zipped search results (e.g. blastp/blastp.zip).
- Add BamView panel to ACT.
- Fix for writing EMBL files out from GFF entries.
- An option has been added in BamView to colour reads by the colour used in the coverage plot - useful when looking at multiple BAM files.
- Plot multiple coverage plots in BamView when multiple BAM files are loaded in.