December 22nd, 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
December 22nd, 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.
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