Version 18
1) Switched build process to use Maven. Changed directory structure. Removed ant and Make files.
2) Retired a number of jars and upgraded others. Removed the ssh-plugin jar.
3) Upgraded to Picard 2.18.14 jar, which has a number of important bug fixes.
4) Removed old documentation functionality. HTML/PDF manuals are now stored in gh-pages branch and exported directly from a word doc.
5) Changed application script jar paths.
6) Rewrote writedb_entry script.
7) Replaced script usage of -Dcom.apple.mrj.application.apple.menu.about.name with -Xdock:name.
8) Fixed incorrect Amigo GO term URL, used in the Artemis gene builder window.
9) Updated README.
Version 17.0.2-test - patch release for Sanger. Changes incorporated into GitHub master.
1) Added bamview_use_htsjdk_file_index_caching property to allow switching off of htsjdk caching for bam files.
This gets around a bug for large bams whereby parts of the bam fail to get loaded - RT ticket #624271.
See htsjdk GitHub issue 1127 for details.
Version 17
Artemis/ACT and associated applications have been upgraded to Java 8. Java 7/6/5 are now no longer supported - RT ticket #589103
BamView fixes/changes -
1) Improved mouse selection of reads.
2) Fixed exceptions thrown when zooming into an area with secondary reads or SNPs enabled - RT ticket #596489: Problem zooming in using isoseq data
3) Removed Samtools (htsjdk) jar and updated Picard jar (which includes htsjdk).
4) Upgraded Apache Commons Net jar - used for ftp'ing.
5) Added Cram file loading and fixed defects around that code area (also related RT ticket #560982: Artemis fails to build from source).
6) Added display of bam secondary & supplementary alignment flags to read details pop-up window.
7) Improved error handling/reporting for standalone BamView application.
8) Added buffer sizing to FTPSeekableStream.
9) Performance tweak for BAM file indexing.
10) Fixed issue in BamView whereby if you went to the end of a long contig and then switched to a shorter one (via the combo), you would end up off the end of the sequence
resulting in a negative array index exception. Code has been changed to reset display to the start of sequence when the combo is changed (i.e. same as Artemis).
11) Added bamview_perform_detailed_validation boolean property that can be set to perform more detailed sam validation during loading - this can be slow for large files.
Added EvoSuite unit tests and additional targeted tests (RT ticket #419534: Develop a test suite for Artemis).
Added Jacoco unit test coverage reporting - manual tests only currently. This may be switched to Clover in the future if this proves compatible with EvoSuite
- for the moment we are stuck with two coverage reports - evosuite and Jacoco.
Removed redundant Corba libraries.
Upgraded JUnit jar.
Changed Travis yml build file. RT ticket #597497: Set up artemis tests to run on travis build.
Changed all build scripts and startup scripts - RT ticket #598617. Removed building of artemis_mac.jar which is not used.
Removed etc/gene_builder script and the gff2embl script (and documentation references) - no longer supported.
Fixed RT ticket #606061 - Using EBI-Dbfetch on ARTEMIS. Change to DbfetchEntrySource.java due to incorrect regular expression and EBI URL.
Resized splash screen, as it was too small to the accommodate text info.
Added error handling for dnaplotter template file loading in standalone mode.
Added Bioconda recipe. RT ticket #341139 .
Fixed RT ticket #467433 - Genbank DBSOURCE field was not recognised by Artemis. DBLINK was already added.
Fixed RT ticket #503254 - Act doesn't detect if file does not exist.
KNOWN ISSUES:
1) Java JDKs 1.8.0_131 and above have a Swing bug related to overlaying of modal dialogs for Mac OS X: https://bugs.openjdk.java.net/browse/JDK-8179335
2) There is a current bug in htsjdk whereby calls to the queryMate functionality can throw an exception on reads with secondaries and/or supplementals.
This affects looking up properties for a selected read on bamview - https://github.com/samtools/htsjdk/issues/1065
Version 16
Add 'Features Within Selection' option to the 'Select' menu to select
features that are contained by a selected base range.
Saving an entry as EMBL submission has an option now to remove products
from CDS features with a pseudogene qualifier.
From the 'View' menu added 'Adjust panel heights...' option in ACT
for adjusting their heights (BAM, VCF, plots, comparisons) by giving
them different weights in order to distribute the space between each
component.
Added ability to hide graph lines. Right click on the graph to get the
popup menu and select 'Configure...'. Then use the 'Line size' slider
to reduce the size of the line(s) that you want to hide to zero.
Labels can optionally be added to the header of base position plots
and these are used in the legend, e.g.
# colour 5:150:55 255:0:0 0:255:0 0:0:255 100:100:100 50:150:50
# label lab1 lab2 lab3 lab4 lab5 lab6
176 2204.8 848.23 0 0 0 536.04
...
In the Feature Editor there is now a button ('User Qualifiers') which
opens a tool for maintaining user defined lists of qualifiers (i.e.
qualifiers in the form tag = value pairs on separate lines) and the
option to read qualifiers from OBO formatted files or URLs. These can
be saved between sessions in the file '.artemis.qualifiers' in the
home directory.
Automatic addition of history qualifier in chado database mode.
Added RNASeq strand specific option to the BAM popup menu ('Colour By' ->
'RNASeq Strand Specific Tag (XS)'). Reads colours are based on the XS
tag (used by TopHat). The RNA strand is then used in the coverage plots
and in calculation of read counts and RPKM values.
Added the following flags:
-Dshow_snps Show SNP marks in BamView
-Dshow_snp_plot Open SNP plot in BamView
-Dshow_cov_plot Open coverage plot in BamView
Add validation checks. This will check the following:
All file types:
- CDS have no internal stop codon
- CDS have valid stop codon
GFF / Chado:
- check complete gene model
- check boundaries are valid
- check all features are on the same strand
- check CDS features have a phase
- check attribute column
- qualifiers have a value (not empty)
- only reserved tags start with uppercase
Validation can be run in two ways:
1. using the option in View->Feature Filters->Validation checks... which shows
'failed' features in feature list windows
2. selecting 'Validation report ...' option in the popup menu when right clicking
on the feature display. This produces a report with an option to auto-fix gene
boundaries and stop codons.
Version 15
Multiple BAM panels can be opened using the bamClone flag this is used with
the -Dbam flag:
art -Dbam='/pathToFile/file1.bam,/pathToFile/file2.bam' -DbamClone=n
(where n is an integer greater than 1). All BAM files are then shown in each
panel. Alternatively the following will open BAM files in separate panels
(using -Dbam[1,2,3...]):
art -Dbam1=fileA.bam -Dbam2=fileB.bam
Add SVG (scalable vector graphics) support for Artemis, ACT and DNAPlotter.
Option added to adjust VCF row height.
Add support for indexed user graphs using tabix. For example file.plot is a tab
delimited file with column 1 containing the sequence name and column 2 the
positions:
(grep ^"#" file.plot; grep -v ^"#" file.plot | sort -k1,1 -k2,2n) | bgzip > sorted.plot.gz ;
tabix -s 1 -b 2 -e 2 sorted.plot.gz
Option added to show or hide the average line in the graphs.
BAM coverage heatmap view added.
Add Rfam sequence search from the RUN menu.
Base similarity graph for each VCF added to the VCF view.
Sense and anti-sense read counts and RPKM values are now reported.
Option added to create features from BAM peaks, i.e. above a threshold of the
number aligned reads.
Option included for defining groups of BAM files so that they can be
switched on and off by their group.
Coverage plots from read alignments (BAM) can be plotted by their strand.
Addition of a Project File Manager used to group files together for
launching in Artemis. When a project has been added or updated the details
are saved at the end of each session in '.artemis.project.properties'
in the user's home directory.
Fix for saving user defined shortcuts between sessions on windows.
Add preliminary support for the CRAM format:
http://www.ebi.ac.uk/ena/about/cram_toolkit
This requires the cramtools.jar to be added to the start of the CLASSPATH.
Improved support for matching GFF feature coordinates to the correct
contig in a multiple FASTA sequences. This works now whether
the sequence is part of the GFF file or a separate multiple-FASTA file.
Add 'Feature Stack View' to visualise overlapping gene features.
Add support for read-only indexed GFF. Features in GFF format are
sorted and indexed with tabix:
http://samtools.sourceforge.net/tabix.shtml
Version 14
Add options in the navigator for searching the forward and
reverse strands individually for base / amino acid patterns.
Add an option to the navigator for searching for matches that
overlap a selected region or feature.
New translation table 24 (Pterobranchia mitochondrial) added.
If the BAM index file is missing then Artemis uses the picard library to
attempt to create the index.
Variant (VCF / BCF) filtering now uses the meta-data in the header to
enable filtering based on INFO, FILTER and FORMAT columns.
Shortcut changes made in the 'Preferences' menu are saved between sessions (the
shortcut_cache flag in the options file can be used to turn this on/off).
More support for GTF format to show CDS and exons as joined features.
BAM record list option added to display as a list the reads and their
properties.
Add options for loading graph, BAM and VCF files into ACT from the
command line. Numbers are used to associate the file with a particular
sequence. e.g. add a BAM to the first (top) sequence in ACT:
act -Dbam1=/pathToFile/file.bam
or, to add a userplot to the second sequence:
act -Duserplot2=/pathToFile/userPlot
Version 13.2.0
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.
Version 13
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.
Version 12
It is now possible to add user plots from the command line using the
JVM userplot option, e.g. art -Duserplot=/pathToFile/userPlot
and for multiple plots this is comma separated
art -Duserplot='/pathToFile/userPlot1,/pathToFile/userPlot2', it
can also read the plots from URL's.
Added support to be able to read BAM files to display read alignments.
It uses picard (http://picard.sourceforge.net/) to read from the BAM file
and so requires Artemis to be run with Java 1.6.
All graphs can now be configured to be plotted as line graphs
or heat maps.
Added support for BLAST tabular format (-m 8 option) and MSPcrunch
format to plot scores.
Added support for wiggle (variableStep/fixedStep) plots that can be
displayed as histograms or heat maps.
Added a new user plot file format with the first column specifying
a base position.
More configure options have been added to the graphs to enable
configuration of the graph line style and size.
GoTo directory option added to file manager to assist navigation.
The database manager is cached between sessions (this can is on by default
and can be switched off with -Ddatabase_manager_cache_off). There is an
option under the File menu to clear this cache.
A checkbox has been added to the window for adding ortholog/paralog links
in the Gene Builder. If this is selected it adds links between existing
ortholog/paralogs and the new ortholog/paralog. By default this is off.
An option has been added to the database manager to display polypeptide
domains in the feature display (as well as the protein map in the Gene
Builder).
An option has been added to the Run menu for doing a search of the Pfam
database.
Added an option to the Write menu for writing a combination of upstream
+ feature + downstream bases for selected features.
Option added in the View->Filter Features menu to search for Duplicate
Systematic Name Qualifier.
LookSeq analysis panel can be displayed by setting the lookseq
value in the options file. An option under the Display menu then
is used to shows the LookSeq read alignment panel in Artemis.
Added options to set the minimum and maximum values of the plots.
Transfer Annotation Tool (TAT) added to feature editor and Gene
Builder.
New graph popup menu option to show the values and average for
a selected range.
Added product_cv database option to define if the product is
stored as a controlled vocabulary or as a feature property (featureprop).
Version 11
Use black_belt_mode to suppress warnings when opening Artemis.
Script (writedb_entry) added to make it easier to write out
multiple entries as EMBL / GFF files from chado. This uses Artemis
read-write libraries and does not require each sequence to be
launched from the database. For command line help run:
etc/writedb_entry -help
On MacOSX - enable dropping files on Artemis application to open sequences
with file extensions: gff, embl, EMBL, genbank, gbk, fasta, seq, art and
dna (defined in Artemis.app/Contents/Info.plist).
Add NCBI search link to run menu. This transfers the sequence automatically
to the NCBI web page.
Add support for writing Sequin table format.
Added print to PostScript option in Artemis and ACT.
Optimisation of reading in user graphs.
New Edit->Selected Feature(s)->Convert Keys option to convert
keys of selected features.
New Edit menu option for finding and replacing qualifier text. This
has an option for boolean searches (e.g. and, or, &, |) of qualifier
text. This includes an option to search for duplicate qualifiers.
Implemented a commit manager for the database mode. This
highlights transactions that produce an error.
Make the chado transaction log messages more human readable.
Add ability to write file formats from Artemis in database mode.
With option to collapse the gene hierarchy (gene, transcript, exon)
into a CDS feature.
Graphs are now added to a split pane. So that their size can be
defined by dragging the divider at the bottom of the graphs.
Provide option to log transform user data plot.
Improved error reporting for contig reordering.
Fix for creating intergenic features for overlapping CDS's. Also
add note based on which one of the 4 cases with respect to the
flanking CDS it belongs to, i.e.:
IGR-F (forward): cds> IGR cds>
IGR-R (reverse): <cds IGR <cds
IGR-B (both): <cds IGR cds>
IGR-X: cds> IGR <cds
Add option to preferences for defining contig ordering features.
Added option to "Create features from graph peaks". For a graph
this creates features in regions above a given cut-off and above
a given feature size.
Add -Dread_only option for read only databases.
Add option to lazy load feature data from database.
Version 10
Add redo function to 'Edit' menu. Also enable/disable undo and
redo menu items when available/not available.
Add option to replace selected bases in 'Edit' menu.
Option to create features in intergenic regions added.
Feature editor now marks hyperlinks to SWALL, EMBL, UniProt,
PMID, PubMed, InterPro, OrthoMCLDB, Pfam that are opened in
the browser. Now configured in the options file.
Added "Convert Qualifier of Selected..." option to the Edit menu.
This allows the user to change the names of qualifiers for all
selected features.
Now using new release of j2ssh (0.2.9). This requires Java1.5+.
Implemented option for ORF creation to take into account boundaries
of multiple fasta sequences, so that they do not cross them.
Implemented the ability to run and store fasta and blast search
results for multiple databases... E.g. fasta searches on uniprot
and on user's own database, stored in multiple fasta_file qualifiers.
"Set Score Cutoffs" in Artemis popup menu uses existing /scores as
the initial min and max values (rather than just 0 and 100).
Added cache to store the entries retrieved for the object editor.
Implement log4j logging to be displayed in log viewer. Using colour
coding depending on level of logging.
Added -Doffset so that Artemis can be opened at a given base.
Version 9
Feature selector can be used to look for features with introns
that do no contain the GT/GC start or AG end.
Contig tool now checks for contigs that contain features that
span the boundaries of the contigs. These features have to be
removed or restricted to the contig boundary before it can
carry out contig reordering.
Fix for converting files from other file formats to
genbank format.
Fix rounding problem for long sequences when writting
out all bases in FASTA or raw format.
Cache the start codons (as per stop codon caching),
to speed their display.
Combine the extend to next exon and the fix stop codons
into one option.
The feature types that appear on the frame lines can be defined
by the user via an option ("Frame Line Features...") in the
feature display popup menu.
Added to File -> Preferences a user defined selection for display names
and systematic names. Also extended popup menu option in feature lists
to allow the user to be able to select multiple qualifiers to display.
For entries opened from the remote side of an SSH connection will search
for results on the remote file system if they are not found locally. They
are transferred via SSH and then stored locally.
For Mac users, the option to send search results to the browser will
display the results in the default browser.
When automatically generating gene names (under the Edit menu), the user
can specify the number of zeros to pad the numbering with. e.g if 5 digits are
selected the format will look like : 00001, 00002 etc.