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 -
Improved mouse selection of reads.
Fixed exceptions thrown when zooming into an area with secondary reads or SNPs enabled - RT ticket #596489: Problem zooming in using isoseq data
Removed Samtools (htsjdk) jar and updated Picard jar (which includes htsjdk).
Upgraded Apache Commons Net jar - used for ftp'ing.
Added Cram file loading and fixed defects around that code area (also related RT ticket #560982: Artemis fails to build from source).
Added display of bam secondary alignment flag to read details pop-up window.
Improved error handling/reporting for standalone BamView application.
Added buffer sizing to FTPSeekableStream.
Performance tweak for BAM file indexing.
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).
Added EvoSuite unit tests and additional targeted tests (RT ticket #419534: Develop a test suite for Artemis).
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@@ -22,8 +24,8 @@ Version 17
Changed Travis yml build file. RT ticket #597497: Set up artemis tests to run on travis.
Changed all build scripts and startup scripts. 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. RT ticket #598617.
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.
