Geneious Basic full changelog

· Sequence Viewer: Fixed hang working with annotation types in tracks that contain '_' or '.' in their type name
· Sequence Viewer: Fixed crash in rare situations when clicking on annotations in contigs
· Sequence Viewer: Fixed crash and/or loss of newly added annotations on consensus sometimes when saving contigs
· Sequence Viewer: Fixed poor performance/hangs viewing large contigs with non-trim annotations on the reads
· Sequence Viewer: Fixed statistics that are too small to read sometimes
· Reference assembly: Fixed crash and/or incorrect results when choosing to map paired reads to all matching locations.
· Reference assembly: Fixed poor sensitivity mapping to genomes of several hundred MB (larger genome sizes (e.g. human genomes) were fine). The increased sensitivity will also slightly improve small genome results.
· Reference assembly: Fixed poor sensitivity mapping reads spanning the origin of circular reference sequences

· Added fastq export option to export paired reads to parallel files

Bugs fixed:
· Read mapping: Fixed incorrect read mapping results and/or poor performance sometimes with circular reference sequences
· 3D Structure Viewer: Fixed a bug where the selection in the tree was being calculated incorrectly, causing the tree and selections to behave incorrectly
· Fixed bug where extraction of multi-interval annotations from long sequences with many annotations could result in extra annotations
· Made PMID show up correctly on PubMed documents
· Fixed extraction of primers from regions of alignments containing gaps
· Fixed crash when concatenating sequence lists or alignments such that that total number of bases was greater than around 2,000,000,000
· Fixed issue where tree viewer options didn't update when saving document
· Fixed issue where jmol viewer selection misbehaved when a PDB document contains HETATM records prior to the last ATOM record

Features:
· Restored the old annotation table view

Bugs fixed:
· Fixed quot;There is already a track on this sequence with name...quot; error message when running various operations such as cloning and SAM import
· Fixed out of memory error when viewing some sequences
· Fixed a bug where the Csv importer wasn't importing Date fields correctly.
· Fixed an error that would occur when searching a server database using a number field
· Fixed an issue with Sassafras licenses not working

Features:
· Restored the old annotation table view

Bugs fixed:
· Fixed quot;There is already a track on this sequence with name...quot; error message when running various operations such as cloning and SAM import
· Fixed out of memory error when viewing some sequences
· Fixed a bug where the Csv importer wasn't importing Date fields correctly.
· Fixed an error that would occur when searching a server database using a number field
· Fixed an issue with Sassafras licenses not working

Features and Improvements:
· Improved fastq import quality format guessing and added dialog asking if the guess is correct if Geneious is unsure of the format
· Better track names when running variant finding
· Batch rename can now rename multiple selected sequence list documents and multiple selected alignments

Bugs fixed:
· Fixed hang using Sequence Logo graph on big alignments/contigs.
· Sequence Viewer: Reduced memory usage when viewing lots (e.g. millions) of annotations
· Fixed occasional failure to copy documents or folders from a server database
· Fixed incorrect assembly results sometimes when mapping to a circular reference sequence
· Fixed a bug where Convert to Oligo was appending a duplicate number to the end of the Oligo's name
· Custom Blast Query-centric alignments no longer double up on annotations
· Fixed a bug that could cause primer documents in a server database to not be available in the primer chooser

Bugs fixed:
· Sequence Search: Fixed crash sometimes when doing a sequence search
· Sequence Viewer: Fixed crash after deleting sequences in genome lists
· Sequence Viewer: Fixed hang/crash when resizing some trim annotations
· Sequence Viewer: Fixed crash clicking 'go to next annotation' button on some restriction site annotations
· Sequence/Contig Viewer: Fixed crash if you delete a track, create one with the same name, and click save
· Sequence/Contig Viewer: Fixed crash when loading a document that previously had an annotation selected in a track, but that track was turned off while viewing another document
· Alignment/Contig Viewer: Fixed not rendering SNP/coverage annotations on the reference sequence that lie past the ends of the reference sequence
· Alignment/Contig Viewer: Fixed it saying you need to zoom in to view reads on contigs that only have a few reads
· Alignment/Contig Viewer: Fixed occasional crash when dragging bases/gaps around during alignment editing

Sequence View Improvements:
· New annotation track functionality that groups annotations from a common source so they can be rearranged, colored, shown/hidden, deleted etc Pro-only
· Added an interactive mini-map that shows your current position in the genome and a summary of annotations
· Added a real-time annotation filter in the annotation controls Pro-only
· Added a chromosome selector when viewing an entire genome as a sequence list (saves memory and improves performance)
· Added a slider for changing the zoom level on genomes
· Redesigned quot;go to positionquot; to have a single input field and a shortcut button in zoom controls on genomes
· Annotations are arranged more efficiently on genomes
· Positions in big sequences are now rendered like 45.2 mb instead of 45,200,000
· Added ability to extract multiple primer annotations simultaneously
· Annotation generators can now run on more than one alignment simultaneously.

Sequence View Improvements:
· New annotation track functionality that groups annotations from a common source so they can be rearranged, colored, shown/hidden, deleted etc Pro-only
· Added an interactive mini-map that shows your current position in the genome and a summary of annotations
· Added a real-time annotation filter in the annotation controls Pro-only
· Added a chromosome selector when viewing an entire genome as a sequence list (saves memory and improves performance)
· Added a slider for changing the zoom level on genomes
· Redesigned quot;go to positionquot; to have a single input field and a shortcut button in zoom controls on genomes
· Annotations are arranged more efficiently on genomes
· Positions in big sequences are now rendered like 45.2 mb instead of 45,200,000
· Added ability to extract multiple primer annotations simultaneously
· Annotation generators can now run on more than one alignment simultaneously.

New features:
· Added quot;Whole Words Onlyquot; checkbox to local documents searching so that you can search for partial words
· Added quot;Find Allquot; button when using quot;Find in Documentquot; on the sequence/alignment viewer
· Can select multiple folders for moving/deleting and for showing the contents of them all at once

Bugs fixed:
· Fixed changes being lost when making changes to an alignment built from a sequence list
· Fixed occasional crash exporting in SAM/BAM format
· Fixed crash that can happen downloading full documents from a tblastn run
· Fixed bug that can cause sequences extracted from tree document to be in the wrong order
· Fixed crash that can occur importing ACE files with reads starting or ending with gaps and having trimmed regions
· Removed possibility of crash from removing invalid bases from sequences with quality/traces on import

Pro-only features now enabled in Geneious Basic:
· All import and export
· Visualisation including circular sequences, chromatograms, color schemes,

New features:
· Added quot;Whole Words Onlyquot; checkbox to local documents searching so that you can search for partial words
· Added quot;Find Allquot; button when using quot;Find in Documentquot; on the sequence/alignment viewer
· Can select multiple folders for moving/deleting and for showing the contents of them all at once

Bugs fixed:
· When a sequence is circularized, annotation intervals extending past the ends of the sequence are now truncated
· When a sequence is de-circularized, annotation intervals spanning the origin are split into multiple intervals
· Fixed poor performance when viewing some sequences with over 100,000 annotations
· Empty sub-folders are now kept when exporting folders
· Separate by barcode works on already paired reads and lets you choose which sequence in the pair has the barcode
· Fixed problem with garbled fonts on some systems
· Fixed de novo assembler running out of file handles on machines with lots of processors