Release Notes - UGENE - Version 1.11 - HTML format

Bug

  • [UGENE-69] - Set data path properly on linux
  • [UGENE-629] - Dotplot files are opened as plain text
  • [UGENE-725] - Can't load BAM file from remote source mounted to file system
  • [UGENE-743] - WD: Write GenBank is saving the sequences not associated to the features
  • [UGENE-747] - Sequence Writer crashes when GFF fromat is chosen
  • [UGENE-757] - WD: remove non-specific document writers (genbank, clustalw etc)
  • [UGENE-760] - UGENE windows installer crashes (with a message) if another version of UGENE is run
  • [UGENE-767] - Users WD script are not functional
  • [UGENE-773] - GFF format: attributes parsing is uncorrect
  • [UGENE-779] - WD: Write annotation element crash
  • [UGENE-783] - QD: repeat element's constraint is not saved
  • [UGENE-787] - WD: create script element dialog - expand slot editor fields
  • [UGENE-801] - Find Dialog crashes in pattern length is graeter than region
  • [UGENE-803] - Include "embl/annotations/qualifier/test_0002" test and make correct parsing of quotes (") in Genbank qualifiers
  • [UGENE-813] - add possibility to on/off crash handler
  • [UGENE-814] - add simpe option dumping log to file
  • [UGENE-821] - Opening Genbank files with a merge mode brakes annotations positions
  • [UGENE-829] - Input the same contig name twice in CAP3
  • [UGENE-835] - Restriction Site Map of deleted sequence (multiple sequences in the Sequence View)
  • [UGENE-839] - Crash when open not a multiple alignment file in Build Matrix dialog
  • [UGENE-841] - Auto-annotations drag&drop doesn't work properly
  • [UGENE-844] - Tandem finder (unoptimized suffix array) crashes
  • [UGENE-864] - Blast worker: tabular form output problems
  • [UGENE-866] - Get File List element couldn't be connected to several inputs
  • [UGENE-875] - Input file is saved and can't be deleted when iterations are used in WD
  • [UGENE-879] - Read sequence worker: adding a file to empty file list is confusing
  • [UGENE-880] - "Unknown property paddling" error in the console
  • [UGENE-886] - Crash when trying to load FASTA file exported from Ensemble
  • [UGENE-888] - WD: wd adds to uwl file string with '#' after each save
  • [UGENE-890] - Update translations for menu for all languages
  • [UGENE-903] - LocalFileAdapter::skip() works incorrect in a very rare case
  • [UGENE-905] - T-Coffee script works incorrectly if working dir contains spaces
  • [UGENE-908] - UGENE WD crashes when a multi input port cmdline element is used
  • [UGENE-910] - "Accomulate objects" parameter in the "Write sequence object" doesn't work
  • [UGENE-913] - HMM in WD truncates files
  • [UGENE-914] - Bad memory management causes crash in WD
  • [UGENE-916] - FASTQ format support
  • [UGENE-924] - Wrong export annotation selection to CSV
  • [UGENE-925] - GFF parser can't read a file
  • [UGENE-926] - Sequence export to alignment ignores complement strand
  • [UGENE-927] - "Auto-saved" state should not be renamed
  • [UGENE-928] - ORF finder dialog crashes UGENE.
  • [UGENE-939] - crash when delete sequence from project tree
  • [UGENE-940] - UGENE crashes when export subalignment to the same file
  • [UGENE-958] - Import annotation from CSV works incorrect in one case
  • [UGENE-962] - UGENE crashes on creating annotation
  • [UGENE-966] - Support "mobile_element" GenBank feature
  • [UGENE-969] - WD every time asks to save schema
  • [UGENE-972] - Align short reads BWA dialog doesn't fit the screen with height 768
  • [UGENE-984] - Publish UGENE package for Ubuntu 12.04
  • [UGENE-985] - Smith-Waterman dialog crashes on custom region selected
  • [UGENE-989] - Incorrect search for a pattern with regular expression containing '*'
  • [UGENE-994] - Get qualifier tooltip crashes UGENE
  • [UGENE-1009] - wrong cloning support: digest sequence
  • [UGENE-1010] - Unloaded files disapper from the project after "Save project as..."

Improvement

  • [UGENE-57] - Support searching/filtering by qualifier in annotation tree
  • [UGENE-240] - Drag and drop in alignment
  • [UGENE-324] - Support DEFENITION entry in Genbank format and reuse it in export of multiple sequences to MSA
  • [UGENE-343] - Sitecon Workflow element parameters
  • [UGENE-392] - Revise Find Pattern dialog
  • [UGENE-407] - Warn a user when a sequence opened contains incorrect characters
  • [UGENE-433] - Highlight mutations/mismatches/SNPs in assembly browser
  • [UGENE-446] - Investigate details about Unpadding element of CIGAR string
  • [UGENE-640] - Export sequence from the Alignment Editor
  • [UGENE-715] - Ugene needs to support openning miltiple sequences from different files as one sequence with merge mode
  • [UGENE-726] - Support the Genome Aligner index directory
  • [UGENE-728] - Add support for lowercase view in a sequence or alignment
  • [UGENE-730] - Mac: small font in external tools preferences
  • [UGENE-731] - Mac: application name is "ugeneui" in dock and menu
  • [UGENE-745] - U2FeatureDbi lacks a method for getting feature keys
  • [UGENE-800] - Check if UGENE has writing rights for temporary directory
  • [UGENE-820] - Improve opening sequences with a merge mode
  • [UGENE-830] - A result file is created when CAP3 fails
  • [UGENE-834] - Circular sequence reverse location
  • [UGENE-847] - Support using unknown file formats for external tool workers
  • [UGENE-855] - Inlcude size of amplicon in primer annotation
  • [UGENE-856] - Primer 3 option: span exon-intron boundaries
  • [UGENE-858] - Copy information about a sequence from the Options Panel
  • [UGENE-859] - Add 'ugene' shell script to Mac bundle
  • [UGENE-861] - Move "Annotations Highlighting" to the Options Panel
  • [UGENE-865] - Optimize Assembly Ruler cursor
  • [UGENE-883] - UGENE installation path on Linux
  • [UGENE-892] - Regular expressions for filters in the File List workflow element
  • [UGENE-894] - Storing of genbank document used whole sequence
  • [UGENE-897] - Update Czech Translations
  • [UGENE-907] - Creation of the Options Panel widget
  • [UGENE-919] - Add filetype association info to Mac bundle
  • [UGENE-920] - Search annotations by qualifiers
  • [UGENE-921] - Invert annotations selection in the Annotations Editor
  • [UGENE-929] - Improve most covered regions list
  • [UGENE-930] - Replace the word 'contig' with 'assembly' where necessary
  • [UGENE-938] - "Navigation" tab on the Options Panel in the Assembly Browser
  • [UGENE-942] - Misleading naming of main menu items: aligner and assembly
  • [UGENE-944] - Garbage collector in WD
  • [UGENE-952] - Merge mode for annotations-only files
  • [UGENE-957] - Improve crash handler logging
  • [UGENE-960] - Add BAM and SAM files to UGENE samples

New Feature

  • [UGENE-41] - Export/highlight all common features in Dotplot
  • [UGENE-442] - Support paired-reads visualization
  • [UGENE-532] - Add description to SITECON models
  • [UGENE-534] - Workflow element that can fetch sequences by their accession IDs from qualifiers
  • [UGENE-578] - Export multiple alignment to vector graphics format
  • [UGENE-597] - Save cutoffs of a graph as annotations
  • [UGENE-658] - Create a widget with online information for the current sequence/alignment/assembly view states
  • [UGENE-661] - ExpertDiscovery recognition window rebuild
  • [UGENE-665] - Add common panel at the right part of a UGENE window
  • [UGENE-753] - Support regexp-based search in find pattern tool
  • [UGENE-775] - Select multiple range option in the Select Range window
  • [UGENE-796] - Showing selected position in the Alignment Editor
  • [UGENE-797] - HMMER2 Support in QD
  • [UGENE-805] - Exclude tandem repeats from repeat finder results
  • [UGENE-808] - Split Fasta in the Write Fasta element
  • [UGENE-817] - Create "Get File List" workflow element
  • [UGENE-819] - Pass an input string "as it is" to a workflow element with a command line tool
  • [UGENE-824] - A new option of Repeat Finder: exclude tandems areas before running
  • [UGENE-828] - Mark sequences by its names
  • [UGENE-853] - Search qualifier in the annotation tree
  • [UGENE-868] - Support bookmarks for AssemblyBrowser
  • [UGENE-871] - "Translate sequence" workflow element
  • [UGENE-873] - "Join sequence into sequence" workflow element
  • [UGENE-898] - Assembly consensus widget
  • [UGENE-899] - Assembly consensus export
  • [UGENE-900] - Add Options panel to Assembly Browser
  • [UGENE-923] - Mac installer package
  • [UGENE-961] - Add name filter to the palette in WD

Task

  • [UGENE-584] - Unit tests for UGENE script functions
  • [UGENE-789] - Change year in headers
  • [UGENE-845] - Create a test suite for workflow elements with command line tools
  • [UGENE-863] - Update web-site with UGENE paper information
  • [UGENE-945] - Remove GPU-BLAST from UGENE

Sub-task

  • [UGENE-889] - Integerate "mRna to genomic" spliced aligner

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