Bug

• [UGENE-88] - Error when "close project" action is cancelled
• [UGENE-93] - Why is the anaglyph view not supported by NVIDIA GeForce 9800 GT
• [UGENE-341] - Custom Workflow elements don't contain script code
• [UGENE-632] - Can't import BAM file (NA12878.chrom1)
• [UGENE-733] - Double extension adding in Write Sequence element
• [UGENE-768] - Add WD script code validation before run
• [UGENE-780] - CMDLine worker problem
• [UGENE-790] - Crash handler fails to send reports with a large log file size
• [UGENE-895] - Ugene craches on assert when qd test is running
• [UGENE-915] - Website layout broken
• [UGENE-986] - UGENE crash on Smith-Waterman search
• [UGENE-995] - WD schemes work slowly when they are run in separate process
• [UGENE-997] - Dot plot don't ask to save the current state
• [UGENE-1013] - MSA Editor improvements
• [UGENE-1016] - "Very high similarity" for a standard Bowtie2 output
• [UGENE-1027] - Problems with Find Pattern tool
• [UGENE-1033] - KAlign can't align COI.aln from samples
• [UGENE-1034] - WD: Converting Huge FASTQ
• [UGENE-1036] - Modifying files in the process of working the Multiple Alignment Tools
• [UGENE-1050] - Unnecessary buttons are enabled in zoom view
• [UGENE-1061] - Text Qualifier Marker fails UGENE
• [UGENE-1062] - Type "D" of optional field while reading a BAM file
• [UGENE-1067] - Dotplot crash while navigating using minimap on max zoom in
• [UGENE-1068] - Workflow designer crash while designing a schema
• [UGENE-1080] - Scheme with remote BLAST + marker + filter fails
• [UGENE-1084] - UGENE Genome Aligner doesn't work with GPU optimization
• [UGENE-1086] - Query Designer Worker: orf finder crash
• [UGENE-1089] - Script samples do not work
• [UGENE-1090] - Samples with filters do not work
• [UGENE-1091] - Samples with groupers do not work
• [UGENE-1094] - WD Samples: Quality filter scheme crashes
• [UGENE-1098] - WD Samples: "Convert UQL schema results to alignment" sample does not work
• [UGENE-1099] - Disable amino translation buttons
• [UGENE-1102] - "Del" hotkey sometimes doesn't work in the Project View
• [UGENE-1108] - Bad deserialization of database attribute of fetch-sequence worker
• [UGENE-1110] - Installing 64-bit UGENE on a 32-bit system
• [UGENE-1114] - Estimation of memory required for one short read in the Genome Aligner
• [UGENE-1116] - Crash on rendering a 3D structure because of bad video driver
• [UGENE-1119] - A gff file with blank lines in the middle crashes UGENE
• [UGENE-1129] - WD: minimal style setting does not work
• [UGENE-1132] - Smith-Waterman crashes on a big sequence (~200mb)
• [UGENE-1137] - "Save a copy" does not work for assemblies
• [UGENE-1138] - AssemblyObject error
• [UGENE-1142] - Russian translation does not work on Linux
• [UGENE-1154] - Genome aligner wrong statistics
• [UGENE-1155] - WD: wrong output path fails UGENE
• [UGENE-1158] - Load pattern from file fails on new annotation document
• [UGENE-1159] - Problems with writing gff file with a sequence.
• [UGENE-1171] - BWA/Bowtie alignment fails
• [UGENE-1173] - GFF file is not visualized right
• [UGENE-1184] - WD: after copying element, copy parameters different
• [UGENE-1187] - Genome aligner: shows error message if user presses cancel on load resulting aligned document dialog
• [UGENE-1188] - Crash handler: send report win x64 information
• [UGENE-1190] - Crash on aligning with Genome Aligner when the first big part of reference sequence contains N's only
• [UGENE-1191] - Crash on aligning with Genome Aligner
• [UGENE-1192] - Genome aligner: memory leak after "build index only" mode finished or cancelled
• [UGENE-1193] - Genome aligner: use GPU optimization checkbox enabled if no gpus are enabled in the settings
• [UGENE-1194] - Genome aligner: "memory leak" in OpenCL mode
• [UGENE-1195] - Genome aligner don't work if run from command-line (ugenecl)
• [UGENE-1197] - Correct physical memory size info for Win, Linux
• [UGENE-1198] - Correct physical memory size info for MacOS
• [UGENE-1201] - Genome aligner dead lock
• [UGENE-1202] - Wrong cuts from enzymes with blunt ends
• [UGENE-1209] - WD: UGENE crashes if 'call variations with SAM tool' worker, has empty 'Source URL' input slots
• [UGENE-1210] - WD: 'call variations with SAM tool' worker problem
• [UGENE-1212] - UGENE hangs up/crashes on region selection (Linux only)
• [UGENE-1215] - MUSCLE memory threshold (x64)
• [UGENE-1224] - Circular molecules are not saved properly
• [UGENE-1229] - Renamed sequences keep old names when exported as multiple alignment
• [UGENE-1230] - Workflow designer incorrect sample schemes
• [UGENE-1231] - Tandem repeats in a 900Mb file
• [UGENE-1232] - DNA statistics error: negative Molar ext. coef.
• [UGENE-1233] - Annotation Selection. Shift+Ctrl modifiers
• [UGENE-1234] - Export 3 translated frames function has artifucts
• [UGENE-1237] - Thresholds of Align short reads dialog are too tight
• [UGENE-1239] - WD: merge annotations worker doesn't work
• [UGENE-1240] - Find patterns crashes on a big pattern
• [UGENE-1246] - UGENE crashes on the Export Document to the SAM format
• [UGENE-1247] - UGENE has error to the Export Document to the BAM format
• [UGENE-1248] - UGENE doesn't open a file without extension
• [UGENE-1253] - Find Pattern: cannot rename annotation/annotation group sometimes
• [UGENE-1255] - Find Pattern. No validation on annotation creation
• [UGENE-1257] - Find Pattern: search button is not disabled if there are errors in parameters
• [UGENE-1259] - Find Pattern: stack overflow when remove a symbol from sequence in FASTA input
• [UGENE-1260] - SAFE_POINT when a subalignment is saved with the same name and different extension
• [UGENE-1262] - Crash when search pattern using deleted annotation document
• [UGENE-1264] - Check if annotation model is ok: CreateAnnotationWidgetController
• [UGENE-1267] - WD Wizards: LineEdit instead of ComboBox for boolean values
• [UGENE-1268] - WD Wizards: bad layout when expend a group with many parameters
• [UGENE-1275] - The associated features are not loaded automatically
• [UGENE-1286] - When subalignment is saved the last column cannot be selected
• [UGENE-1288] - Wrong default parameters of input slots of Find Pattern element
• [UGENE-1289] - Tabbed view crash
• [UGENE-1290] - "Filter results" cleans dotplot
• [UGENE-1296] - T-Coffee exit with error 127 (MacOS)
• [UGENE-1301] - Duplicate names in U2 namespace
• [UGENE-1307] - MAlignment edit works wrong
• [UGENE-1308] - UGENE shows warnings on application start
• [UGENE-1315] - Primer3 doesn't produce any results when searching for single primer
• [UGENE-1320] - WD datasets: iterations bug
• [UGENE-1324] - WD: default decimals in property editor
• [UGENE-1325] - UGENE crash on loading a long GFF file
• [UGENE-1326] - WD wizards: create unresizable dialog
• [UGENE-1327] - Workflow designer report: no output files
• [UGENE-1333] - Find pattern area widgets are not shown correctly
• [UGENE-1337] - Merge sequences warning is shown only first time
• [UGENE-1338] - WD: Cannot switch properties in combo boxes
• [UGENE-1339] - Quality scores conversion error
• [UGENE-1342] - WD crashes when trying to add element using context menu
• [UGENE-1348] - Workflow designer crash with adding removed worker
• [UGENE-1349] - Workflow designer: can't use drag-n-drop on custom elements with non-English names
• [UGENE-1350] - Wrong data in UGENE copy of JASPAR database
• [UGENE-1353] - Need refactoring FindAlgorithm
• [UGENE-1356] - "Export document" doesn't work for ACE format
• [UGENE-1357] - WD: cmdline tryed to guess unset parameter
• [UGENE-1358] - UGENE crashes when running scheme in WD
• [UGENE-1359] - Workflow Samples are not loaded
• [UGENE-1360] - WD datasets: sometimes docs are not updated
• [UGENE-1361] - Tabs have not close buttons
• [UGENE-1362] - MSA: incorrect values in distance matrix including gaps
• [UGENE-1364] - WD datasets: last open directory is not saved
• [UGENE-1365] - "Save" button on the main toolbar is disabled when WD is opened
• [UGENE-1366] - Scene is not refreshed after adding an element
• [UGENE-1367] - Undo option works incorrect in MSA editor
• [UGENE-1368] - Crash: sam file opening
• [UGENE-1369] - Transfer remove item in the project view to the top level context menu
• [UGENE-1371] - MSA: unable to open file BL060C3.ace from samples
• [UGENE-1373] - Update right column on UGENE web site
• [UGENE-1377] - Defects in translations of some transcription factor workflow elements
• [UGENE-1378] - Several edit lines are able to contain cursor in Smith-Waterman Search dialog
• [UGENE-1381] - Zooming problems in Dotplot
• [UGENE-1383] - Resizing elements in Query Designer works incorrect
• [UGENE-1387] - Crash on removing columns with percentage of gaps
• [UGENE-1399] - Wrong numeration in Export alignment to amino translation dialog
• [UGENE-1402] - Undo/redo for remove columns of gaps
• [UGENE-1405] - SAFE_POINT is triggered on deletion of columns with gaps
• [UGENE-1406] - Sequence is not renamed when replacing selected row with reverse-complement
• [UGENE-1407] - Smith-Waterman algorithm use int values, task settings and dialog allow float values
• [UGENE-1408] - Import annotation from CSV works incorrect
• [UGENE-1409] - Sequence Viewer: F2 works in the annotation editor but doesn't work in the sequence view
• [UGENE-1411] - Annotations are split incorrectly during insert of a sub-sequence
• [UGENE-1415] - "No data to write" error when there are two input alignment
• [UGENE-1418] - UGENE crashes if command line worker has quotes in execution string
• [UGENE-1419] - QObject::moveToThread errors
• [UGENE-1421] - UGENE crashes when building tree
• [UGENE-1422] - UGENE crashes when exporting it into SAM format
• [UGENE-1424] - UGENE crashes when using undo option in MSA
• [UGENE-1425] - WD offers dividing input file list into separate iterations on deleting read element
• [UGENE-1428] - Double export from the project view
• [UGENE-1429] - Aligner index builder: bowtie building crashes on assert
• [UGENE-1430] - Incorrect layout of Dataset directory options ui (Mac)
• [UGENE-1433] - Problem with bowtie aligning
• [UGENE-1436] - WD: join quality worker works wrong
• [UGENE-1437] - WD: hmm2-build workers works wrong
• [UGENE-1438] - UGENE tries to import empty fasta (headers only) to db
• [UGENE-1439] - MUSCLE align to profile failed
• [UGENE-1440] - UGENE crashes when using editing MSA
• [UGENE-1443] - Crash on constructing circular molecules
• [UGENE-1444] - UGENE crashes when assemly browser is used
• [UGENE-1445] - UGENE crash on removing last sequence from alignment
• [UGENE-1450] - Some assamblies can not be opened by UGENE
• [UGENE-1451] - Sequences can not be deleted from alignment in MSA
• [UGENE-1455] - WD doesn't load scheme with script element
• [UGENE-1457] - Position field in "Navigation" tab of options panel in assembly doesn't work
• [UGENE-1458] - 'Export document' project action works incorrect for documents with 2 or more MAlignmentObjects
• [UGENE-1460] - 'Export document' dialog didn't applies right extension to file name
• [UGENE-1461] - Crash on assert while using the Smith-Waterman algorithm with incorrect matrix.
• [UGENE-1464] - Wrong export to NEXUS format
• [UGENE-1468] - UGENE crashes when saving subalignment in msa
• [UGENE-1470] - Gaps are not inserted to the end of sequence in MSA
• [UGENE-1471] - Broken layout fo the dialog
• [UGENE-1472] - Sequence widgets are presented in random order in sequence viewer
• [UGENE-1474] - Repeat finder incorrect homology
• [UGENE-1475] - Incorrect format detection
• [UGENE-1476] - Bad parsing of a file in NEXUS format
• [UGENE-1480] - WD: repeat finder special parameters doesn't work as it suppose to work
• [UGENE-1481] - "Zoom in to see the reads" button doesn't enable navigation in the Assembly Viewer
• [UGENE-1482] - Regular crashes related to time comparison when running tests on Linux in multithreaded mode
• [UGENE-1483] - Crash on sequences selection in MSAEditor with collapsing mode
• [UGENE-1485] - Nothing is done when there is no result using "Call Variants"
• [UGENE-1489] - "Call variants" pipeline results differes from original tool
• [UGENE-1490] - Wrong discription of "Call Variants" workflow element
• [UGENE-1491] - Multiple Sequence Reading Mode Dialog: Bad swapping behavior
• [UGENE-1494] - Redo Win hotkey differs from Linux Redo hotkey
• [UGENE-1496] - There's no UGENE assembler anymore in v. 1.11.5
• [UGENE-1499] - MSA - Tree View: sort alignment by tree crash
• [UGENE-1503] - Grouper doesn't output alignments if group by test pattern
• [UGENE-1504] - No arrows in collapsible lists
• [UGENE-1506] - Crash: tree view zoom
• [UGENE-1507] - Clustering works incorrenct
• [UGENE-1508] - Crash: refine option in MUSCLE
• [UGENE-1510] - Call variant worker crash for non-assembly input files
• [UGENE-1511] - Selection is not removed after pressing ESC button
• [UGENE-1512] - Crash on resizing alignment in MSAEditor with tree view
• [UGENE-1514] - Zoom option works wrong in new tree view
• [UGENE-1515] - UGENE crashes when rewriting .nwk file
• [UGENE-1516] - Tree view is closed wrong
• [UGENE-1521] - UGENE crashes when opening 2 files simultaneously
• [UGENE-1523] - UGENE crashes on opening an .idx file as text
• [UGENE-1524] - Conservation plot: handle spaces in label field
• [UGENE-1526] - Cistrome pipeline: hg19 as default assembly/annotation table by default of every element
• [UGENE-1527] - Crash when aligning to an empty alignment
• [UGENE-1530] - Alignment highlighting doesn't work when scrolling
• [UGENE-1531] - Hint on the "Sequence statistics" tab of the Alignment Editor Options Panel
• [UGENE-1532] - Strange zooming when building tree in MSA
• [UGENE-1534] - SNP format indexing error
• [UGENE-1535] - Name labels have wrong initial alignment
• [UGENE-1536] - Export sequence to alignment take too long
• [UGENE-1537] - Crash on canceling "Open msa task"
• [UGENE-1538] - Wrong visualization of enzyme cuts for BsaI restriction site
• [UGENE-1539] - Gap insertion works wrong
• [UGENE-1541] - Wrong size of clusterization line in MSAEditor tree views
• [UGENE-1542] - Fix parser of test runner suites list
• [UGENE-1543] - MSA: adding gaps works wrong
• [UGENE-1544] - Incorrect layout in "Tree settings" options panel tab
• [UGENE-1546] - Very contrast highlighting of clusterization groups in MSAEditor tree viewer
• [UGENE-1548] - Incorrect sorting of sequences in multiple alignment by tree
• [UGENE-1551] - Unexpected appearance of the rename sequence dialog
• [UGENE-1552] - Remove columns with percentage of gaps works wrong
• [UGENE-1553] - Undo works wrong when removing columns of gaps in alignment
• [UGENE-1555] - Incorrect alignment object name in Project View after its renaming
• [UGENE-1556] - Undo button is disables after alignment renaming
• [UGENE-1557] - Warnings at UGENE start
• [UGENE-1559] - Objects in project view losing their tags after rename
• [UGENE-1560] - Crash on adding reference to assembly
• [UGENE-1568] - Crash on opening MSAEditor with unloaded tree on Mac
• [UGENE-1569] - QD elements can increase height downwards on resizing upwards
• [UGENE-1570] - MACS doesn't use control annotations
• [UGENE-1573] - Incorrect selection in MSA Editor after another selection
• [UGENE-1574] - Incorrect selection with enabled collapsing option
• [UGENE-1575] - Incorrect behavior in collapsed mode
• [UGENE-1578] - Crash while dragging an alignment object from one project to another
• [UGENE-1580] - fix GUI test GUITest_regression_scenarios_test_1255
• [UGENE-1584] - Genbank header: wrong number of whitespaces
• [UGENE-1585] - Shifting MSA region works wrong with collapsing mode enabled
• [UGENE-1586] - Undo works wrong for MUSCLE aligner
• [UGENE-1594] - MACS: bad progress on Mac OS X
• [UGENE-1596] - No Smith-Waterman and UGENE Genome Aligner plugins
• [UGENE-1597] - Creating new table during searching for a pattern does not work
• [UGENE-1598] - Incorrect validation of a search region for a sequence on the Options Panel
• [UGENE-1600] - Fix undo/redo on collapsible mode
• [UGENE-1602] - Strange behavior during importing AltaiNea
• [UGENE-1603] - Crash due opening second msa view with tree on Mac
• [UGENE-1604] - UGENE is very slow with several opened Tree Views on Mac OS
• [UGENE-1607] - Read Plain Text-->Write Variations scheme crashes
• [UGENE-1609] - Deleted file still presents in project
• [UGENE-1613] - SAFE_POINT is triggered on selection in the MSA Editor
• [UGENE-1614] - Need compile uMuscle plugin for Windows x64
• [UGENE-1616] - Assertion fails after enabling collapsed mode
• [UGENE-1620] - Undo/redo stopped working
• [UGENE-1621] - Crash on checking "Show distances column" on "Statistics" tab
• [UGENE-1625] - Crash with primer span intron feature
• [UGENE-1626] - Problems with FASTA multiple alignment file
• [UGENE-1627] - Assertion fails during the dotplot building
• [UGENE-1628] - Incorrect undo/redo for renaming when unicode characters are used
• [UGENE-1629] - "Open As" is not available when there is no project in UGENE
• [UGENE-1635] - Opening view when performing pairwise alignment
• [UGENE-1636] - UGENE crashes when you toggle the statistics column in MSA View
• [UGENE-1639] - Cuffdiff shows errors
• [UGENE-1640] - MSA View: empty selection
• [UGENE-1641] - Incorrect values in distances column in MSA Editor
• [UGENE-1645] - Crash during unloading the document
• [UGENE-1650] - Crash on trying to load large reference sequence in Genome Aligner
• [UGENE-1653] - Wrong initial state of find pattern option panel
• [UGENE-1654] - find pattern option can be blocked
• [UGENE-1658] - UGENE crashes on removing tree file
• [UGENE-1659] - Set up unicode NSIS and configure UGENE install scripts
• [UGENE-1660] - UGENE crashes when using "custom region" in fild pattern option panel
• [UGENE-1661] - Changing region settings in find pattern works wrong
• [UGENE-1663] - Shift+arrow shifts selection on Mac
• [UGENE-1664] - Crash during modifying an msa selection with a keyboard
• [UGENE-1665] - Undo for renaming sequence works wrong
• [UGENE-1667] - GTFFormat: file with multiple sequence ids are not recognized
• [UGENE-1668] - MSA Editor: save chosen sequences for PWA
• [UGENE-1670] - MSAEditor: capital letters for sequence choose widget
• [UGENE-1672] - Incorrect result of distance algorithm
• [UGENE-1680] - Shift+arrows selection doesn't work in the name list of the MSA Editor
• [UGENE-1683] - Assert triggered during shifting selected region in alignment
• [UGENE-1688] - Crash on loading large FASTA file containing short reads on x32
• [UGENE-1689] - Last saved value of the consensus threshold is incorrect
• [UGENE-1693] - WD crashes when using pipelines
• [UGENE-1696] - Crash on loading large FASTQ file containing short reads on x32
• [UGENE-1700] - Crash on x32 because of BioStruct3DPlugin memory leak
• [UGENE-1702] - AppResource needs to be thread-safe
• [UGENE-1704] - UGENE cannot save/read Pfam annotations
• [UGENE-1708] - Undo after align 'eats' sequences
• [UGENE-1711] - ugeneui fails to link
• [UGENE-1712] - TaskScheduler must try to lock resources without blocking calls
• [UGENE-1714] - Crash on selecting python external tool
• [UGENE-1715] - Crash during clicking undo in msa
• [UGENE-1716] - UGENE crashes when trying to open Geneious application.lock
• [UGENE-1717] - Access remote database window resize
• [UGENE-1718] - Crash on simultaneous loading many files in UGENE
• [UGENE-1720] - Error when loading a remote document but the document is in the project
• [UGENE-1725] - When external tool pack path is selected in settings not all the tools are found
• [UGENE-1726] - Memory leak during logging
• [UGENE-1728] - Graphs in sequence viewer work slow
• [UGENE-1731] - Identity columns in MSA shows incorrect data
• [UGENE-1738] - Call Variants pipeline cannot be stoped on big files
• [UGENE-1744] - Errors during UGENE installation and uninstallation on Windows
• [UGENE-1747] - Progress for "Generate distance matrix" task is incorrect
• [UGENE-1748] - Assertion fails after selecting region in sequence graphs
• [UGENE-1752] - Search TFBS with matrices algorithm creates invalid annotation qualifiers

New Feature

• [UGENE-117] - Import SAM files into ugenedb
• [UGENE-326] - Assembly: support VCF (Variant Call Format)
• [UGENE-501] - Export PHRED quality values
• [UGENE-701] - Add support for automatically checking updates
• [UGENE-737] - Consider integration of Clustal Omega into UGENE
• [UGENE-1037] - Support variants visualizatoin for Assembly Browser
• [UGENE-1038] - New WD type: assembly
• [UGENE-1039] - Read Assembly element
• [UGENE-1040] - Write Assembly element
• [UGENE-1041] - Assembly to sequences element
• [UGENE-1049] - Group statistics of multiple alignment
• [UGENE-1056] - No "Read annotation" element in WD
• [UGENE-1082] - support join into alignment sequences opened from several files
• [UGENE-1100] - Allow Smith-Waterman worker to take sequences from two "Read Sequence" element
• [UGENE-1115] - Allow to export BLAST hits into multiple alignment
• [UGENE-1117] - Add "export consensus variations" option in assembly browser
• [UGENE-1128] - Introduce "reference" sequence in MSA Editor
• [UGENE-1151] - Find Pattern: load patterns from a file
• [UGENE-1161] - UGENE storage for produced files
• [UGENE-1167] - Local pairwise alignment with SW algorithm
• [UGENE-1178] - Integrate CEAS report into WD
• [UGENE-1183] - "Read Sequence" reads from all directory's files
• [UGENE-1222] - Edit sequence usability and shortcuts
• [UGENE-1263] - Allow to create PCR product of primers pair
• [UGENE-1265] - Create sample with a wizard for Call Variants Pipeline
• [UGENE-1313] - Team City: Write a script that performs pre-commit of the changes and autocommit then
• [UGENE-1323] - WD: MACS integration
• [UGENE-1331] - New workflow element to annotate a region between two annotations.
• [UGENE-1336] - WD: Read annotations - "Merge annotations" parameter
• [UGENE-1388] - Allow to show/hide different signals of chromotogram
• [UGENE-1412] - Support Workflow Designer wizards
• [UGENE-1420] - BWA: add support for long reads alignment
• [UGENE-1462] - Gene-by-gene approach for genome characteristic worker
• [UGENE-1484] - "GC-content" element in the Query Designer
• [UGENE-1525] - WD Reports: Open Containig folder
• [UGENE-1662] - TopHat: one run for one dataset when input files are used
• [UGENE-1681] - Support Tuxedo simplified pipelines
• [UGENE-1713] - Workflow Designer dashboard
• [UGENE-1719] - Workflow sample wizards

Task

• [UGENE-460] - Fix Nightly Tests
• [UGENE-860] - Update bwa in external tool package to latest version 0.6.1
• [UGENE-1030] - New WD type: variation track
• [UGENE-1088] - Configure test computers to run GPU tests and create a test for UGENE Genome Aligner
• [UGENE-1097] - Code review of import quality scores
• [UGENE-1134] - Samtools sorting bug
• [UGENE-1140] - Create the task for "Save a copy"
• [UGENE-1146] - U2SequenceObject::clone() - not all sequence attributes are copied
• [UGENE-1147] - PhyTreeObject::clone() - PhyTree has not a copy constructor
• [UGENE-1149] - VariantTrackObject::clone() - variants are always imported to the same database
• [UGENE-1170] - Add tests for ImportQuality and ExportQuality tasks
• [UGENE-1177] - Integrate Cistrome pipeline
• [UGENE-1218] - Try to crash UGENE with corrupted fasta files
• [UGENE-1228] - Replace UWL header
• [UGENE-1251] - Investigate the problem of schemas with a script
• [UGENE-1261] - Validation of annotation controller: separation of concerns is disturbed
• [UGENE-1467] - MSAEditor: common sequence choose widget
• [UGENE-1478] - Fix SW cmdline tests
• [UGENE-1479] - Update bowtie at UBUNTU 10 machine
• [UGENE-1493] - Tuxedo pipeline tests don't pass
• [UGENE-1509] - Include license.3rd_party into all UGENE packages
• [UGENE-1583] - WD validate: remove copy-paste
• [UGENE-1608] - Remove CUDA dead code from Genome Aligner plugin
• [UGENE-1649] - Genome Aligner refactoring
• [UGENE-1676] - Genome Aligner binary find optimization and refactoring
• [UGENE-1706] - Trace to log UGENE memory usage to be able to have that information in crash reports
• [UGENE-1707] - Solve 'disk space' problem on test servers
• [UGENE-1723] - MacOS: temporary switch off running workflows in separate process

Improvement

• [UGENE-547] - Make datawrite workers auto-complete files without extension
• [UGENE-627] - Add hints to every field of Primer dialog
• [UGENE-643] - Improve cancelling propagation in tasks
• [UGENE-663] - Protein statistics
• [UGENE-698] - CLONE - Data storage for a WD-schema running process
• [UGENE-709] - Issue with "Unable to unload document" error message
• [UGENE-736] - Switch to DBI MSA model
• [UGENE-792] - WD: better support for "all-files-in-folder" processing
• [UGENE-826] - Improve names of copied output files in the Workflow Designer
• [UGENE-872] - User should be able to select the language during UGENE installation
• [UGENE-891] - Disable the "Edit" and "Remove" buttons in the Marker workflow element
• [UGENE-902] - Visualization information about graph dots
• [UGENE-976] - "Exact" match algorithm for "Search in Sequence"
• [UGENE-991] - Short read alignment: add generic support for paired-end reads in GUI and provide this option for Bowtie and BWA
• [UGENE-996] - WD: Sequence writer in split mode should create normal names
• [UGENE-1029] - Add "Hide all circular views" option
• [UGENE-1069] - Improve auto-annotations behaviour with long sequences
• [UGENE-1079] - Show "White spaces error" before closing BLAST dialog
• [UGENE-1093] - Genome Aligner: strange error
• [UGENE-1101] - Read assembly worker: sort unsorted BAMs before using
• [UGENE-1123] - Allow sequences in SCF and ABI format as input for CAP3
• [UGENE-1124] - Improve input description for CAP3
• [UGENE-1126] - Convert SAM/BAM files to sorted indexed BAM before using
• [UGENE-1130] - Support sequence length attribute for samtools DBI
• [UGENE-1131] - Support paired-reads alignment
• [UGENE-1133] - In pattern field of SW Search dialog space symbols (in particular, new line symbol) aren't skipped
• [UGENE-1135] - Support comments in FASTA files
• [UGENE-1148] - Crash Handler reports: include in report "ppa" mark if it's a version from ppa
• [UGENE-1150] - Improve "Save a copy" functionality to "Export document"
• [UGENE-1152] - Support multiple patterns in Find Patterns
• [UGENE-1157] - Collocalion search worker: save original annotations
• [UGENE-1175] - Validate an external tool before launching a workflow scheme
• [UGENE-1182] - WD: new grouper slot - group size
• [UGENE-1189] - Add "selected region" to "Region" combo box of Option Panel of Sequence View
• [UGENE-1196] - Correct physical memory size info
• [UGENE-1204] - Enlarge the maximum number of hits for remote BLAST results
• [UGENE-1219] - Visual enhancement of Smith-Waterman Search dialog
• [UGENE-1227] - Selecting a bunch of rows with Shift modifier in MsaView
• [UGENE-1252] - WD: bind all avaiable incoming slots to the destination slot
• [UGENE-1258] - FindPattern allow using sequence names as annotation names when FASTA format is provided
• [UGENE-1266] - Add descriptions of parameters in WD Wizards
• [UGENE-1269] - WD Wizards: file format and file path are not synchronized
• [UGENE-1272] - Review all persistent settings parameters to make them versioned
• [UGENE-1276] - "Construct molecule" dialog improvements
• [UGENE-1277] - Improve the concept and format of enzymes selection
• [UGENE-1285] - Find Substring element - load pattern from files and use names of sequence for annotations
• [UGENE-1300] - Project View Usability: improve view managment
• [UGENE-1304] - Do blast on selected regions
• [UGENE-1305] - Change red cross of tabbed view to something more neutral
• [UGENE-1341] - BED format: allow opening simple files without headers
• [UGENE-1372] - Repeat find and Find tandems tasks should work with a part of sequence
• [UGENE-1427] - Default name when loading sequence from plain text
• [UGENE-1431] - WD Wizards: Highlight required parameters in bold like in Parameters Editor
• [UGENE-1434] - Find pattern with regexps
• [UGENE-1442] - Allow to open PWM matrices in its own view
• [UGENE-1447] - WD Scripts: add script functions to write and read files
• [UGENE-1463] - Sort enzymes in the "Restrictions sites map" alphabetically
• [UGENE-1488] - 64-bit version of Bowtie on Windows
• [UGENE-1502] - README file for users
• [UGENE-1513] - External tools must be able to specify their runner if required
• [UGENE-1540] - Add the format selection combobox to the "Save subalignment" dialog
• [UGENE-1547] - Create options panel tab to add tree in MSAEditor
• [UGENE-1579] - Cistrome pipeline: add extensions for files in the file selector dialog
• [UGENE-1587] - Do not stop workflow when input file is incorrect
• [UGENE-1595] - Datasets widget: add shortcut for deleting files
• [UGENE-1633] - "General" tab of MSA View
• [UGENE-1634] - Create a "ghost" tab on the options panel of MSA View
• [UGENE-1669] - MSAEditor: text alignment of sequence choose widget
• [UGENE-1671] - MSAEditor: double enter for sequence choose widget
• [UGENE-1673] - Only one tab at a time on the Options Panel
• [UGENE-1677] - Paired reads in wizards
• [UGENE-1687] - MSA Editor: reference hint
• [UGENE-1710] - Improve WD validation messages
• [UGENE-1727] - MACS and seqpos output

Edit/Copy Release Notes

The text area below allows the project release notes to be edited and copied to another document.