--- Release notes MEGAN6 V6_25_9 (Tue, 16 Jan 2024): --- - fixed bug in zooming buttons for cluster viewer --- Release notes MEGAN6 V6_25_8 (Mon, 15 Jan 2024): --- - fixed bug that caused nodes to disappear in PCoA plot when labels turned off --- Release notes MEGAN6 V6_25_7 (Fri, 1 Dec 2023): --- - fixed bug that caused bar chart and stacked bar chart to be incorrectly scaled when using percentages --- Release notes MEGAN6 V6_25_6 (Fri, 10 Nov 2023): --- - added new tool to UE that merges multiple (sorted) accession to id mappings into one table for import into an sqlite MEGAN mapping database - added new UE export command for saving all annotated KEGG map images to PDF files --- Release notes MEGAN6 V6_25_5 (Wed, 8 Nov 2023): --- - fixed newly introduced bug that caused to functional classification to sometimes fail --- Release notes MEGAN6 V6_25_4 (Tue, 24 Oct 2023): --- - modified usage report read-extractor - attempted to fix array size exceeds VM Limit - other minor fixes --- Release notes MEGAN6 V6_25_3 (Fri, 15 Sep 2023): --- - fixed a bug that prevented download of MeganServer files in MEGAN UE --- Release notes MEGAN6 V6_25_2 (Wed, 13 Sep 2023): --- - added -ar and -br options to taxonomony2function tool --- Release notes MEGAN6 V6_25_1 (Thu, 31 Aug 2023): --- CRITICAL update - fixed bug that sometimes caused meganization to hang during writing phase --- Release notes MEGAN6 V6_25_0 (Wed, 30 Aug 2023): --- -created installers for ARM (e.g. Linux running on Apple M1 or M2 chip) --- Release notes MEGAN6 V6_24_26 (Mon, 14 Aug 2023): --- - fixed build error that prevented program from starting --- Release notes MEGAN6 V6_24_25 (Wed, 9 Aug 2023): --- - fixed build error that prevented program from starting --- Release notes MEGAN6 V6_24_24 (Mon, 7 Aug 2023): --- - added options that report KPCOFGS assignments of taxa in text export --- Release notes MEGAN6 V6_24_23 (Tue, 9 May 2023): --- - reduced number of accessions fetched per SQLITE query to prevent a SQLITE_TOOBIG exception. - You can now add a line like this: AccessionChunkSize=1000 to the properties file Megan.def to reduce the number further (or type command - Use statement like ChartLineWidth=2.5 to change line width in line charts --- Release notes MEGAN6 V6_24_22 (Thu, 13 Apr 2023): --- - fixed MeganServer bug that caused problems when downloading classifications during SQLITE file generation --- Release notes MEGAN6 V6_24_21 (Fri, 17 Mar 2023): --- - fixed issues associated with using place-holders in file names when exporting reads and similar --- Release notes MEGAN6 V6_24_20 (Sun, 5 Feb 2023): --- - improved version of SQLite exporter in UE --- Release notes MEGAN6 V6_24_19 (Fri, 3 Feb 2023): --- - improved version of SQLite exporter in UE --- Release notes MEGAN6 V6_24_18 (Thu, 2 Feb 2023): --- - improved version of SQLite exporter in UE --- Release notes MEGAN6 V6_24_17 (Thu, 2 Feb 2023): --- - Fixed bug that caused first letter of sequence name to be omitted in alignment viewer - prevent GFF export when nothing selected - fixed bug that prevent correct replacement of %t or %i in output file name templates - installer-builder update should fix issue that program doesn’t install on MacOS venture - First version of SQLite exporter in UE --- Release notes MEGAN6 V6_24_16 (Mon, 16 Jan 2023): --- - Fixed bug that prevented opening of MeganServer client --- Release notes MEGAN6 V6_24_15 (Sat, 14 Jan 2023): --- - fixed selection bug in sidebar tree - added -mro option to taxonomy2function program: when using the NCBI taxonomy, this option ensures that all reported taxa have major ranks (ie KPCOFGS) --- Release notes MEGAN6 V6_24_14 (Fri, 13 Jan 2023): --- - added new %f place holder for export file names- it will be replaced by the input file name - fixed bug that prevented display of 3D PCoA plot in UE - fixed bug that caused *normalized to* to show 0 --- Release notes MEGAN6 V6_24_13 (Fri, 6 Jan 2023): --- - fixed newly introduced bug that cause exception at end of run in command-line mode --- Release notes MEGAN6 V6_24_12 (Wed, 4 Jan 2023): --- - added menu item for scaling bi-plot and try-plot arrows - added memory messages --- Release notes MEGAN6 V6_24_11 (Thu, 1 Dec 2022): --- - more bug fixes megan-server (paper just submitted to BioRxiv and Bioinformatics) --- Release notes MEGAN6 V6_24_10 (Wed, 30 Nov 2022): --- - fixed newly introduced megan-server bugs --- Release notes MEGAN6 V6_24_9 (Wed, 30 Nov 2022): --- - fixed newly introduced megan-server bugs --- Release notes MEGAN6 V6_24_8 (Wed, 30 Nov 2022): --- - fixed megan server help screen --- Release notes MEGAN6 V6_24_7 (Wed, 30 Nov 2022): --- - fixed update URL - megan server - base URL now serves help screen --- Release notes MEGAN6 V6_24_6 (Wed, 16 Nov 2022): --- - fixed bug that sometimes prevented connecting to an instance of megan server --- Release notes MEGAN6 V6_24_5 (Sun, 13 Nov 2022): --- - Now using in-memory caching for Sqlite with cache size -10000, this should hopefully fix the out-of-memory problem sometimes encountered during meganization - This setting can be changed using a new command-line option -cs - The command-line options -tsm has been removed from programs where they have no effect - The command-line option -tsd has been removed because the corresponding SQLite pragma has been deprecated --- Release notes MEGAN6 V6_24_4 (Mon, 31 Oct 2022): --- - Updated SqlIte driver, show now work on apple silicon chips --- Release notes MEGAN6 V6_24_2 (Tue, 25 Oct 2022): --- Megan: - Fixed bug in daa2info that caused the bacteriaOnly flag to be ignored. - Fixed bug in parameter parser that caused problems when a minimum read length is specified - Minor issues that occur during computation of comparisons are no longer shown as notifications. --- Release notes MEGAN6 V6_24_1 (Thu, 15 Sep 2022): --- CRITICAL BUG FIX - Second attempt to fix bug that can cause meganization to exceed max SQLITE query length - Added property file specification option -P to all tools --- Release notes MEGAN6 V6_24_0 (Sat, 3 Sep 2022): --- - Added support for the PGPT analyzer - Added another tool to tools/utils - Fixed bug that can cause meganization to exceed max SQLITE query length - Fixed bug that prevented reporting of multiple paths that end in the same functional class (only first was reported) --- Release notes MEGAN6 V6_23_4 (Wed, 27 Jul 2022): --- - In samples viewer- added new menu item *remove low abundance* that removes all nodes for which all samples show a percent abundance that does not exceed a given threshold --- Release notes MEGAN6 V6_23_3 (Thu, 14 Jul 2022): --- - fixed bug that sometimes made megan server fail - added shutdown command to megan server --- Release notes MEGAN6 V6_23_2 (Mon, 9 May 2022): --- - fixed minor bug in merge-files command --- Release notes MEGAN6 V6_23_1 (Mon, 9 May 2022): --- CRITICAL BUG FIX - recent update causes problems with some summary files that contain references to embedded files - removed support for (little used) embedded files, as this was causing issues with the newly implemented merged files concept --- Release notes MEGAN6 V6_23_0 (Fri, 6 May 2022): --- - New merge-files tool: merges multiple meganized DAA files or RMA files as one MEGAN file virtually. Individual reads and alignments can be accessed from the merged file. Internally, MEGAN iterates over all merged input files - UE only: menu item for merging files and dialog for reattaching input files to a merged file when file locations have changed. --- Release notes MEGAN6 V6_22_2 (Thu, 10 Mar 2022): --- MAJOR bug fix - fixed a bug that caused order of data not to change in viewers, even though labels and colors changed. --- Release notes MEGAN6 V6_22_1 (Mon, 7 Mar 2022): --- - fixed bug in meganizer that caused option -t4t to be ignored - fixed exception that occurs when message0 is null --- Release notes MEGAN6 V6_22_0 (Sat, 19 Feb 2022): --- MAJOR update - Updated mapping DB - built Feb 2022 - Updated taxonomy and functional hierarchies - Bug files - Some new command-line tools (UE) - Runs on MacOS M1 chip --- Release notes MEGAN6 V6_21_18 (Fri, 21 Jan 2022): --- - export read names to matches now reports taxon-id, bit score, match length and percent identity --- Release notes MEGAN6 V6_21_17 (Thu, 20 Jan 2022): --- - implemented *add classification* command in Community Edition - added first version of daa2gff3 tool, this probably needs work, please send feedback! - major refactoring of code base, please report any (new) bugs encountered --- Release notes MEGAN6 V6_21_16 (Thu, 28 Oct 2021): --- - Modified taxon2function so that it now can report paths for the classification entities and can be run on multiple files --- Release notes MEGAN6 V6_21_15 (Sun, 17 Oct 2021): --- - fixed a minor issue with the enable software feature menu item (and added software-feature switch that tolerates hyphens in accession strings) --- Release notes MEGAN6 V6_21_14 (Fri, 15 Oct 2021): --- - fixed a minor issue with the enable software feature menu item (and added software-feature switch that tolerates hyphens in accession strings) --- Release notes MEGAN6 V6_21_13 (Wed, 13 Oct 2021): --- - Added new tool taxonomy2function that outputs a taxonomy-by-function table reporting number of reads, or names of reads, assigned to each pair. --- Release notes MEGAN6 V6_21_12 (Wed, 25 Aug 2021): --- - Fixed bugs in Import CSV, now either full names or ids for functional classes can be supplied as -*class name* --- Release notes MEGAN6 V6_21_11 (Fri, 20 Aug 2021): --- - Fixed newly introduce bug in Project menu - Fixed minor bug in rma2info --- Release notes MEGAN6 V6_21_10 (Thu, 29 Jul 2021): --- - Fixed bug in chart labeling - fixed bug in alignment viewer tool bar - Projection also applies to GTDB taxonomy, if the viewer is open --- Release notes MEGAN6 V6_21_9 (Mon, 12 Jul 2021): --- - Fixed bug that prevented MeganServer from serving symbolically linked directories - Megan server now supports files that describe samples. If a directory contains a file called About.txt, then the content will be displayed with the directory. If for a dataset foo.daa or foo.rma there is also a file called foo.txt, then the content will be displayed with the dataset --- Release notes MEGAN6 V6_21_8 (Mon, 5 Jul 2021): --- - added *allBelow* option to read extractor tool - output to standard out in MEGAN UE no longer sent to file. --- Release notes MEGAN6 V6_21_7 (Wed, 23 Jun 2021): --- - added new *sum* option to rma2info and daa2info that uses summarized counts, rather than assigned counts, when listing class-to-counts. --- Release notes MEGAN6 V6_21_6 (Tue, 22 Jun 2021): --- - Fixed bug in gc-assembler that caused program to hang after assembly has completed - Fixed bug in Meganizer dialog that caused program to ignore MinSupport setting when set to 1 - Updated RDP parser to accommodate changes to format --- Release notes MEGAN6 V6_21_5 (Wed, 5 May 2021): --- - Fixed bug in daa2info UE that caused KEGG2011 to be used rather than KEGG - Fixed bug in MEGAN export of path to count to report only one path per leaf label even if the leaf label appears multiple times in a functional classification --- Release notes MEGAN6 V6_21_4 (Wed, 28 Apr 2021): --- CRITICAL UPDATE! - Fixed stupid editing bug: all instances of the word extract where replaced by extractSubGraph in the source code, breaking any features related to extracting something. - sam2rma: allow -inf and inf as values for integer and float variables in SAM format --- Release notes MEGAN6 V6_21_3 (Sat, 17 Apr 2021): --- - added menu item to UE that allows easy incorporation of additional classifications --- Release notes MEGAN6 V6_21_2 (Sun, 14 Mar 2021): --- - improved scale bar, fixed some issues - fixed bug in color-by-attribute menu item - tree layout now places internals nodes closer to the root rather than to leaves - extensive internal refactoring --- Release notes MEGAN6 V6_21_1 (Sun, 21 Feb 2021): --- - Show scale bar in classifications viewers (can turn off/on using Layout->Show Scale Bar menu item) - Show scale when drawing annotated KEGG pathways (MEGAN UE) - allow longer reads and more matches in sam2rma --- Release notes MEGAN6 V6_21_0 (Thu, 18 Feb 2021): --- - Updated built-in hierarchies to version Jan 2021 - Update classifications in map db to Jan2021 - fixed a bug in MeganServer that caused the same read to be served multiple times --- Release notes MEGAN6 V6_20_19 (Tue, 5 Jan 2021): --- - fixed bug that caused MEGAN UE not to run under some linux editions --- Release notes MEGAN6 V6_20_18 (Tue, 15 Dec 2020): --- - fixed newly introduced bug that broke the extract reads feature - fixed bug in guest user in megan server UE --- Release notes MEGAN6 V6_20_17 (Fri, 20 Nov 2020): --- - fixed bug that caused megan to forget labels set for samples in Samples Viewer - added new split samples by attribute menu item in Samples Viewer that allows one to put samples into different files based on the values of an attribute --- Release notes MEGAN6 V6_20_16 (Tue, 17 Nov 2020): --- - fixed bugs in samples viewer reordering - fixed bugs in color-by-samples menu --- Release notes MEGAN6 V6_20_15 (Mon, 16 Nov 2020): --- - fixed bug in compute-comparison that failed to compare read-assignment modes - fixed minor layout issues in remote browser - fixed bug in AadderBuild using mapping database --- Release notes MEGAN6 V6_20_14 (Wed, 11 Nov 2020): --- - Added command line options to daa-meganizer and similar programs for selecting the location for temporary SQLITE storage during mapping, use -tsm to place temporary storage in memory or -tsd to set the directory for temporary storage (.e.g /dev/shm on linux) - started work on support of opened MEGAN by double-clicking a MEGAN file - fixed recent issued that prevented some programs (such as daa2info) to run on a linux server (with no X11 server) --- Release notes MEGAN6 V6_20_13 (Thu, 5 Nov 2020): --- - Improvement of MeganServer (incompatible with previous versions of MEGAN) --- Release notes MEGAN6 V6_20_12 (Wed, 4 Nov 2020): --- - Fixed issue in MeganServer that causes the program chokes on some files - Running MEGAN with option -d now reports all MEGAN requests to MeganServer in Message Window - Some URLs in MeganServer output were missing a forward slash --- Release notes MEGAN6 V6_20_11 (Mon, 2 Nov 2020): --- - Minor modifications of daa-meganizer program - Fixed bug in MeganServer that prevented inspection of reads --- Release notes MEGAN6 V6_20_10 (Sun, 1 Nov 2020): --- - MeganServer crucial bug fix. --- Release notes MEGAN6 V6_20_9 (Sun, 1 Nov 2020): --- - MeganServer now uses bcrypt for password hashing. --- Release notes MEGAN6 V6_20_8 (Wed, 28 Oct 2020): --- - Improvements and minor bug fixes in compare-comparison program --- Release notes MEGAN6 V6_20_7 (Tue, 27 Oct 2020): --- - Rewrote compute-comparison tool to make it more efficient and able to run on a server in console mode (without an X server) - Minor bug fixes megan-server --- Release notes MEGAN6 V6_20_6 (Mon, 26 Oct 2020): --- - some changes to MeganServer option names - MeganServer UE now support multiple endpoints --- Release notes MEGAN6 V6_20_5 (Wed, 21 Oct 2020): --- CRITICAL UPDATE - Bug fixes in MeganServer --- Release notes MEGAN6 V6_20_4 (Tue, 20 Oct 2020): --- - Bug fixes in MeganServer --- Release notes MEGAN6 V6_20_3 (Tue, 20 Oct 2020): --- - Bug fixes in MeganServer --- Release notes MEGAN6 V6_20_2 (Wed, 14 Oct 2020): --- - Fixed bug introduced in previous release --- Release notes MEGAN6 V6_20_1 (Wed, 14 Oct 2020): --- - Bug fixes in new megan-server client code --- Release notes MEGAN6 V6_20_0 (Tue, 13 Oct 2020): --- - Contains a completely new implementation of MeganServer. - tools/megan-server is a standalone http-server that can server megan files from a server to the web. Files can be opened via a webbrowser or within MEGAN. Access is password protected --- Release notes MEGAN6 V6_19_9 (Fri, 11 Sep 2020): --- - Fixed bug that sometimes caused ignorable exception to be thrown when using mapping files --- Release notes MEGAN6 V6_19_8 (Thu, 27 Aug 2020): --- - Fixed bug in extract reads tool that prevented use of relative paths for output files - Fixed bug in Meganization dialog that caused minSupportPercent to be set to 0, when minSupport=1. Now, minSupportPercent is only set to 0 if MinSupport >1 - Fixed bug that caused reordering of rows in sample viewer to be ignored in classification viewers - modified MEGAN comparison format so that all lines in data table have same length - added metadata file input to compute-comparison tool - compute-comparison now also supports directory input - fixed bug that caused MEGAN to throw an exception (which can be ignored) when loading a synonyms file - fixed error in read-assignment usage message in sam2rma and similar tools --- Release notes MEGAN6 V6_19_7 (Fri, 14 Aug 2020): --- - Enabled and tested contaminant filtering --- Release notes MEGAN6 V6_19_6 (Thu, 30 Jul 2020): --- MAJOR bug fix - Fixed a bug in the processing of blast alignments that occurs when the same query has multiple alignments to the same subject in short read mode that causes all other alignments for the given query, including to other references to be skipped. --- Release notes MEGAN6 V6_19_5 (Tue, 28 Jul 2020): --- MAJOR feature update, MAJOR bug fix - updated GTDB viewer to GTDB release 95 - Download and use mapping file megan-map-Jul2020-2.db.zip or newer to benefit from GTDB update - Fixed a bug in the processing of blast alignments that occurs when the same query has multiple alignments to the same subject in short read mode that causes all other alignments for the given query, including to other references to be skipped. --- Release notes MEGAN6 /V6_19_4 (Thu, 16 Jul 2020): --- - Fixed bug in daa2info and rma2info that caused the Kingdom node to missing from eukaryotic paths - Fixed bug that caused Check for Updates to fail --- Release notes MEGAN6 V6_19_3 (Fri, 10 Jul 2020): --- NEW FEATURES release. - Added EC enzyme classification viewer - Updated NCBI taxonomy in July 2020 - Updated taxonomy in map database to July 2020 - Added EC to map database --- Release notes MEGAN6 V6_19_2 (Wed, 17 Jun 2020): --- MEGAN 6.19.2: Minor bug fix. - removed the word none that appeared at the end of some labels in the new GTDB taxonomy viewer - uploaded new extended mapping db that contain many more accessions. This larger db file should be employed when not aligning against a recent version of the NCBI-nr database - modified the UE program CreateMappingDB to allow the creation of extended mapping db files --- Release notes MEGAN6 V6_19_1 (Mon, 8 Jun 2020): --- CRICTICAL bug fix. - Due to an internal change in DIAMOND, long read analyses performed with DIAMOND releases after Feb 2020 are not compatible with previous releases of MEGAN. - This release of MEGAN is compatible both with old DAA files (created with DIAMOND build versions before 134) and with new DAA files (created with DIAMOND build versions 134 or higher). --- Release notes MEGAN6 V6_19_0 (Mon, 8 Jun 2020): --- MAJOR update in which the taxonomy and most of the functional classifications have been updated. - Updated Taxonomy, COG, SEED and KEGG to May 2020 versions (Interpro2GO not updated) - SEED classification is now based on Patric database (source: https://www.patricbrc.org) - New mapping databases: megan-map-May2020.db and megan-map-May2020-ue.db - Added new GTDB viewer for taxonomic analysis of bacterial content (source: http://gtdb.ecogenomic.org) - Improved performance of UE tool create-accession-db - Removed VFDB classification, as it needs work - Fixed bug that sometimes caused functional viewers to open empty Currently unresolved issue: - No fix yet for reported bug that MEGAN sometimes fails to meganize DIAMOND files aligned with long-reads option --- Release notes MEGAN6 V6_18_11 (Mon, 25 May 2020): --- - modified relative comparison calculation to reduce rounding-induced discrepancies. - added tags4t option to daa-meganizer and similar tools - fixed bug that caused some options of daa-meganizer and similar tools to be ignored - changed number of cores option to -t to fix collisions with other uses of -p --- Release notes MEGAN6 V6_18_10 (Thu, 30 Apr 2020): --- - If Windows version doesn’t start after this update, please completely uninstall and then reinstall - Updated to openjdk14/jdk-14.0.1+7 and OpenJFX 14 - JDK now also bundled on linux platform - Added option to turn off functional classifications during meganization or creation of RMA files --- Release notes MEGAN6 V6_18_9 (Sat, 4 Apr 2020): --- - fixed bugs that prevented parsing of old RMA3 files (as produced by older versions of MALT) --- Release notes MEGAN6 V6_18_8 (Thu, 2 Apr 2020): --- - fixed bug that caused *parse names* taxonomy options to sometimes be ignored - fixed bug that broke accession mapping when using XML files and mapping DB --- Release notes MEGAN6 V6_18_7 (Wed, 1 Apr 2020): --- - fixed bug in *check for updates* menu item --- Release notes MEGAN6 V6_18_6 (Mon, 30 Mar 2020): --- - fixed bug in extract reads tool - minor bug fixes --- Release notes MEGAN6 V6_18_5 (Fri, 14 Feb 2020): --- - fixed bug that prevented blast2rma from working - fixed bug in calculation of z-scores for heat-map - number of other bug fixes --- Release notes MEGAN6 V6_18_4 (Wed, 29 Jan 2020): --- - fixed numerous bugs in LR-inspector - notarized MacOS installer to be compatible with latest Catalina OS - updated to OpenJDK 13 - added export read name to covered bases - added map.db support to Aadder-build - added mechanism for incorporating external classifications into UE --- Release notes MEGAN6 V6_18_3 (Tue, 17 Dec 2019): --- - Added new menu item *Reanalyze Files* that can be used to rerun the LCA ataxonomic analysis and functional analyses on DAA and RMA files - Added new commandline program *Reanalyzer* that can be used to rerun the LCA taxonomic analysis and functional analyses on DAA and RMA files --- Release notes MEGAN6 V6_18_2 (Wed, 11 Dec 2019): --- - fixed bug in extended mapping mode that caused it to fail (bug introduced in 6.18.0) --- Release notes MEGAN6 V6_18_1: --- - fixed bug in new db-mapping code that sometimes caused incorrect assignment of class-ids to matches when important into an RMA file - fixed newly introduced bug in increase/decrease font - fixed bug by which sorting rows in sample viewer was sometimes ignored - fixed Java12-related bug that prevented export biom1 format to work - catches any *UnsupportedOperationException: PERPIXEL_TRANSLUCENT translucency is not supported* exception - fixed bug that prevented use of mapping database when parsing ids during import of a CSV file - added UE tool to create DNA mapping DB from NCBI download - added mapping db for genomic DNA sequences --- Release notes MEGAN6 V6_18_0: --- - Major update - Mapping of reference accessions to taxonomy and functional classifications is now performed using a single unified lookup file, called megan-map-Oct2019.db. - The Ultimate Edition uses mapping file megan-map-Oct2019-ue.db - New mapping code faster than previous approach - New mapping file smaller than previous mapping files (including smaller download, less than 1GB in total) - These mapping files are sqlite databases and so can be interactively viewed and modified by other program such as sqlite3 - These mappings reference only the first accession in each NCBI-nr header line - We will later provide a tool for extracting mappings to other accessions (that appear within header lines) - Fixed a number of minor bugs - Code improvements using automated inspection routines - NCBI taxonomy updated to October 2019 - eggNOG and InterPro2Go updated to October 2019 - software repository moved to software-ab.informatik.uni-tuebingen.de --- Release notes MEGAN6 V6_17_0 (2019/08/07): --- - Updated NCBI taxonomy to July 2019 version - Updated taxonomic mapping files to July 2019 version - Updated InterPro2GO hierarchy and mapping files to July 2019 version - Updated eggNOG (COG) mapping files to July 2019 version - Updated Kegg hierarchy and mapping files to July 2019 version (UE only) - Number of minor bug fixes --- Release notes MEGAN6 V6_16_4: --- - fixed critical bug that caused meganization to fail to classify any reads --- Release notes MEGAN6 V6_16_3: --- - fixed bug that prevented turning bi- and tri-plots on and off - fixed bug that prevented turning convex hull on and off - fixed bug that prevented selection of items in charts view - Added Pearson’s r and Kendall’s tau to co-occurrence graph - Fixed bug that didn’t disable collapse to rank in functional viewer - Fixed numerous bugs associated with showing or hiding bi- and tri-plots in PCoA - Fixed *Set Groups Linewidth and Color…* menu item in Cluster Viewer --- Release notes MEGAN6 V6_16_2: --- - fixed bug that prevented check for updates to work correctly --- Release notes MEGAN6 V6_16_1: --- - fixed bug that caused Quit command to fail on MacOS - Fixed bug that caused Check for Updates to hang --- Release notes MEGAN6 V6_16_0: --- - MEGAN now runs under Java 12 and comes with JavaFX bundled - Samples Viewer was rewritten due to incompatibility issues - Notifications disabled due to incompatibility problems - class/resources directory addition of external classifications no longer supported due to incompatibility problems - if you need this, please contact daniel huson - NCBI taxonomy updated to current version - NCBI mapping files will be updated in the next few days --- Release notes MEGAN6 V6_15_2: --- - Fixed bug that caused usePercentIdentityFilter to be ignored when using the naive LCA - Changed context message in command input dialog in MEGAN UE to reflect then name expected in the set context command - Removed component-wise installation - Major refactoring of base code - might cause strange bugs - please report them to the community web page --- Release notes MEGAN6 V6_15_1: --- - Fixed bug that prevented Export-CSV to work in some cases - Fixed bug that caused functional classifications to disappear after computing core biome or similar --- Release notes MEGAN6 V6_15_0: --- - Added new VFDB functional classification (Virulence Factor Database, www.mgc.ac.cn/VFs) - Added mapping file for VFDB to MEGAN download webpage - Fixed a number of broken menu items in the Cluster Viewer, such as HFlip and VFlip - Added menu items for setting color and line-width of items in PCoA viewer - Added new set scale menu item to PCoA viewer - Refactored *Segmentation of reads* export - Fixed some minor issues with the *Export Frame-shift corrected reads* --- Release notes MEGAN6 V6_14_3: --- - Fixed bug that prevented use of extract to new document on long reads --- Release notes MEGAN6 V6_14_2: --- -added 'extract all' option to extract-reads tool - fixed bug in "Export Read Lengths and Coverage" --- Release notes MEGAN6 V6_14_1: --- -fixed bug in extract-reads tool --- Release notes MEGAN6 V6_14_0: --- - added menu item to Inspector Window that allows one to save currently selected text to a file - added a new tools program that allows one to extract reads from a DAA or RMA file, by taxonomic or functional classes - updated Silva to NCBI mapping file to use latest NCBI taxonomy --- Release notes MEGAN6 V6_13_5: --- - Added functional classification to taxa CSV export - Fixed some bugs in CSV export --- Release notes MEGAN6 V6_13_4: --- - added export frame-shift corrected reads --- Release notes MEGAN6 V6_13_3: --- - Fixed bug that caused min zombie window to open when using the cluster viewer --- Release notes MEGAN6 V6_13_2: --- - Fixed bug in BIOM parser that caused null pointer exception on some inputs - Fixed bug that prevented reopening of ClusterViewer - Fixed bug that prevented sample color/shape from updating in sample column in sample viewer - Fixed bug in *set color* command. Now this will work: "set color=#00FF00 attribute=Gender state=male;" - Added compute-comparison tool to CE --- Release notes MEGAN6 V6_13_2: --- - Fixed bug in SAM parser that caused Minimap files to fail - Fixed bug in BIOM parser that caused null pointer exception on some inputs - Fixed bug that prevented reopening of ClusterViewer - Fixed bug that prevented sample color/shape from updating in sample column in sample viewer - Fixed bug in *set color* command. Now this will work: set color=#00FF00 attribute=Gender state=male; - Added compute-comparisons to CE --- Release notes MEGAN6 V6_13_1: --- - fixed bug that slowed down export of reads and CSV from meganized DAA files - speed up of loading alignments from DAA file - to reduce the number of alignments from DAA file, added filter that requires protein alignment to cover 80% of reference sequence --- Release notes MEGAN6 V6_13_0: --- - Updated to latest NCBI taxonomy, now over 2 million nodes - Updated taxonomic mapping files, NCBI-nr now contains over 170 million references --- Release notes MEGAN6 V6_12_8: --- - Updated bundled Java version for Windows and MacOS - Fixed incompatibility with MacOS Mojave --- Release notes MEGAN6 V6_12_7: --- - Fixed bug that caused incorrect functional binning of long reads in rare cases - Fixed bug that caused MEGAN to forget which taxa have been disabled. --- Release notes MEGAN6 V6_12_6: --- - added support for layered functional export to STAMP - implemented export from long read inspector to file --- Release notes MEGAN6 V6_12_5: --- - added taxdump2tree to UE --- Release notes MEGAN6 V6_12_4: --- - Fixed bug that caused problems when parsing SAM format produced by minimal --- Release notes MEGAN6 V6_12_3: --- - Fixed bug that caused + (positive alignment) to be missing in print out of protein and translated alignments (note that positive score is determined using Blosum62, independent of what was originally used to align the sequences) - Fixed bug that caused too many files to be opened when exporting data. - Added experimental code for correcting erroneous frame-shifts in long reads - Added new command-line tool *extract-biome* that extracts the total, core or rare biome from a MEGAN comparison file - UE only: added command-line tool *compute-comparison* that computes a comparison file for a list of RMA, .megan and meganized DAA files --- Release notes MEGAN6 V6_12_2: --- - Fixed bug that cause dominance filter to be ignored when parsing long reads alignments in a DAA file (dominated alignments were not removed from consideration as the should have been) - Updated read-to-frameshiftsPerKb export to report on all reads on or below a selected, collapsed taxonomy node --- Release notes MEGAN6 V6_12_1: --- - Fixed bugs associated with exporting counts - Added new selection menu item - Fixed minor bugs --- Release notes MEGAN6 V6_12_0: --- - Added experimental contaminant filter. A forthcoming paper will describe and evaluate this new feature - Updated InterPro 2 GO classification to latest metagenomic GO slim and latest InterPro families (downloaded June 2018) - Updated InterPro 2 GO mapping files on MEGAN6 download page - Updated taxonomic classification to latest NCBI taxonomy (downloaded June 2018) - Updated INCBI taxonomy mapping files on MEGAN6 download page - Fixed bug that caused computation of "rare biome" to produce incorrect results --- Release notes MEGAN6 V6_11_7: --- - Fixed bug that caused Chi square distance calculation to fail - Reimplemented all distance calculations (except Goodall) - Added Goodall distance (back) to menu - More work on UniFrac distances, unweighted is correct, and pretty certain that weighted calculation is also correct --- Release notes MEGAN6 V6_11_6: --- - Enabled Unweighted and Weighted UniFrac in Cluster Viewer --- Release notes MEGAN6 V6_11_5: --- - Fixed bug that caused turning off of Parse Taxon Names to be ignored - Choices made in meganize dialog are now remembered - RDP standalone files should now be recognized correctly - Wrong file suffix now produces only a warning, not an exception - Removed some unused menu items --- Release notes MEGAN6 V6_11_4: --- - removed debugging output --- Release notes MEGAN6 V6_11_3: --- - Fixed bug that occurred when selecting different layout in Layout menu of alignment viewer - Fixed bug that potentially cause some KEGG assignments to be missed --- Release notes MEGAN6 V6_11_2: --- - Fixed multiple bugs that prevented use of the RDP standalone and details file importer --- Release notes MEGAN6 V6_11_1: --- - Fixed bug that caused the setting "Min Support Percent =0" to be overwritten with "Min Support Percent =0.05" during meganization - Fixed a number of minor bugs - Produced new Silva to NCBI mapping file (Silva release 132), available on the MEGAN 6 download site - This is the first official release of MEGAN-LR, meaning that the long read additions to the software have been tested enough to be considered usable. A paper describing these additions is to appear in Biology Direct To perform long read analysis, first run Diamond in long read mode, using the options: --range-culling --frameshift 15 --top 10 Then meganize the resulting DAA file using the --longReads option. --- Release notes MEGAN6 V6_11_0: --- -Update NCBI taxonomic tree in MEGAN using data downloaded from NCBI in March 2018. Taxonomy now has 1.7 million nodes - Updated taxonomy mapping files on http://ab.inf.uni-tuebingen.de/data/software/megan6/download/welcome.html using data downloaded from NCBI in March 2018 - Fixed bug that caused MEGAN UE *help* option to be write to error.log instead of to console - GFF export: Domination filter now only removes a match if it dominated by a match that itself is not dominated by any match. In case of a bit-score tie, the shorter of two matches dominates - Added new experimental *frame-shifts per kb-aligned-sequence* export feature for long reads --- Release notes MEGAN6 V6_10_13: --- - fixed fatal bug that was introduced with previous release --- Release notes MEGAN6 V6_10_12: --- - Fixed bug that caused very slow access to information in a meganized-DAA fille. Export to CSV files should now run many times faster. --- Release notes MEGAN6 V6_10_11: --- - fixed -r2c bug in RMA2Info and DAA2Info --- Release notes MEGAN6 V6_10_10: --- - Fixed bug in long-read best hit functional binning algorithm that resulted in duplicate reporting of the same gene in many cases - Fixed bug that caused *strong domination filter* not to be applied when importing long reads from a DAA file - The *strong domination filter* default values are MinPercentCoverToStronglyDominate=90% and TopPercentScoreToStronglyDominate=90% (see the paper on MEGAN-LR for details) - Print command for LR-inspector now produces vector-pdf, not pixel-pdf --- Release notes MEGAN6 V6_10_9: --- - noncritical internal changes --- Release notes MEGAN6 V6_10_8: --- - Fixed bug that shows some amino acids in lower case in inspector window --- Release notes MEGAN6 V6_10_7: --- - Fixed a bug in the samples viewer that caused some menu items to be disabled - Updated DAA parser to accept latest version of DAA files generated by Diamond - Updated version of controlsfx.jar used - Updated bundle JRE to 1.8.0_162 --- Release notes MEGAN6 V6_10_6: --- - Fixed bug in long read inspector that caused read lengths to appear as 0 - Fixed bug that caused samples to disappear when importing an incorrect metadata file - Fixed bug that caused incorrect parsing of taxon ids during CSV import - Removed redundant classification option from meganizer and other tools, desired classification is now inferred from given mapping files - Updated KEGG to December 2017 in UE --- Release notes MEGAN6 V6_10_5: --- - Added *disable taxon* context menu item to Inspector window - Allow SAM files to start with @PG (as produced by minimap) (- Contaminant file can now be specified in LCA Parameters dialog) --- Release notes MEGAN6 V6_10_4: --- - Fixed tool bar problems in Alignment Viewer - Added Edit-Preferences-Enable Feature… menu item that allows users to turn experimental features to help with testing - (Added experimental contamination filter for testing, not enabled yet) --- Release notes MEGAN6 V6_10_3: --- - Added minPercentIdentity option to blast2rma and daa2rma programs --- Release notes MEGAN6 V6_10_2: --- - Updated the NCBI protein and nucleotide mapping files. Note that due to large number of protein accessions (over 400 million), the new protein mapping file only maps the first identifier on each line of the NCBI-nr database, and thus only contains just over 100 million accessions. For a given header line, the first accession is mapped to the LCA of all taxa that are referenced on the header line, so some assignments will be less specific than when using previous mapping files - Fixed bug that caused interval-union algorithm to sometimes fail with a "No root" runtime exception - Modified LCA mode ExtendMappingUsingReferenceFastA so that ancestral taxa are not ignored, so if an entry has both a strain and a species assignment, then the species assignment is used - Modified coloring of arrows in long read inspector such that "by Label" uses taxonomic labels, while "By Position" uses label of highest ancestor below taxonomic assignment rank for coloring --- Release notes MEGAN6 V6_10_1: --- - Fixed splash screen scaling bug - Fixed PCoA ghost window bug - Added menu items for setting axes colors in PCoA viewer - Added handling of underscores in names to be looked up - Updated NCBI tree to version of Oct 19th, 2017 - Updated NCBI taxonomy mapping files - NCBI mapping files are currently being computed and will be available before the end of Oct 2017 - We now round bitscores from meganized DAA files so that the results are the same as what you get from RMA files - Added new menu items for keeping non-prokaryotic, non-eukaryotic or non-virus nodes collapsed - Fixed bug that caused different reads with the same name not to both be exported in CSV export --- Release notes MEGAN6 V6_10_0: --- - First release of MEGAN-LR (MEGAN long read) - Added maf2daa to tools (converts LAST MAF output to DAA format for processing with MEGAN) - Fixed a number of bugs associated with taxon disabling - Fixed bug that caused List disabled taxa to fail - Added -Disable Default- menu item to taxon disabling --- Release notes MEGAN6 V6_9_4: --- - Fixed bug that caused daa2info to throw an exception when given an non-meganized file - Fixed bug that caused recent files menu not to be disabled during recompute - MinSupportPercent is now based on assignment mode, not number of reads. So if the value is set to 0.1%, say, and the assignment mode is aligned bases, say, then a taxon will have to attract 0.1% of all assigned bases to appear in the tree. If this number is not achieved, then the reads are pushed up the tree. - Based on simulation study results, default value for MinSupportPercent increased to 0.05% --- Release notes MEGAN6 V6_9_3: --- - Fixed bug that caused parameters not to be saved in Summary file - Added -vo (viruses only) flag to daa2info and rma2info - Implemented "scroll to match" in long read inspector - a number of bug fixes - report summary of node selection to message window (and as tooltip for status bar) --- Release notes MEGAN6 V6_9_2: --- - Finished implementing GFF3 export and this now allows one to export annotated long read and contig in such a way that the resulting files can be opened in the Artemis genome browser. --- Release notes MEGAN6 V6_9_1: --- - Improved coloring of alignments in long-read inspector - Minor improvement of long-read inspector - Taxon disabling now applies recursively to all the descendants of any node selected or specified --- Release notes MEGAN6 V6_9_0: --- - First version of BIOM2 format parser, hopefully compatible with latest QIIME - Fixed bug that prevented use of additional classifications with daa2info and rma2info - Some bug fixes - UE compare command now allows specified megan file to be a directory. In this case all suitable files in the directory are recursively involved in the comparison --- Release notes MEGAN6 V6_8_20: --- - Fixed bug that caused UE to not save -rc code in command line mode - Close all long-read inspectors on recompute - Color taxa in long-read inspectors by next lower taxonomic rank - Better node labeling for very large numbers of samples - Allow Percent chart to be calculated with respect to total assigned reads (or bases) --- Release notes MEGAN6 V6_8_19: --- - Naive LCA algorithm now takes LCA weight into account: if this is set to less than 100 %, then read is place above given percent of all taxa that to which the read has a significant alignment - Added "unknown" ranks when exporting taxonomy paths in MEGAN, daa2info and rma2info - Fixed bug that caused null pointer exception when using weighted LCA - Added path export to rma2info and daa2info for functional classifications - Attempted to fix old problem that causes newly opened windows to sometimes open behind already existing ones - Improved heuristic for identifying header line in CSV import - Fixed bug in CSV import that prevented use of the Samples Viewer - Attempted to fix bug that sometimes causes image export to fail on certain linux platforms --- Release notes MEGAN6 V6_8_18: --- - fixed bug that prevented saving of comparison files --- Release notes MEGAN6 V6_8_17: --- - Fixed another bug that caused number of aligned bases to sometimes be incorrect in long read taxonomic assignment when parsing DAA file produced from a MAF file - Fixed newly introduced bug that broke zooming classification tree --- Release notes MEGAN6 V6_8_16: --- - Fixed bug in code that processes DAA input containing frame-shifts. --- Release notes MEGAN6 V6_8_15: --- - Fixed bug that caused number of aligned bases to sometimes be incorrect --- Release notes MEGAN6 V6_8_14: --- - More work on long read taxonomic binning algorithm. Long read algorithm is now interval-set based (again). - Optimised PCoA so that it can now handle 1000 samples or more. - A number of minor bug fixes --- Release notes MEGAN6 V6_8_13: --- - Extract to new document available for comparison documents (if original input documents still present at original location, todo: add dialog for finding files if moved) - Improved handling of minSupport and minSupportPercent options in blast2rma, daa2rma and daa-meganizer - rma2info and daa2info have new option --ranks for outputting rank information for taxonomic assignments, rma2info and daa2info both now always honor --majorRanksOnly option for taxonomic output - rma2info and daa2info can now output summary files - Implemented new "segment-based LCA" algorithm for taxonomic binning of long reads - Weighted LCA now takes "read assignment mode" into account. --- Release notes MEGAN6 V6_8_12: --- - Fixed bug that caused problems with LCA when importing from CSV - Fixed bug that sometimes caused problems in new parallelized assignment algorithm (experimental algorithm, activate in UE with set prop UseParallelDataProcessor=true;) --- Release notes MEGAN6 V6_8_11: --- - Fixed bug that sometimes caused problems when importing CSV files - Fixed bug that caused some alignments to not be assigned when importing XML files --- Release notes MEGAN6 V6_8_10: --- - Fixed newly introduced bug that prevented loading of files into comparison window - Command line input now explicitly shows the active "command context" (UE) - Added options to rma2info and daa2info tools to request that taxonomic paths are reported --- Release notes MEGAN6 V6_8_9: --- - Fixed bug that prevented switching to bar charts when viewing KEGG pathway - Fixed bug that caused incorrect colors in comparison document - Now reference default server directly --- Release notes MEGAN6 V6_8_8: --- - Fixed bug that caused problems when analyzing comparison documents (incompatibility with new inspector feature for comparisons document) --- Release notes MEGAN6 V6_8_7: --- - Fixed menu bug in UE KeggViewer - Added zoom menu items to popup menu for pathway tabs - KeggViewer now supports use selected color scheme in pathway tabs for heatmaps --- Release notes MEGAN6 V6_8_6: --- - Improved long read LCA binning algorithm - Added new feature that allows users to use inspector and other read or alignment access methods on comparison files. This gives a unified view of multiple samples as one. (Need to add code to allow users to reattach comparison files to underlying source files if the source files have been moved.) --- Release notes MEGAN6 V6_8_5: --- - fixed (recently introduced) bug that caused problems when parsing blast-tab files (and possibly other parsers, too) --- Release notes MEGAN6 V6_8_4: --- - Fixed major bug in long read LCA algorithm - Added experimental CollapseSpeciesLongReadLCA that has the effect that multiple different alignments to the same species (e.g. at the strain level) are represented only by one alignment during the long read LCA algorithm. This reduces the effect of over abundance in the reference database of some strains e.g. E.coli - Updated long read LCA algorithm so that alignments to any disabled taxa are ignored during taxonomic binning - Windows and MacOS versions now use Java 1.8.0_131 --- Release notes MEGAN6 V6_8_3: --- - Updated NCBI taxonomy and mapping files to May 22nd, 2017 - Fixed bug that suppressed some of the status bar messages - Implemented parallel version of DataProcessor. This is still under development and aims at speeding up the meganization and analysis process. To active this, set the UseParallelDataProcessor variable to true - Updated long read LCA algorithm slightly --- Release notes MEGAN6 V6_8_2: --- - Fixed bug that sometimes caused reads with no alignments to appear under Unassigned rather than No Hits - Now use much less aggressive filtering of alignments in long read mode. Now an alignment is only ignored if it is dominated by another alignment that covers at least 90% and is such that the bitscore of the alignment does not achieve 90% of the dominators bitscore (In the UE, the two thresholds can be changed by setting the variables MinPercentCoverToDominate and TopPercentScoreToDominate) - Rewrote SAM parser so that it supports long read mode --- Release notes MEGAN6 V6_8_1: --- - Fixed bug that prevented Long Read inspector from opening in CE - Fixed bug that caused Import from Blast Dialog to ignore chosen ReadAssignmentMode - Fixed bug that prevented use of LCA percent weight with long read mode in Import Blast Dialog - Fixed some issues associated with parsing SAM files that come from programs other than DIAMOND or MALT --- Release notes MEGAN6 V6_8_0: --- - Added experimental long read inspector to MEGAN CE - Fixed bug that caused Attribute Correlation Plot to break after intermediately saving data - Fixed bug that prevented KEGG viewer (UE) for shown Metabolism overview diagram - Fixed bug that prevented KEGG viewer (UE) from highlighting nodes in sidebar tree - Fixed bug that prevented KEGG Viewer (UE) from updating visualization to heat maps in pathways that are already showing --- Release notes MEGAN6 V6_7_21: --- - More work on faster loading of remote files - Fixed bug that caused problems opening rma2 files - Fixed problems with status bar - blast on NCBI dialog provides better preselected directories --- Release notes MEGAN6 V6_7_20: --- - Fixed recent bug in *compare from remote server* that caused initial loading of files to take a very long time with no feedback to user - Improved display in parallel coordinates viewer - Fixed bug that might cause problems when closing windows --- Release notes MEGAN6 V6_7_19: --- - Fixed bug in make-acc2interpro - Simplified long read LCA processing: there is now only one algorithm, Long Read LCA, that can be used with long reads. - Added different definitions of "assigned reads" in the taxonomy viewer: counts, lengths, aligned bases and magnitudes - Statusbar modified so that it can wrap around when too long --- Release notes MEGAN6 V6_7_18: --- - - Fixed newly introduced bug that caused problems when computing comparisons of samples that have read magnitudes --- Release notes MEGAN6 V6_7_17: --- - Fixed bug that sometimes prevents *Import from Blast* dialog from opening --- Release notes MEGAN6 V6_7_16: --- - More work on long read analysis: - NaiveMultiGene LCA algorithm now named NaiveLongRead - CoverageMultiGene LCA algorithm now named CoverageLongRead - CoverageLongRead algorithm now more conservative: weight of higher order taxa now must lie below read placement node - In long read mode, *min support* parameter now refers to number of base pairs rather than number of reads - Added *minPercentReadToCover* option to LCA algorithm - when used, a read is only binned if the given percent of its full length is covered by alignments - Removed filter from long read inspector: now all alignments are shown, none are removed (this may need further work) - Improved Collapse and Expand node commands: program now scrolls to the nodes affected --- Release notes MEGAN6 V6_7_15: --- - Fixed bug that caused alignment viewer to fail on some meganized DAA files --- Release notes MEGAN6 V6_7_14: --- - Fixed bug that caused gene-centric assembly to throw an exception --- Release notes MEGAN6 V6_7_13: --- - Fixed bug that caused blast2lca fail when used for KEGG assignments - Added *export reads in GFF format* menu item - Added new experimental coverage-based LCA taxonomic assignment algorithm for long reads - Added minPercentReadCovered filter that only bins reads taxonomically if a given percentage of their length is covered by alignments - Long read analysis now turns off topPercent filter (as it makes no sense to use it in this case) - Added scroll to selected menu item --- Release notes MEGAN6 V6_7_12: --- - Added new Option *Use Read Weights for Assignments*. When selected, viewers report read weights rather than number of reads. The read weight of a node differs from the number of reads assigned to a node if (a) the reads were parsed with magnitudes or (b) long read mode is being used - Added support for frame-shift alignments - Added new menu items to Samples Viewer - Added "Updating" item to window menu items for windows that are currently being updated - More work on long read inspector --- Release notes MEGAN6 V6_7_11: --- - Added long reads option to NCBI blast dialog - Fixed minor bug in parallel coordinates viewer (UE) - Fixed incomplete version update --- Release notes MEGAN6 V6_7_10: --- - Fixed a subtle bug in RMA6 file accessor that caused problems in rare cases, causing the accessor to throw an exception and to then ignore reads from that point forward. --- Release notes MEGAN6 V6_7_10: --- - Added command for listing summary of all metadata - Bug fixes in new parallel coordinates viewer (UE) --- Release notes MEGAN6 V6_7_9: --- - Fixed some issues in menus - Fixed multiple bugs in parallel coordinates viewer (UE) --- Release notes MEGAN6 V6_7_8: --- - Improved visualization for large comparisons of 500+ samples - Added new column squeeze command to samples viewer - Implemented "Select from Previous" in groups viewer - Fixed some problems with grouping by attributes --- Release notes MEGAN6 V6_7_7: --- - Improved visualization for large comparisons of 500+ samples - Added new column squeeze command to samples viewer - Implemented "Select from Previous" in groups viewer - Fixed some problems with grouping by attributes --- Release notes MEGAN6 V6_7_6: --- - Fixed bug that caused inspector window to show the same alignments for all reads - Modified remote blast dialog to only show blast program options that work with MEGAN --- Release notes MEGAN6 V6_7_5: --- - Added preference to set desired search engine (default is google.com) - Fixed bug that caused problems in side-bar heat map view - Fixed minor bug in in BlastP parser - Added new feature that allows one to run blast remotely at NCBI and then to capture the results in a MEGAN file - More work on improving the long read inspector (UE) --- Release notes MEGAN6 V6_7_4: --- - Added preference for web search engine URL - Fixed bug in sidebar heatmap numbers - More work on long read viewer (UE) --- Release notes MEGAN6 V6_7_3: --- - Fixed bug in biom1 import that sometimes caused import to fail - Implemented support for Last BlastX-like alignments that contain frame shifts (as represented in MAF format) in Inspector window and also in visual long read inspector (UE) - Improved internal representation of RMA6 files - Fixed import and meganization missing Taxonomy bug --- Release notes MEGAN6 V6_7_2: --- - Fixed bug that caused Open From URL… to fail - Fixed bug in sort-last-maf that prevented use of fastq files as sort key - Fixed newly introduced bug that caused Taxonomy tab to sometimes be missing in Import Blast or Meganize dialogs - Note: new Last MAF parser currently does not handle frame shifts, will be fixed in next update --- Release notes MEGAN6 V6_7_1: --- - Fixed major bug in new MAF format parser that caused position and frame of BlastX alignments on reverse strand to be incorrect. - Fixed a number of bugs in Export Image - Fixed bug that prevented use of SeedPath_to_RPK in CSV export - Fixed bug that prevented export of legend from working - Updated blast-tab format parser to support use of long read mode. - Improved long read parsing algorithm and long read inspector algorithms - Improved long read visual inspector in UE --- Release notes MEGAN6 V6_7_0: --- - Implemented new "long read mode". This entails: (a) new parsing algorithm that imports significant along whole read, (b) a new "long read" LCA for taxonomic binning and (c) a new "multi-gene" algorithm for functional binning. - Added new long read inspector to UE - Added a number of new node shapes for PCoA plots - Leaves now selected when constructing chart for functional classification - Add feature that allows one to request taxon name parsing on command line - Added support for Last’s MAF output format. WARNING: Last does not report the alignments associated with a given read consecutively. This causes MEGAN to report the same read more than once. - When importing metadata, samples are reordered to reflect ordering in metadata file. - Added CSV export of functional binning to RPK "reads per kilo-base" values. - Added blastMode option to blast2rma program - Updated to latest NCBI tree - Updated to latest JRE (windows and mac) - Fixed bug that sometimes caused "can’t seek backward" exception when updating DAA files - Fixed bug in CSV import that caused import of "read name,taxon,score" to fail - Fixed bug that caused coloring by position to break when opening a previously saved file --- Release notes MEGAN6 V6_6_7: --- - Fixed bug that prevented daa2info from working (Classification not found problem) - Updated ControlsFX version --- Release notes MEGAN6 V6_6_6: --- - Fixed bug that caused Import Blast dialog to forget set format and mode when sswitching between tabs - Fixed bug that caused BIOM export of function to allow multiple occurrences of the same class id --- Release notes MEGAN6 V6_6_4: --- - Modified daa2info so that header lines are not shown when general info lines not requested - Added new tool rma2info that can be used to extract annotations from an RMA file (similar to daa2info) - Fixed bug that prevented recognition of blast tab files that start with comment lines (such as produced by last) - New updated acc2kegg-Nov2016X-ue.abin.zip KEGG mapping file replaces previous one (cc2kegg-Oct2016X-ue.abin.zip), which was missing all archaea annotations due to an error - Minor bug fix in find dialog - Updated installer --- Release notes MEGAN6 V6_6_3: --- - Fixed newly introduced bug (6.6.2) that causes Compare to throw an exception - Modified blast2rma, daa2rma and similar programs to set -fwa to true by default, which is required to correctly perform mapping when using an ncbi-NR reference database downloaded Sept-2016 or later. - Fixed minor bug in daa2info - New acc to interpro mapping file (acc2interpro-Nov2016XX.abin) that maps 17 of 106 million ncbi-NR references to some interpro family --- Release notes MEGAN6 V6_6_2: --- - Fixed bug in color assignment when switching from "by Label" to "by Position" - Change of color table or color mode now causes program to undo any previous selection of attribute to color - Added code to recover from a "buffer underflow" exception caused when opening a meganized Diamond file that has been corrupted by an incomplete update of file - Comparison calculation now throws an exception and terminates if there is any problem reading any of the input files --- Release notes MEGAN6 V6_6_1: --- - Added new daa2info tool for querying a meganized DAA file - Fixed a number of minor bugs - updated KEGG classification tree in UE (removed superfluous intermediate nodes labeled null) - More work on accession mapping files --- Release notes MEGAN6 V6_6_0: --- This is a major update that fixes many issues. - Updated NR parser to take into account that since September 2016 accessions are no longer prefixed with gb| or ref| - Previous releases of MEGAN6 do not handle recent versions of NR correctly. - New accession to KEGG and accession to InterPro2GO mapping files - Now 5.2 million entries in NR receive a KEGG assignment - Now 8.7 million entries in NR receive an InterPro assignment (with gi mapping file this number was 16 million, this issue is being studied) - Added code that allows one to override MEGAN’s functional classification algorithm - Updated access to NCBI so as to use https rather than http - Fixed bug in "References_as_FastA" parser that caused problem at the end of the file - Fixed bug that prevented recognition of fastA files when compressed and no fastA suffix in name - Command line tools in MEGAN UE can now use UE-only mapping files - Fixed bug in show/hide selected command in chart viewer - Fixed bug in import of functional classifications from CSV - Fixed bug in UE representation of latest KEGG hierarchy - Updated interpro2go to new release of metagenomic GO slim - Did some work on how KEGG classification appears --- Release notes MEGAN6 V6_5_10: --- - Fixed bug in open file in command line mode that failed to update connection to latest file - Updated to latest Java 1.8.0_102 (MacOS and Windows) --- Release notes MEGAN6 V6_5_9: --- - Fixed bug that caused assigned rather than summarized counts to be exported when performing Export CSV - Fixed a bug that caused exception when exporting PDF image of PCoA plot - Added new CSV Export format "readName_to_taxonPathPercent". In this variant of taxon-path export, the path only contains taxa that have an official NCBI rank assignment (such as phylum etc), each taxon name has a prefix indicating its rank (e.g. g__ for genus) and each taxon is accompanied by a number that indicates the percentage of significant alignments of the read to that taxon. - Program properties topTreeSpace and rightTreeSpace implemented to allow determine the size of trees in HeatMap and AttributeCorrelationPlot --- Release notes MEGAN6 V6_5_8: --- - Added ability to use ellipses to indicate groups in PCoA plot - Fixed bug in use of alternative taxonomy - Implemented clustering by classes and attributes in attributes correlation chart - Implemented transposed mode in attributes correlation chart - Implemented clustering by series or classes in correlation chart - Implemented transposed mode in correlation chart - MALT is now open source (see https://github.com/danielhuson/malt) --- Release notes MEGAN6 V6_5_7: --- - Export data for Attribute correlation plot and correlation plot now exports correlation values --- Release notes MEGAN6 V6_5_6: --- - Now allow .csv files for metadata - Now allow repeated loading of metadata, with the option to delete previous metadata - Now allow user to ‘expand’ an attribute in the Samples viewer which means one new column will be generated for each value that the attribute has. This allows such values to appear in a PCoA plot or attribute correlation plot - Now support find and replace in Samples Viewer, including replace only within selected cells --- Release notes MEGAN6 V6_5_5: --- - Fixed bug in CSV exporter headerline - Fixed bug in 'none' mode of gc-assembler --- Release notes MEGAN6 V6_5_4: --- - Major improvement of MEGAN UE’s representation of the KEGG hierarchy. - Fixed bug that prevented use of Export Overlap Graph… menu item - Find command sets focus to find dialog - Fixed bug that sometimes prevented Alignment Viewer from opening - Fixed bug in Alignment Viewer close command - Added "none" classification mode to gc-assembler - Inspect command still has problems (window jumps to back…) --- Release notes MEGAN6 V6_5_3: --- - Fixed a number of minor bugs in GUI - Now apply topPercent filter to functional analysis as well (as in most previous releases) --- Release notes MEGAN6 V6_5_2: --- (Versions 6.5.0 and 6.5.1 were not publicly released) - Major update: MEGAN UE now contains licensed uptodate version of KEGG - KEGG mapping in UE now assigns many more reads to KOs than previously assigned - Updated protein and nucleotide accession to NCBI taxonomy mapping files - Updated GI mapping files - Modified remote service browser so that it opens connection much quicker (no longer queries file sizes) - Fixed bug that caused all samples to appear "grouped" after a grouping has been added and then removed - Fixed bug in "order by enabled" button in Chart Viewer - Fixed bug that prevented gc-assembler from working with self-defined classifications in UE - Fixed bug that prevented multiple use of Export Summary command - Added "Compute Core Biome" menu item to main viewer - Cleaned up Export CSV dialog --- Release notes MEGAN6 V6_4_24: --- - Inspector window now shows length of reads and number of matches - Fixed a number of bugs that caused assignments to KEGG to be lower than when using MEGAN5 - In particular, MEGAN6 was missing the Unclassified category containing reads that align to a KO, but the KO is not contained in a path - Added a stand-alone version of the gene-centric assembler called gc-assembler --- Release notes MEGAN6 V6_4_23: --- - Fixed bug that caused all console output to go to error.log - Fixed CSV export problem of double quotes when label already has quotes around it - Fixed CSV export problem that sometimes allowed lines with 0 entries to be created - More work on fixing problem that causes Inspector window to open behind window instead of in front --- Release notes MEGAN6 V6_4_22: --- - Can now click on individual points in whisker plot to select both series (i.e. samples) and classes (e.g. taxa) - Can now apply "Compare Relative" menu item in Samples Viewer to produce relative comparison of a set of samples that are contained in a comparison document - Fixed issue in convex hull computation that caused problems in PCoA plot of large numbers of samples --- Release notes MEGAN6 V6_4_21: --- - fixed bug that caused KEGG chart not to show when using transposed option due to very long KEGG labels - updated accession parser to allow KEGG accessions that contain a colon : - improved code for parsing and using gi and accession number maps - minor improvement of BIOM1 importer (can import yet another variant of this underspecified "format") --- Release notes MEGAN6 V6_4_20: --- - Fixed bug in BlastXML parser that sometimes caused parser to freeze. - Modified blast2rma6 and daa2rma6 tools so that now both are able to handle paired reads and their alignments inputed in pairs of files. - Modified algorithm for handling paired reads: if only one read has taxonomic assignment, then it is used for other read as well. Otherwise, if first read has lca A and second read has lca B, then both are assigned to A, if A lies on or below B, or B, if B lies below A. If neither is the case, that is, if A and B are in different parts of the taxonomy and thus conflicting, then both reads are assigned to the LCA of A and B. - Improved LCA mapping algorithm - Gene-centric assembly implementation now constructs overlap graph for contigs to merge contigs that have a significant overlap - There appears to be a bug in the code that computes the consensus sequence in the alignment viewer. The consensus sequence is sometimes wrong- will try to fix… --- Release notes MEGAN6 V6_4_19: --- - Fixed newly introduced bug that prevented use of some GI mapping files - More work on putting PCoA computation into separate thread to allow analysis of 600+ samples --- Release notes MEGAN6 V6_4_18: --- - PCoA and trees computed in additional thread --- Release notes MEGAN6 V6_4_17: --- - Fix bug that caused Compare to fail when number of samples exceeded 100 x number of cores - Increased default timeout for PCoA calculation to 120s (to accommodate calculations on large number of samples). In UE, PCoA timeout can be set to 3000, say, using "setprop PCoAMaxTimeSeconds=300" - PCoA is currently calculated in main Event thread, leading to GUI freeze during computation, something that will to be fixed soon --- Release notes MEGAN6 V6_4_16: --- - Updated eggNOG and InterPro2GO classifications - More work on fixing focus-related problems (that sometimes cause menu short cuts to not work) - Fixed bug that caused Import from Blast dialog and Meganize dialog to forget chosen analyses --- Release notes MEGAN6 V6_4_15: --- - Fixed bug that caused some assignments in mapping file gi2tax.bin mapping files to be incorrect. Please update to mapping file gi2tax-July2016.bin - Modified biom1 parser to allow multiple columns to contain the same taxon (or functional class) - Better error handling in command line mode of UE --- Release notes MEGAN6 V6_4_14: --- - Fixed minor bugs in box chart - Added LCA feature to extend mapping program so as to use LCA when extending NCBI taxonomy mapping - Fixed internal bug that caused problems when taxonomy not selected when computing classifications - Updated GI-to-eggNOG mapping file --- Release notes MEGAN6 V6_4_13: --- - Added Attribute Correlation Plot and Correlation Plot to MEGAN CE - Added Clustering and Z-score calculation to HeatMap in MEGAN CE - Added Meganize DAA Files menu item to MEGAN CE --- Release notes MEGAN6 V6_4_12: --- - Box chart now reports the attribute by which samples are grouped - Fixed minor bugs in chart UI --- Release notes MEGAN6 V6_4_11: --- - Fixed some minor bugs that impacted the chart drawing gui - Added a box chart drawer (whisker plot) - BlastXML parser now accepts .txt as file ending - Fixed a problem that caused BlastXML parser to hang when a problem is encountered --- Release notes MEGAN6 V6_4_10: --- - Added new CSV export feature that exports Rank:taxon and then counts or lengths, etc - Fixed bug that prevented status bar from appearing - Fixed bug that caused focus on wrong window after computing a comparison --- Release notes MEGAN6 V6_4_9: --- - Fixed bug that caused wrong window to grab focus after computation (took two days to find…) - Modified Color by position" feature to use whole color scheme if more colors available than attributes. With this, now can color by gradient: simply sort column then color by position - Fixed synchronization bug in SamplesViewer column sorting commands - Meganizer command in UE does not stop on exception but rather attempts to meganize all given files, reporting how many failures happened at the end - Sample viewer now keeps selection of multiple rows when setting color etc, so now possible to set color for multiple samples simultaneously - Fixed bug that caused color picker to apply wrong color to samples" --- Release notes MEGAN6 V6_4_8: --- - Fixed broken libary that caused MEGAN to use old code causing recent versions to miss some fixes --- Release notes MEGAN6 V6_4_7: --- - Fixed bug in blastn parser --- Release notes MEGAN6 V6_4_6: --- - Fixed bug in "extract reads" command that prevented it from working on user-defined classifications - Fixed bug in ExtendMapping program that caused problems - Fixed issues with version reporting in command line tools - Added close all other windows menu item - Fixed some usability issues with the interactive meganize command in UE - Updated NCBI taxonomy to latest version (June 2016) - Updated NCBI accession mapping files to latest version (June 2016) --- Release notes MEGAN6 V6_4_5: --- - Modified side-bar tree so that it now shows number of reads assigned to nodes, independent of how much of the tree has been opened on the right-hand tree viewer - Fixed bug that caused "Use ID parsing" option to be ignored - Added code to warn user that files cannot be meganized in UE while they are open - Fixed bug that prevented "extract reads" to work on DAA files when no nodes selected - Fixed a number of bugs in "ExtendMappingUsingReferenceFastA" program that caused extended mapping files to be incomplete --- Release notes MEGAN6 V6_4_4: --- Fixed bug that caused some CE tools to hang (due to a missing library) - Made ID parser more robust - Remote file browser displays number of reads (in tooltip) --- Release notes MEGAN6 V6_4_3: --- - Turned off multi-threading in main data analysis algorithm as it sometimes causes reads to be placed incorrectly. - Fixed bug that caused read sequences not to be extracted when using Extract To New Document - Improved alignment viewer command so that all reads below a collapsed leaf node are also loaded into the viewer - Modified blast-tab parser so that it ignores lines starting with ‘# ‘ (hash+space) - Modified blast-text parser so that it allows additional text between reference header line and score line, as encountered when downloading blast results as text from NCBI --- Release notes MEGAN6 V6_4_2: --- - Modified biom1 file filter so that it does not allow user to select biom2 files (as they are not supported) - Extract To New Document menu item now also includes reads that are summarized by a selected leaf node - Added weightedLCAPercent option to UI - now uses open-source megan-ce code-base --- Release notes MEGAN6 V6_4_1: --- - Distance calculation for PCoA plots now uses assigned counts on internal nodes and summarized counts on leaves - FIxed subtle bug that caused weighted-LCA to sometimes assigned reads to related, but incorrect taxa - When rerunning LCA algorithm, now removes state entries from Inspector window --- Release notes MEGAN6 V6_4_0: --- - First release based on GitHub open source repository danielhuson/megan-ce - Fixed a number of problems associated with scripts in the tools directory (both CE and UE) --- Release notes MEGAN6 V6_3_11: --- - Fixed bug that prevented previous release from starting. --- Release notes MEGAN6 V6_3_10: --- - fixed bug that prevented daa-meganizer from working in Community Edition - update bundled java version - fixed issue with updater when not using install4j - Community Edition source code now available on GitHub (danielhuson/megan-ce) --- Release notes MEGAN6 V6_3_9: --- - fixed bug that prevented use of daa-meganizer in CE --- Release notes MEGAN6 V6_3_8: --- - Nothing changed --- Release notes MEGAN6 V6_3_7: --- - fixed bug that prevented correct "Extract to Document" for RMA6 files when paired reads set to true --- Release notes MEGAN6 V6_3_6: --- - fixed recently introduced bug that caused id-assignment to sometimes assign random taxa or functions to reference sequences - fixed bug that prevented import of KEGG assignments in biom format from PieCrust - Updated Windows and MacOS JREs to latest version --- Release notes MEGAN6 V6_3_5: --- - fixed bug in 2D PCoA viewer that caused some nodes to have gray borders - fixed bug that caused null-exception in Alignment export. - modified weighted-LCA to use max weight assigned to a specific taxon rather than sum - fixed bug that caused some assignable reads to get placed on Not assigned node - added Select All and Select None to Inspector window - fixed bug that caused reordering of samples in sample viewer to sometimes be ignored by other viewers - enabled drag-and-drop reordering of samples in comparison dialog - fixed bug that caused problems recognizing blast files in tab format when the file suffix wasn’t specific --- Release notes MEGAN6 V6_3_4: --- - Fixed bug that broke layout of BLASTN alignments - Fixed related bug that caused problems in weighted-lca algorithm - Better multi-threading of main analysis algorithm - Added code to uncollapse tree before running Project Assignments To Rank,… algorithm. --- Release notes MEGAN6 V6_3_3: --- - More work on speeding up weighted LCA. Now takes only less than 3 times as long as the naive LCA, however memory usage may be a problem - Added Project Assignments to Rank… menu item to Options menu, it replaces the somewhat cryptical "Taxonomic Profiling" dialog - Added "Meganize DAA Files…" menu item to UE --- Release notes MEGAN6 V6_3_2: --- - Fixed a bug that caused all BLASTP alignments imported from DIAMOND to be labeled with query start position 1, even if they start at some other position - Main read assignment algorithm is now multi-threaded - Fixed some minor issues in Weighted-LCA - Fixed some minor issues that caused progress bar task label to sometimes not appear - Updated manual --- Release notes MEGAN6 V6_3_1: --- - Fixed minor bug in alignment code (that is used to remove contained contigs in gene centric assembler) - Removed some redundant libraries (such as picard) - Updated GSON library in the hope that this would fix an incompatibility with BIOM1 files generated by mothur (unfortunately, it didn’t…) - Fixed a bug in UE that prevented incorporation of uptodate KEGG files (for those you have a KEGG license) --- Release notes MEGAN6 V6_3_0: --- - Major update that includes support for accession to taxon and functional class mapping. This addresses the issue that NCBI intends to discontinue the use of GI numbers. MEGAN uses an optimised file-based hash-table to store and use accession to taxon id (and other id) mappings. You will notice that the Use RefSeq feature in the Import Blast flag as been replaced by a Use Accession feature. This feature expects either a text file containing accession value pairs or a MEGAN .abin file that contains a hash table (as mentioned above). MEGAN now also provides a new tool contained references-annotator that can be run on a reference fasta file before it is used to build a BLAST or similar index. This program will annotate each reference by the taxon (and/or functions) that it is associated with. Then, when running MEGAN, mapping of references is done simply by parsing the augmented reference header lines . - This version also contains a bug fix related to parsing SAM files generated by MALT - A number of other bug fixes --- Release notes MEGAN6 V6_2_40: --- - Fixed bug that prevented blast2rma6 from operating correctly --- Release notes MEGAN6 V6_2_39: --- - fixed some mapping-related bugs (in connection with MALT) - simplified Parameters dialog - removed LCA Percent parameter - updated Heat Map chart --- Release notes MEGAN6 V6_2_38: --- - Added z-score and hierarchical clustering to Heat Map in UE - Fixed bug that prevented number of contained reads from being correctly used in gene-centric assembly - Fixed bug that prevented files ending on .blastp to be recognized as legitimate blasttab files --- Release notes MEGAN6 V6_2_37: --- - Fixed bug that caused previous window to briefly jump to the front when opening a new window - Added missing popup menus to some viewers - Fixed bug that caused new lines to be missing when exporting an assembly from the alignment viewer - Fixed a bug that sometimes resulted in a deadlock between Swing and JavaFx, causing the GUI to freeze --- Release notes MEGAN6 V6_2_36: --- - Fixed minor bug in tools (duplicated options for taxonomy features) - Fixed bug in weighted LCA algorithm (incorrect weights) - Speed up of weighted LCA algorithm for meganized DAA files --- Release notes MEGAN6 V6_2_35: --- - Fixed recently introduced problem that made taxonomy viewer very sluggish on large trees - Updated NCBI taxonomy to latest version (as of Feb 2016), now contains over 1.4 million nodes --- Release notes MEGAN6 V6_2_34: --- - Fixed major bug in MEGAN that caused Export-Alignments feature to output badly corrupted alignments - Fixed minor bug in BLAST text format input that caused small number of alignments to be incorrectly parsed - Fixed problem with rarefaction analysis - Fixed problems related to new Program Colors table --- Release notes MEGAN6 V6_2_33: --- - Added new Program Color Table menu item that tells MEGAN to use the same color table (and edits to the table, e.g. change of the color of a particular species) on all opened documents, rather than using document-specific color tables (default) - Added new weighted LCA algorithm implementation. This is the same algorithm as used in our Metascope software that won the 2013 DTRA Algorithms challenge. It is much more specific than the naive LCA algorithm at the expense of requiring substantially more time to run - Fixed a recent bug that caused some windows to appear multiple times in the Windows menu --- Release notes MEGAN6 V6_2_32: --- - fixed commandline programs in UE --- Release notes MEGAN6 V6_2_31: --- - fixed new bug in Chart Viewer throws many exceptions --- Release notes MEGAN6 V6_2_30: --- - Added new Attribute Correlation Plot chart to UE - fixed issue that caused summary files to be a couple of Mb in size (rather than just kb) when some nodes collapsed - fixed problem with Collapse to Rank menu item - fixed bug that caused sample attributes table columns to get permuted when saving and reopening - saved bug that caused dirty flag not be be erased when saving while Samples Viewer is open and has changes - added Paste by Attribute menu item in Samples Viewer that allows one to paste e.g. Age for Subjects that represented by multiple samples (each sample associated with the same Subject will get the same Age value) - fixed problems with tools in UE --- Release notes MEGAN6 V6_2_29: --- - Fixed bug in PCoA viewer that sometimes caused the bi-plot and tri-plot vectors to initially be placed incorrectly --- Release notes MEGAN6 V6_2_28: --- - Uploaded new GI-to-Taxon-Id mapping file gi2tax-Feb2016X.bin.zip to replace gi2tax-Nov2015.bin.zip which unfortunately contains errors (association between GI numbers and taxon-ids was off by 1, so most assignments ok, but some completely random) - Fixed bug in program that computes binary gi-to-taxon-id .bin file, which caused the problems mentioned above - Updated ExtendMapping utility so that it can handle the latest NR database (which caused problems due to its increased size…) - Added large color table containing 250 random colors - Increased the number of colors in the Yellow-Red table to 224 colors - Added new node context menu item for computing correlation coefficients between node assignments and attribute values --- Release notes MEGAN6 V6_2_27: --- - Fixed bug that prevented setting of individual colors for individual samples or classes - individually set colors are now a property of the given document, no longer a program wide property - fixed bug that prevented chart windows from using * to indicate that a document has been changed - fixed minor bug in KEGG UE update - fixed bug that prevented use of context menu on sidebar tree in classification viewers - fixed bug that cause export assembly to fail when no paths detected in overlap graph --- Release notes MEGAN6 V6_2_26: --- - Fixed bug that disabled Edit-Preferences-Fix Taxon Mapping items - Fixed bug that prevented use of Edit-Preferences- Taxon Disabling items - Fixed bug that cause exception when Export Assembly resulted in 0 contigs (e.g. due to filtering) --- Release notes MEGAN6 V6_2_25: --- - Updated manual - Fixed some color-scheme related bugs - Parallelized path extraction and containment calculation in gene-centric assembly --- Release notes MEGAN6 V6_2_24: --- - Fixed by in *use 16S percent identity filter* that caused reads assigned to a non-rank node not to be pushed up the tree to an appropriate node - Added item to color table menu that allows user to turn off *color samples by attribute* --- Release notes MEGAN6 V6_2_23: --- - Added option to normalized comparison to always keep at least a count of 1 when normalizing, this is helpful, say, when comparing results of different algorithms to avoid wrong false negatives --- Release notes MEGAN6 V6_2_22: --- - Fixed bug that prevented use of command-line mode (UE) - User can now choose between different color schemes for heat maps in main viewer and in chart viewer - Fixed bug that prevented color choices to be saved with a document - Fixed bug that prevented import of CVS files - Added option for user to turn on use of "magnitudes", i.e. weights on reads - Fixed a number of other bugs (it might be more accurate to say that I replaced old bugs by new ones…) --- Release notes MEGAN6 V6_2_21: --- - Fixed a bug that caused some alignments to differ by lower vs upper-case letters - Percent identity filter now applies to BLASTX and BLASTP alignments, too - Now remember choice of ColorByPosition or ColorByLabel - Modified KEGG tools so that KO number appears as prefix of label (UE) --- Release notes MEGAN6 V6_2_20: --- - fixed recently introduced bug that prevented use of MEGAN6 UE in command-line mode --- Release notes MEGAN6 V6_2_19: --- - fixed bug in gene-centric assembly dialog that caused Apply button to be disabled - speed up of remove contained contigs in gene-centric assembly --- Release notes MEGAN6 V6_2_18: --- - fixed bug that caused "Show Alignment" menu item to be disabled when it should be enabled - added GUI element to allow users to set up gene centric assembly calculation on any node or any alignment - genetic centric assembly now has filter to remove "contained" contigs whose percent identity to the containing contig is or exceeds "maxPercentIdentity" --- Release notes MEGAN6 V6_2_17: --- - changing the order of samples in the samples viewer now immediately changes the order of samples in the taxonomy and functional viewers. - the color by position flag is now also observed when colouring by attributes. - user mouse interaction in the 3D PCoA viewer how works as expected --- Release notes MEGAN6 V6_2_16: --- - Fixed newly introduced bug that prevented use of Charts in Community Edition --- Release notes MEGAN6 V6_2_15: --- - Fixed bug that caused choice of color table to be lost - Chart drawers now use their preferred scaling option, e.g. word cloud uses sqrt scaling - Added Color By… options to Color Table popup menu for easier access - Fixed a couple of minor bugs --- Release notes MEGAN6 V6_2_14: --- - Fixed bug that caused header and sequence of contigs to appear in a single line - Modified tool bar so now all charts immediately available from viewer toolbar - Updated viewer so that it will hopefully use much less memory that recent updates and should open faster (JTree in new MainViewer side-bar is now built on command) --- Release notes MEGAN6 V6_2_13: --- - Charts now provide multiple color tables - Color table choice is now the property of a document, not of the running program, so different documents can use different color schemes. - Implemented new "Color Classes By Position" option so that e.g. in a bar chart, the first bar gets the first color, the second gets the second etc. - Fixed bug in "Color By Rank" feature - Fixed a number of minor bugs - Cleaned up some of the icons --- Release notes MEGAN6 V6_2_12: --- - More work on new color table feature - Added a number of different color schemes - When color scheme is changed, now ask whether to delete individual changes made --- Release notes MEGAN6 V6_2_11: --- - Fixed bug that caused problems when changing fonts in charts - Added new color schemes (Edit-Preferences-Set Color Scheme…) --- Release notes MEGAN6 V6_2_10: --- - Fixed serious bug in contig containment removal; - Fixed bug in Meganizer that caused program to fail sometimes --- Release notes MEGAN6 V6_2_9: --- - Added filter that removes "contained" contigs from assembly - Fixed bug that impacted KeggViewer Overviewer Tree in UE --- Release notes MEGAN6 V6_2_8: --- - Taxonomy viewer and functional viewers now use same code - This was a major change of code, so might have some unexpected consequences, please notify me (the author) if you notice anything weird - As a result, taxonomy viewer how offers split pane with additional "Overview Tree" and "Heat Map" - This might make the program slower to start up and more memory hungry, but that will soon be fixed - Fixed bug that prevented use of Meganizer in Community Edition - UE now supports use of multiple different taxonomies simultaneously - Meganizer in UE supports arbitrary additional classifications - Updated MacOS and Windows bundled JRE to latest (1.8.0.71) --- Release notes MEGAN6 V6_2_7: --- - Added "report only official ranks" option to BIOM1 output - Minor bug fixes GUI --- Release notes MEGAN6 V6_2_6: --- - Updated MacOS and Windows bundled JRE to latest (1.8.0.66) - Added output of query length to Matches export --- Release notes MEGAN6 V6_2_5: --- - FIXED newly introduced bug that prevented use of functional viewers such as InterPro2GO, SEED, etc - Modified multilevel STAMP export such that missing taxon rank labels are replaced by labels in brackets - Fixed some bugs in new 3D PCoA panel (UE) --- Release notes MEGAN6 V6_2_4: --- - Added new Export to STAMP command that allows both single level and multiple export (the latter for taxonomic data) - Finished implementing 3D PCoA viewer (based on JavaFX) in UE --- Release notes MEGAN6 V6_2_3: --- - added parser for Illumina Reporter output (use "Import From Blast" menu item) --- Release notes MEGAN6 V6_2_2: --- - fixed scale representation in 2D and 3D PCoA plot - added "percent explained" to PCs in PCoA plot - fixed bug in i x j and i x j x k features of PCoA --- Release notes MEGAN6 V6_2_1: --- - Fixed bug in "Compute Taxonomic Profile" that caused failure on first application. - Fixed bug that caused weird counts of Unassigned to sometimes appear after "Compute Taxonomic Profile" - Fixed bug that caused Attributes to be lost when using "Compute Taxonomic Profile" - Some work on 3D PCoA plot: axes labels are now 2D (not 3D) --- Release notes MEGAN6 V6_2: --- - First official non-alpha, non-beta release of MEGAN6 - Added new correlation plot chart drawer to Ultimate Edition - Minor bug fixes --- Release notes MEGAN6 V6_1_42beta: --- - added code that determines BLAST type associated with a given RMA or DAA file, if not already known - this addresses the problem that some commands failed due to "unknown blast mode" - Updated "Extract to New Document" so that progress bar is active and user can cancel, upon cancel, reads extracted so far are placed in new document, --- Release notes MEGAN6 V6_1_41beta: --- - MeganServer JSON format has changed, this version of MEGAN6 has been changed accordingly, older releases will not operate correctly with up-to-date MeganServer instances - Fixed bug in CSV exporter that prevented export of read name to seed-path and similar - Added anti-aliasing to Coffee Bean chart --- Release notes MEGAN6 V6_1_40beta: --- - added first version of correlation coffee bean chart to UE - fixed some chart-enabling related issues - fixed bug that sometimes prevented alignment viewer from being enabled --- Release notes MEGAN6 V6_1_39beta: --- - fixed bug that affected older megan comparison files created using subsampling, causing them to not open correctly, causing weird problems such as missing colors - added triangulation test to Cluster Viewer Options menu --- Release notes MEGAN6 V6_1_38beta: --- - fixed (hopefully?) bug that caused Windows version to throw many null exceptions… - fixed bug in daa2rma and blast2rma that prevented useMagnitude switch from working - fixed bug that prevented export of TaxonName_to_Percent and TaxonPath_to_Percent - removed gi2tax-Nov2015.bin.zip mapping file due to it missing many important taxa, will be recomputed and then added back very soon --- Release notes MEGAN6 V6_1_37beta: --- - fixed bugs related to sample viewer and metadata - added more text on biom format to manual --- Release notes MEGAN6 V6_1_36beta: --- - added icons in Samples Viewer to show which color and shape are being used to represent a given sample - added menu items for setting color and shape for individual samples - updated chart viewer so that percentages are always based on all classes listed in the side bar of the chart viewer, whether enabled or not - numerous bug fixes --- Release notes MEGAN6 V6_1_35beta: --- - fixed bug in paste to sample viewer table on windows - Hide Labels menu item in PCoA viewer now no longer hides biplot and triplot labels - Sizes are no longer added to metadata (there was always problems with this feature) - removed subsampling code (had bugs and is not really necessary) - fixed installer bug that prevented from tools/kegg from being populated with tools - Made "Apply Order to Viewers" more prominent - Added some missing tooltips - updated manual - fixed bug that caused metadata to be listed twice in sample viewer after Extract… command --- Release notes MEGAN6 V6_1_34beta: --- - fixed bug that prevented use of Cluster Analyzer in Community Edition - Check for Update now disables other commands while running --- Release notes MEGAN6 V6_1_33beta: --- - added tools for updating to latest KEGG version from KEGG ftp download for users that have a valid KEGG license - added mapping extension tool - fixed a number of minor bugs --- Release notes MEGAN6 V6_1_32beta: --- - fixed newly introduced bug that prevented Import from Blast from completing - changed default values for daa-meganizer, blast2rma and sam2rma: default min support percent is now 0.01 (not 0, as previously set) --- Release notes MEGAN6 V6_1_31beta: --- - fixed bug that prevented use of cluster viewer for functional analysis - fixed bug that prevented use of meganizer in some cases - improved log output of meganizer, and now also outputs total number of alignments --- Release notes MEGAN6 V6_1_30beta: --- - fixed bug that caused problems for RMA and DAA files in Sample Viewer - Extract to New Document… can now also be applied to meganized DAA files, not just RMA6 files --- Release notes MEGAN6 V6_1_29beta: --- - this is the first beta release, has no expiry date - fixed bug that occurs when an RMA or DAA file is renamed, causing the Sample Viewer to show the old name (or even multiple sample names) - updated NCBI taxonomy to Nov 2015 version - uploaded new GI to taxon-ID mapping file to MEGAN6 download page --- Release notes MEGAN6 V6_1_28alpha: --- - fixed bug that caused export using taxon paths to fail - extended expiry date to Jan 30, 2016 --- Release notes MEGAN6 V6_1_27alpha: --- - fixed serious bug in DAA parser that prevented import of DAA files - fixed serious bug in SampleViewer that caused loss of values entered by hand --- Release notes MEGAN6 V6_1_26alpha: --- - updated SEED hierarchy based on files downloaded from the SEED API in Nov 2015. This is a significant clean-up compared to the previous version. - Minor bug fixes --- Release notes MEGAN6 V6_1_25alpha: --- - Can how export assignment counts as percentages (of counts for all nodes selected) - In transposed chart, percentages are now based on percentages per sample (based on selected nodes), not percentage of reads assigned to a given class (which didn’t really make sense) - InterPro2GO is now recommended functional analyzer - COG analyzer has been updated - KEGG analyzer reflects early 2011 version of KEGG (before licensing changed) - Todo: update SEED analyzer --- Release notes MEGAN6 V6_1_24alpha: --- - Fixed bug the prevented use of "taxonomic profile" in command-line mode --- Release notes MEGAN6 V6_1_23alpha: --- - Added first version of 3D PCoA plot viewer to UE - Fixed fatal bug in DAA-parser and DAA-meganizer (UE) - Fixed recent bug that prevented opening of command input window (UE) - Worked on compatibility issues (windows) - fix minor bugs associated with remote browser - fixed minor bugs associate - added option to turn off notifications --- Release notes MEGAN6 V6_1_22alpha: --- - fixed serious bug in move column left or right in samples viewer - fixed bug that prevented use of sort by sample in samples viewer --- Release notes MEGAN6 V6_1_21alpha: --- - fixed bugs related to opening files in comparison window --- Release notes MEGAN6 V6_1_20alpha: --- - fixed issue that prevented import of additional metadata --- Release notes MEGAN6 V6_1_19alpha: --- - Modified Compare Window to allow comparison of unopened documents - Samples viewer now supports "Compare By Attribute" in which samples that have the same value for a given attribute are pooled and then compared against each other - Samples viewer now supports reordering of attributes and/or samples - Hide and unhide debugged - shape by attribute added - more work on selection color scheme --- Release notes MEGAN6 V6_1_18alpha: --- - fixed numerous "samples viewer" related bugs - changed selection color scheme --- Release notes MEGAN6 V6_1_17alpha: --- - fixed numerous "samples viewer" related bugs --- Release notes MEGAN6 V6_1_16alpha: --- - fixed bug that caused previous version not to start on some systems - fixed bug that caused previous version not to be able to save a file - first version of Excel-like metadata table aka "samples viewer" - more work toward integrating JavaFX --- Release notes MEGAN6 V6_1_15alpha: --- - added daa-meganizer to UE - added notifications - started working on JavaFX integration --- Release notes MEGAN6 V6_1_14alpha: --- - fixed newly introduced bug that caused MEGAN UE to freeze --- Release notes MEGAN6 V6_1_13alpha: --- - fixed java path problem in daa2rma --- Release notes MEGAN6 V6_1_12alpha: --- - added daa2rma script to tools directory - minor bug fixes --- Release notes MEGAN6 V6_1_11alpha: --- - first version of daa2rma parser, this can parse DAA files generated by DIAMOND --- Release notes MEGAN6 V6_1_9alpha: --- - fixed bug that prevented parsing of BlastTab format --- Release notes MEGAN6 V6_1_9alpha: --- - fixed Blast2LCA problem --- Release notes MEGAN6 V6_1_8alpha: --- - updated format produced by 'export blast' so that the output can be parsed by MEGAN - added option to paired reads dialog that explicitly allows reads not to differ by suffix - fixed paired reads related bug that caused 'change lca parameters' to fail - fixed bug that caused turning off of paired reads to be ignored in 'change lca parameters dialog' --- Release notes MEGAN6 V6_1_7alpha: --- - fixed a bug in enable/disable of some menu items in functional viewers - fixed a bug that sometimes caused a black box to appear in saved images in command line mode - updated blast2lca options and output format - some other minor bug fixes - fixed some problems in manual - fixed bug in export read-names to refSeq-ids - added export read-names to reference headers --- Release notes MEGAN6 V6_1_6alpha: --- - Speed up of SAM to RMA and BLAST to RMA computation (but more speed improvements necessary) - Fixed bug in computation of consensus sequence in alignment viewer - Simplified y axis in chart drawing --- Release notes MEGAN6 V6_1_5alpha: --- - fixed new bug that prevented creation of RMA files --- Release notes MEGAN6 V6_1_4alpha: --- - fixed bug introduced in previous version that prevented use of .map files in GI mapping --- Release notes MEGAN6 V6_1_3alpha: --- - more work on GI to ID mapping --- Release notes MEGAN6 V6_1_2alpha: --- - Major speedup of import from BLAST, sam2rma and blast2rma. Is now at least twice as fast. Turning off compression is now an option and gains an additional speed up of 20% (but without compression RMA files are about 4 times the size) --- Release notes MEGAN6 V6_1_1alpha: --- - added Open From URL… to File menu --- Release notes MEGAN6 V6_1_0alpha: --- - fixed bug caused by removal of taxon "Beta" - fixed some bugs associated with missing metadata - fixed bug that caused different copies of the same file to be considered one copy (and thus opened read-only) - added open from URL command in remote browser - updated registration code capture --- Release notes MEGAN6 V6_0_20alpha: --- - fixed two bugs in sam2rma - fixed bug that caused "uptodate" message even when not uptodate --- Release notes MEGAN6 V6_0_19alpha: --- - updated manual to MEGAN6 - fixed bug that prevented command line image generation for KEGG and other functional viewers - updated MeganServer access --- Release notes MEGAN6 V6_0_18alpha: --- - added min percent identity filter - fixed broken URL links - fixed minor bug in BIOM export - other small fixes --- Release notes MEGAN6 V6_0_17alpha: --- - more work on BIOM format - added Help menu --- Release notes MEGAN6 V6_0_16alpha: --- - More work on BIOM problems… - Fixed bug that caused read magnitudes to be ignored - Fixed bug associated with chart attributes command - Fixed progress bar bug in export assembly - Remote file browser displays descriptions as tool tips (if available) --- Release notes MEGAN6 V6_0_15alpha: --- - fixed bugs in BIOM import and export - more work on times series viewer - some work on remote file browser --- Release notes MEGAN6 V6_0_14alpha: --- - fixed a missing libraries issue (introduced in a very recent release) that broke a number of features --- Release notes MEGAN6 V6_0_13alpha: --- - another attempt to fix BIOM export --- Release notes MEGAN6 V6_0_12alpha: --- - fixed bug that prevented export BIOM - Added new group comparison and more work on time series viewer - modified remote file access to choose not to save credentials - remote file access does not display password --- Release notes MEGAN6 V6_0_11alpha: --- - assembly algorithm aims at path that maximizes total overlap of reads - minor bug fixes and clean up of export methods --- Release notes MEGAN6 V6_0_10alpha: --- - modified "List Paths" command so that it lists number of reads summarized at each path - Added blast2rma tool - Fixed bugs in sam2rma tool --- Release notes MEGAN6 V6_0_9alpha: --- - bug fix in Extract Reads… menu item - bug fix in Sample Viewer tables - added option to list command that allows one to list to a file - changed syntax of list commands - started work on Times Series Viewer (but not operating yet) --- Release notes MEGAN6 V6_0_8alpha: --- - fixed bug in Import CSV dialog - fixed bug in set context command (UE) --- Release notes MEGAN6 V6_0_7alpha: --- - Improved Export Tree command so that it uses the labels as displayed in the viewer and also work for the functional viewers - fixed bug that prevented the Set Context command from appearing (UE) --- Release notes MEGAN6 V6_0_6alpha: --- - fixed bug that prevented MEGAN from correctly accepting BLAST files that have no suffix - fixed bug that prevented parsing of BLAST files - fixed bug that broke some of the alignment context menu items --- Release notes MEGAN6 V6_0_5alpha: --- - set license to GPL3 - fixed minor bugs - updated Voronoi tree map (UE) --- Release notes MEGAN6 V6_0_4alpha: --- - some bug fixes - updated default MeganServer URL - updated license to GPL --- Release notes MEGAN6 V6_0_3alpha: --- - fixed bug that prevented export of overlap graph on older datasets - modified find algorithm to also take node ids (when displayed) into account --- Release notes MEGAN6 V6_0_2alpha: --- - Updated license text - Fixed bug that prevented Voronoi tree from working (UE) - Fixed bug in Overlap Graph exporter - Other bug fixes - Added readName_to_taxonMatches CSV export option --- Release notes MEGAN6 V6_0_1alpha: --- - early alpha version of MEGAN6 - fixed numerous bugs - Export of overlap graph seems to work --- Release notes MEGAN6 V6_0_0alpha: --- - New file format RMA6. Much faster to construct and uses less space than previous RMA versions, this included rewriting all BLAST importers - Rewrote all functional viewers - Rewrote read and taxon show commands in inspector - RAPSearch2 alignments can now be loaded into Alignment Viewer - XML alignments are now correctly formatted and can be loaded into the Alignment Viewer - Dots in RAPSearch2 queries are replaced by Xs - Parsing of RDP and similar taxonomic paths improved, now maps path to lowest taxon that lies in an NCBI path that is consistent with the RDP path - Much faster "Extract to New Document" command --- Release notes MEGAN6 V6_1_42beta: --- - added code that determines BLAST type associated with a given RMA or DAA file, if not already known - this addresses the problem that some commands failed due to "unknown blast mode" - Updated "Extract to New Document" so that progress bar is active and user can cancel, upon cancel, reads extracted so far are placed in new document, --- Release notes MEGAN6 V6_1_41beta: --- - MeganServer JSON format has changed, this version of MEGAN6 has been changed accordingly, older releases will not operate correctly with up-to-date MeganServer instances - Fixed bug in CSV exporter that prevented export of read name to seed-path and similar - Added anti-aliasing to Coffee Bean chart --- Release notes MEGAN6 V6_1_40beta: --- - added first version of correlation coffee bean chart to UE - fixed some chart-enabling related issues - fixed bug that sometimes prevented alignment viewer from being enabled --- Release notes MEGAN6 V6_1_39beta: --- - fixed bug that affected older megan comparison files created using subsampling, causing them to not open correctly, causing weird problems such as missing colors - added triangulation test to Cluster Viewer Options menu --- Release notes MEGAN6 V6_1_38beta: --- - fixed (hopefully?) bug that caused Windows version to throw many null exceptions… - fixed bug in daa2rma and blast2rma that prevented useMagnitude switch from working - fixed bug that prevented export of TaxonName_to_Percent and TaxonPath_to_Percent - removed gi2tax-Nov2015.bin.zip mapping file due to it missing many important taxa, will be recomputed and then added back very soon --- Release notes MEGAN6 V6_1_37beta: --- - fixed bugs related to sample viewer and metadata - added more text on biom format to manual --- Release notes MEGAN6 V6_1_36beta: --- - added icons in Samples Viewer to show which color and shape are being used to represent a given sample - added menu items for setting color and shape for individual samples - updated chart viewer so that percentages are always based on all classes listed in the side bar of the chart viewer, whether enabled or not - numerous bug fixes --- Release notes MEGAN6 V6_1_35beta: --- - fixed bug in paste to sample viewer table on windows - Hide Labels menu item in PCoA viewer now no longer hides biplot and triplot labels - Sizes are no longer added to metadata (there was always problems with this feature) - removed subsampling code (had bugs and is not really necessary) - fixed installer bug that prevented from tools/kegg from being populated with tools - Made "Apply Order to Viewers" more prominent - Added some missing tooltips - updated manual - fixed bug that caused metadata to be listed twice in sample viewer after Extract… command --- Release notes MEGAN6 V6_1_34beta: --- - fixed bug that prevented use of Cluster Analyzer in Community Edition - Check for Update now disables other commands while running --- Release notes MEGAN6 V6_1_33beta: --- - added tools for updating to latest KEGG version from KEGG ftp download for users that have a valid KEGG license - added mapping extension tool - fixed a number of minor bugs --- Release notes MEGAN6 V6_1_32beta: --- - fixed newly introduced bug that prevented Import from Blast from completing - changed default values for daa-meganizer, blast2rma and sam2rma: default min support percent is now 0.01 (not 0, as previously set) --- Release notes MEGAN6 V6_1_31beta: --- - fixed bug that prevented use of cluster viewer for functional analysis - fixed bug that prevented use of meganizer in some cases - improved log output of meganizer, and now also outputs total number of alignments --- Release notes MEGAN6 V6_1_30beta: --- - fixed bug that caused problems for RMA and DAA files in Sample Viewer - Extract to New Document… can now also be applied to meganized DAA files, not just RMA6 files --- Release notes MEGAN6 V6_1_29beta: --- - this is the first beta release, has no expiry date - fixed bug that occurs when an RMA or DAA file is renamed, causing the Sample Viewer to show the old name (or even multiple sample names) - updated NCBI taxonomy to Nov 2015 version - uploaded new GI to taxon-ID mapping file to MEGAN6 download page --- Release notes MEGAN6 V6_1_28alpha: --- - fixed bug that caused export using taxon paths to fail - extended expiry date to Jan 30, 2016 --- Release notes MEGAN6 V6_1_27alpha: --- - fixed serious bug in DAA parser that prevented import of DAA files - fixed serious bug in SampleViewer that caused loss of values entered by hand --- Release notes MEGAN6 V6_1_26alpha: --- - updated SEED hierarchy based on files downloaded from the SEED API in Nov 2015. This is a significant clean-up compared to the previous version. - Minor bug fixes --- Release notes MEGAN6 V6_1_25alpha: --- - Can how export assignment counts as percentages (of counts for all nodes selected) - In transposed chart, percentages are now based on percentages per sample (based on selected nodes), not percentage of reads assigned to a given class (which didn’t really make sense) - InterPro2GO is now recommended functional analyzer - COG analyzer has been updated - KEGG analyzer reflects early 2011 version of KEGG (before licensing changed) - Todo: update SEED analyzer --- Release notes MEGAN6 V6_1_24alpha: --- - Fixed bug the prevented use of "taxonomic profile" in command-line mode --- Release notes MEGAN6 V6_1_23alpha: --- - Added first version of 3D PCoA plot viewer to UE - Fixed fatal bug in DAA-parser and DAA-meganizer (UE) - Fixed recent bug that prevented opening of command input window (UE) - Worked on compatibility issues (windows) - fix minor bugs associated with remote browser - fixed minor bugs associate - added option to turn off notifications --- Release notes MEGAN6 V6_1_22alpha: --- - fixed serious bug in move column left or right in samples viewer - fixed bug that prevented use of sort by sample in samples viewer --- Release notes MEGAN6 V6_1_21alpha: --- - fixed bugs related to opening files in comparison window --- Release notes MEGAN6 V6_1_20alpha: --- - fixed issue that prevented import of additional metadata --- Release notes MEGAN6 V6_1_19alpha: --- - Modified Compare Window to allow comparison of unopened documents - Samples viewer now supports "Compare By Attribute" in which samples that have the same value for a given attribute are pooled and then compared against each other - Samples viewer now supports reordering of attributes and/or samples - Hide and unhide debugged - shape by attribute added - more work on selection color scheme --- Release notes MEGAN6 V6_1_18alpha: --- - fixed numerous "samples viewer" related bugs - changed selection color scheme --- Release notes MEGAN6 V6_1_17alpha: --- - fixed numerous "samples viewer" related bugs --- Release notes MEGAN6 V6_1_16alpha: --- - fixed bug that caused previous version not to start on some systems - fixed bug that caused previous version not to be able to save a file - first version of Excel-like metadata table aka "samples viewer" - more work toward integrating JavaFX --- Release notes MEGAN6 V6_1_15alpha: --- - added daa-meganizer to UE - added notifications - started working on JavaFX integration --- Release notes MEGAN6 V6_1_14alpha: --- - fixed newly introduced bug that caused MEGAN UE to freeze --- Release notes MEGAN6 V6_1_13alpha: --- - fixed java path problem in daa2rma --- Release notes MEGAN6 V6_1_12alpha: --- - added daa2rma script to tools directory - minor bug fixes --- Release notes MEGAN6 V6_1_11alpha: --- - first version of daa2rma parser, this can parse DAA files generated by DIAMOND --- Release notes MEGAN6 V6_1_9alpha: --- - fixed bug that prevented parsing of BlastTab format --- Release notes MEGAN6 V6_1_9alpha: --- - fixed Blast2LCA problem --- Release notes MEGAN6 V6_1_8alpha: --- - updated format produced by 'export blast' so that the output can be parsed by MEGAN - added option to paired reads dialog that explicitly allows reads not to differ by suffix - fixed paired reads related bug that caused 'change lca parameters' to fail - fixed bug that caused turning off of paired reads to be ignored in 'change lca parameters dialog' --- Release notes MEGAN6 V6_1_7alpha: --- - fixed a bug in enable/disable of some menu items in functional viewers - fixed a bug that sometimes caused a black box to appear in saved images in command line mode - updated blast2lca options and output format - some other minor bug fixes - fixed some problems in manual - fixed bug in export read-names to refSeq-ids - added export read-names to reference headers --- Release notes MEGAN6 V6_1_6alpha: --- - Speed up of SAM to RMA and BLAST to RMA computation (but more speed improvements necessary) - Fixed bug in computation of consensus sequence in alignment viewer - Simplified y axis in chart drawing --- Release notes MEGAN6 V6_1_5alpha: --- - fixed new bug that prevented creation of RMA files --- Release notes MEGAN6 V6_1_4alpha: --- - fixed bug introduced in previous version that prevented use of .map files in GI mapping --- Release notes MEGAN6 V6_1_3alpha: --- - more work on GI to ID mapping --- Release notes MEGAN6 V6_1_2alpha: --- - Major speedup of import from BLAST, sam2rma and blast2rma. Is now at least twice as fast. Turning off compression is now an option and gains an additional speed up of 20% (but without compression RMA files are about 4 times the size) --- Release notes MEGAN6 V6_1_1alpha: --- - added Open From URL… to File menu --- Release notes MEGAN6 V6_1_0alpha: --- - fixed bug caused by removal of taxon "Beta" - fixed some bugs associated with missing metadata - fixed bug that caused different copies of the same file to be considered one copy (and thus opened read-only) - added open from URL command in remote browser - updated registration code capture --- Release notes MEGAN6 V6_0_20alpha: --- - fixed two bugs in sam2rma - fixed bug that caused "uptodate" message even when not uptodate --- Release notes MEGAN6 V6_0_19alpha: --- - updated manual to MEGAN6 - fixed bug that prevented command line image generation for KEGG and other functional viewers - updated MeganServer access --- Release notes MEGAN6 V6_0_18alpha: --- - added min percent identity filter - fixed broken URL links - fixed minor bug in BIOM export - other small fixes --- Release notes MEGAN6 V6_0_17alpha: --- - more work on BIOM format - added Help menu --- Release notes MEGAN6 V6_0_16alpha: --- - More work on BIOM problems… - Fixed bug that caused read magnitudes to be ignored - Fixed bug associated with chart attributes command - Fixed progress bar bug in export assembly - Remote file browser displays descriptions as tool tips (if available) --- Release notes MEGAN6 V6_0_15alpha: --- - fixed bugs in BIOM import and export - more work on times series viewer - some work on remote file browser --- Release notes MEGAN6 V6_0_14alpha: --- - fixed a missing libraries issue (introduced in a very recent release) that broke a number of features --- Release notes MEGAN6 V6_0_13alpha: --- - another attempt to fix BIOM export --- Release notes MEGAN6 V6_0_12alpha: --- - fixed bug that prevented export BIOM - Added new group comparison and more work on time series viewer - modified remote file access to choose not to save credentials - remote file access does not display password --- Release notes MEGAN6 V6_0_11alpha: --- - assembly algorithm aims at path that maximizes total overlap of reads - minor bug fixes and clean up of export methods --- Release notes MEGAN6 V6_0_10alpha: --- - modified "List Paths" command so that it lists number of reads summarized at each path - Added blast2rma tool - Fixed bugs in sam2rma tool --- Release notes MEGAN6 V6_0_9alpha: --- - bug fix in Extract Reads… menu item - bug fix in Sample Viewer tables - added option to list command that allows one to list to a file - changed syntax of list commands - started work on Times Series Viewer (but not operating yet) --- Release notes MEGAN6 V6_0_8alpha: --- - fixed bug in Import CSV dialog - fixed bug in set context command (UE) --- Release notes MEGAN6 V6_0_7alpha: --- - Improved Export Tree command so that it uses the labels as displayed in the viewer and also work for the functional viewers - fixed bug that prevented the Set Context command from appearing (UE) --- Release notes MEGAN6 V6_0_6alpha: --- - fixed bug that prevented MEGAN from correctly accepting BLAST files that have no suffix - fixed bug that prevented parsing of BLAST files - fixed bug that broke some of the alignment context menu items --- Release notes MEGAN6 V6_0_5alpha: --- - set license to GPL3 - fixed minor bugs - updated Voronoi tree map (UE) --- Release notes MEGAN6 V6_0_4alpha: --- - some bug fixes - updated default MeganServer URL - updated license to GPL --- Release notes MEGAN6 V6_0_3alpha: --- - fixed bug that prevented export of overlap graph on older datasets - modified find algorithm to also take node ids (when displayed) into account --- Release notes MEGAN6 V6_0_2alpha: --- - Updated license text - Fixed bug that prevented Voronoi tree from working (UE) - Fixed bug in Overlap Graph exporter - Other bug fixes - Added readName_to_taxonMatches CSV export option --- Release notes MEGAN6 V6_0_1alpha: --- - early alpha version of MEGAN6 - fixed numerous bugs - Export of overlap graph seems to work --- Release notes MEGAN6 V6_0_0alpha: --- - New file format RMA6. Much faster to construct and uses less space than previous RMA versions, this included rewriting all BLAST importers - Rewrote all functional viewers - Rewrote read and taxon show commands in inspector - RAPSearch2 alignments can now be loaded into Alignment Viewer - XML alignments are now correctly formatted and can be loaded into the Alignment Viewer - Dots in RAPSearch2 queries are replaced by Xs - Parsing of RDP and similar taxonomic paths improved, now maps path to lowest taxon that lies in an NCBI path that is consistent with the RDP path - Much faster "Extract to New Document" command --- Release notes MEGAN6 V6_1_42beta: --- - added code that determines BLAST type associated with a given RMA or DAA file, if not already known - this addresses the problem that some commands failed due to "unknown blast mode" - Updated "Extract to New Document" so that progress bar is active and user can cancel, upon cancel, reads extracted so far are placed in new document, --- Release notes MEGAN6 V6_1_41beta: --- - MeganServer JSON format has changed, this version of MEGAN6 has been changed accordingly, older releases will not operate correctly with up-to-date MeganServer instances - Fixed bug in CSV exporter that prevented export of read name to seed-path and similar - Added anti-aliasing to Coffee Bean chart --- Release notes MEGAN6 V6_1_40beta: --- - added first version of correlation coffee bean chart to UE - fixed some chart-enabling related issues - fixed bug that sometimes prevented alignment viewer from being enabled --- Release notes MEGAN6 V6_1_39beta: --- - fixed bug that affected older megan comparison files created using subsampling, causing them to not open correctly, causing weird problems such as missing colors - added triangulation test to Cluster Viewer Options menu --- Release notes MEGAN6 V6_1_38beta: --- - fixed (hopefully?) bug that caused Windows version to throw many null exceptions… - fixed bug in daa2rma and blast2rma that prevented useMagnitude switch from working - fixed bug that prevented export of TaxonName_to_Percent and TaxonPath_to_Percent - removed gi2tax-Nov2015.bin.zip mapping file due to it missing many important taxa, will be recomputed and then added back very soon --- Release notes MEGAN6 V6_1_37beta: --- - fixed bugs related to sample viewer and metadata - added more text on biom format to manual --- Release notes MEGAN6 V6_1_36beta: --- - added icons in Samples Viewer to show which color and shape are being used to represent a given sample - added menu items for setting color and shape for individual samples - updated chart viewer so that percentages are always based on all classes listed in the side bar of the chart viewer, whether enabled or not - numerous bug fixes --- Release notes MEGAN6 V6_1_35beta: --- - fixed bug in paste to sample viewer table on windows - Hide Labels menu item in PCoA viewer now no longer hides biplot and triplot labels - Sizes are no longer added to metadata (there was always problems with this feature) - removed subsampling code (had bugs and is not really necessary) - fixed installer bug that prevented from tools/kegg from being populated with tools - Made "Apply Order to Viewers" more prominent - Added some missing tooltips - updated manual - fixed bug that caused metadata to be listed twice in sample viewer after Extract… command --- Release notes MEGAN6 V6_1_34beta: --- - fixed bug that prevented use of Cluster Analyzer in Community Edition - Check for Update now disables other commands while running --- Release notes MEGAN6 V6_1_33beta: --- - added tools for updating to latest KEGG version from KEGG ftp download for users that have a valid KEGG license - added mapping extension tool - fixed a number of minor bugs --- Release notes MEGAN6 V6_1_32beta: --- - fixed newly introduced bug that prevented Import from Blast from completing - changed default values for daa-meganizer, blast2rma and sam2rma: default min support percent is now 0.01 (not 0, as previously set) --- Release notes MEGAN6 V6_1_31beta: --- - fixed bug that prevented use of cluster viewer for functional analysis - fixed bug that prevented use of meganizer in some cases - improved log output of meganizer, and now also outputs total number of alignments --- Release notes MEGAN6 V6_1_30beta: --- - fixed bug that caused problems for RMA and DAA files in Sample Viewer - Extract to New Document… can now also be applied to meganized DAA files, not just RMA6 files --- Release notes MEGAN6 V6_1_29beta: --- - this is the first beta release, has no expiry date - fixed bug that occurs when an RMA or DAA file is renamed, causing the Sample Viewer to show the old name (or even multiple sample names) - updated NCBI taxonomy to Nov 2015 version - uploaded new GI to taxon-ID mapping file to MEGAN6 download page --- Release notes MEGAN6 V6_1_28alpha: --- - fixed bug that caused export using taxon paths to fail - extended expiry date to Jan 30, 2016 --- Release notes MEGAN6 V6_1_27alpha: --- - fixed serious bug in DAA parser that prevented import of DAA files - fixed serious bug in SampleViewer that caused loss of values entered by hand --- Release notes MEGAN6 V6_1_26alpha: --- - updated SEED hierarchy based on files downloaded from the SEED API in Nov 2015. This is a significant clean-up compared to the previous version. - Minor bug fixes --- Release notes MEGAN6 V6_1_25alpha: --- - Can how export assignment counts as percentages (of counts for all nodes selected) - In transposed chart, percentages are now based on percentages per sample (based on selected nodes), not percentage of reads assigned to a given class (which didn’t really make sense) - InterPro2GO is now recommended functional analyzer - COG analyzer has been updated - KEGG analyzer reflects early 2011 version of KEGG (before licensing changed) - Todo: update SEED analyzer --- Release notes MEGAN6 V6_1_24alpha: --- - Fixed bug the prevented use of "taxonomic profile" in command-line mode --- Release notes MEGAN6 V6_1_23alpha: --- - Added first version of 3D PCoA plot viewer to UE - Fixed fatal bug in DAA-parser and DAA-meganizer (UE) - Fixed recent bug that prevented opening of command input window (UE) - Worked on compatibility issues (windows) - fix minor bugs associated with remote browser - fixed minor bugs associate - added option to turn off notifications --- Release notes MEGAN6 V6_1_22alpha: --- - fixed serious bug in move column left or right in samples viewer - fixed bug that prevented use of sort by sample in samples viewer --- Release notes MEGAN6 V6_1_21alpha: --- - fixed bugs related to opening files in comparison window --- Release notes MEGAN6 V6_1_20alpha: --- - fixed issue that prevented import of additional metadata --- Release notes MEGAN6 V6_1_19alpha: --- - Modified Compare Window to allow comparison of unopened documents - Samples viewer now supports "Compare By Attribute" in which samples that have the same value for a given attribute are pooled and then compared against each other - Samples viewer now supports reordering of attributes and/or samples - Hide and unhide debugged - shape by attribute added - more work on selection color scheme --- Release notes MEGAN6 V6_1_18alpha: --- - fixed numerous "samples viewer" related bugs - changed selection color scheme --- Release notes MEGAN6 V6_1_17alpha: --- - fixed numerous "samples viewer" related bugs --- Release notes MEGAN6 V6_1_16alpha: --- - fixed bug that caused previous version not to start on some systems - fixed bug that caused previous version not to be able to save a file - first version of Excel-like metadata table aka "samples viewer" - more work toward integrating JavaFX --- Release notes MEGAN6 V6_1_15alpha: --- - added daa-meganizer to UE - added notifications - started working on JavaFX integration --- Release notes MEGAN6 V6_1_14alpha: --- - fixed newly introduced bug that caused MEGAN UE to freeze --- Release notes MEGAN6 V6_1_13alpha: --- - fixed java path problem in daa2rma --- Release notes MEGAN6 V6_1_12alpha: --- - added daa2rma script to tools directory - minor bug fixes --- Release notes MEGAN6 V6_1_11alpha: --- - first version of daa2rma parser, this can parse DAA files generated by DIAMOND --- Release notes MEGAN6 V6_1_9alpha: --- - fixed bug that prevented parsing of BlastTab format --- Release notes MEGAN6 V6_1_9alpha: --- - fixed Blast2LCA problem --- Release notes MEGAN6 V6_1_8alpha: --- - updated format produced by 'export blast' so that the output can be parsed by MEGAN - added option to paired reads dialog that explicitly allows reads not to differ by suffix - fixed paired reads related bug that caused 'change lca parameters' to fail - fixed bug that caused turning off of paired reads to be ignored in 'change lca parameters dialog' --- Release notes MEGAN6 V6_1_7alpha: --- - fixed a bug in enable/disable of some menu items in functional viewers - fixed a bug that sometimes caused a black box to appear in saved images in command line mode - updated blast2lca options and output format - some other minor bug fixes - fixed some problems in manual - fixed bug in export read-names to refSeq-ids - added export read-names to reference headers --- Release notes MEGAN6 V6_1_6alpha: --- - Speed up of SAM to RMA and BLAST to RMA computation (but more speed improvements necessary) - Fixed bug in computation of consensus sequence in alignment viewer - Simplified y axis in chart drawing --- Release notes MEGAN6 V6_1_5alpha: --- - fixed new bug that prevented creation of RMA files --- Release notes MEGAN6 V6_1_4alpha: --- - fixed bug introduced in previous version that prevented use of .map files in GI mapping --- Release notes MEGAN6 V6_1_3alpha: --- - more work on GI to ID mapping --- Release notes MEGAN6 V6_1_2alpha: --- - Major speedup of import from BLAST, sam2rma and blast2rma. Is now at least twice as fast. Turning off compression is now an option and gains an additional speed up of 20% (but without compression RMA files are about 4 times the size) --- Release notes MEGAN6 V6_1_1alpha: --- - added Open From URL… to File menu --- Release notes MEGAN6 V6_1_0alpha: --- - fixed bug caused by removal of taxon "Beta" - fixed some bugs associated with missing metadata - fixed bug that caused different copies of the same file to be considered one copy (and thus opened read-only) - added open from URL command in remote browser - updated registration code capture --- Release notes MEGAN6 V6_0_20alpha: --- - fixed two bugs in sam2rma - fixed bug that caused "uptodate" message even when not uptodate --- Release notes MEGAN6 V6_0_19alpha: --- - updated manual to MEGAN6 - fixed bug that prevented command line image generation for KEGG and other functional viewers - updated MeganServer access --- Release notes MEGAN6 V6_0_18alpha: --- - added min percent identity filter - fixed broken URL links - fixed minor bug in BIOM export - other small fixes --- Release notes MEGAN6 V6_0_17alpha: --- - more work on BIOM format - added Help menu --- Release notes MEGAN6 V6_0_16alpha: --- - More work on BIOM problems… - Fixed bug that caused read magnitudes to be ignored - Fixed bug associated with chart attributes command - Fixed progress bar bug in export assembly - Remote file browser displays descriptions as tool tips (if available) --- Release notes MEGAN6 V6_0_15alpha: --- - fixed bugs in BIOM import and export - more work on times series viewer - some work on remote file browser --- Release notes MEGAN6 V6_0_14alpha: --- - fixed a missing libraries issue (introduced in a very recent release) that broke a number of features --- Release notes MEGAN6 V6_0_13alpha: --- - another attempt to fix BIOM export --- Release notes MEGAN6 V6_0_12alpha: --- - fixed bug that prevented export BIOM - Added new group comparison and more work on time series viewer - modified remote file access to choose not to save credentials - remote file access does not display password --- Release notes MEGAN6 V6_0_11alpha: --- - assembly algorithm aims at path that maximizes total overlap of reads - minor bug fixes and clean up of export methods --- Release notes MEGAN6 V6_0_10alpha: --- - modified "List Paths" command so that it lists number of reads summarized at each path - Added blast2rma tool - Fixed bugs in sam2rma tool --- Release notes MEGAN6 V6_0_9alpha: --- - bug fix in Extract Reads… menu item - bug fix in Sample Viewer tables - added option to list command that allows one to list to a file - changed syntax of list commands - started work on Times Series Viewer (but not operating yet) --- Release notes MEGAN6 V6_0_8alpha: --- - fixed bug in Import CSV dialog - fixed bug in set context command (UE) --- Release notes MEGAN6 V6_0_7alpha: --- - Improved Export Tree command so that it uses the labels as displayed in the viewer and also work for the functional viewers - fixed bug that prevented the Set Context command from appearing (UE) --- Release notes MEGAN6 V6_0_6alpha: --- - fixed bug that prevented MEGAN from correctly accepting BLAST files that have no suffix - fixed bug that prevented parsing of BLAST files - fixed bug that broke some of the alignment context menu items --- Release notes MEGAN6 V6_0_5alpha: --- - set license to GPL3 - fixed minor bugs - updated Voronoi tree map (UE) --- Release notes MEGAN6 V6_0_4alpha: --- - some bug fixes - updated default MeganServer URL - updated license to GPL --- Release notes MEGAN6 V6_0_3alpha: --- - fixed bug that prevented export of overlap graph on older datasets - modified find algorithm to also take node ids (when displayed) into account --- Release notes MEGAN6 V6_0_2alpha: --- - Updated license text - Fixed bug that prevented Voronoi tree from working (UE) - Fixed bug in Overlap Graph exporter - Other bug fixes - Added readName_to_taxonMatches CSV export option --- Release notes MEGAN6 V6_0_1alpha: --- - early alpha version of MEGAN6 - fixed numerous bugs - Export of overlap graph seems to work --- Release notes MEGAN6 V6_0_0alpha: --- - New file format RMA6. Much faster to construct and uses less space than previous RMA versions, this included rewriting all BLAST importers - Rewrote all functional viewers - Rewrote read and taxon show commands in inspector - RAPSearch2 alignments can now be loaded into Alignment Viewer - XML alignments are now correctly formatted and can be loaded into the Alignment Viewer - Dots in RAPSearch2 queries are replaced by Xs - Parsing of RDP and similar taxonomic paths improved, now maps path to lowest taxon that lies in an NCBI path that is consistent with the RDP path - Much faster "Extract to New Document" command --- Release notes MEGAN6 V6_1_42beta: --- - added code that determines BLAST type associated with a given RMA or DAA file, if not already known - this addresses the problem that some commands failed due to "unknown blast mode" - Updated "Extract to New Document" so that progress bar is active and user can cancel, upon cancel, reads extracted so far are placed in new document, --- Release notes MEGAN6 V6_1_41beta: --- - MeganServer JSON format has changed, this version of MEGAN6 has been changed accordingly, older releases will not operate correctly with up-to-date MeganServer instances - Fixed bug in CSV exporter that prevented export of read name to seed-path and similar - Added anti-aliasing to Coffee Bean chart --- Release notes MEGAN6 V6_1_40beta: --- - added first version of correlation coffee bean chart to UE - fixed some chart-enabling related issues - fixed bug that sometimes prevented alignment viewer from being enabled --- Release notes MEGAN6 V6_1_39beta: --- - fixed bug that affected older megan comparison files created using subsampling, causing them to not open correctly, causing weird problems such as missing colors - added triangulation test to Cluster Viewer Options menu --- Release notes MEGAN6 V6_1_38beta: --- - fixed (hopefully?) bug that caused Windows version to throw many null exceptions… - fixed bug in daa2rma and blast2rma that prevented useMagnitude switch from working - fixed bug that prevented export of TaxonName_to_Percent and TaxonPath_to_Percent - removed gi2tax-Nov2015.bin.zip mapping file due to it missing many important taxa, will be recomputed and then added back very soon --- Release notes MEGAN6 V6_1_37beta: --- - fixed bugs related to sample viewer and metadata - added more text on biom format to manual --- Release notes MEGAN6 V6_1_36beta: --- - added icons in Samples Viewer to show which color and shape are being used to represent a given sample - added menu items for setting color and shape for individual samples - updated chart viewer so that percentages are always based on all classes listed in the side bar of the chart viewer, whether enabled or not - numerous bug fixes --- Release notes MEGAN6 V6_1_35beta: --- - fixed bug in paste to sample viewer table on windows - Hide Labels menu item in PCoA viewer now no longer hides biplot and triplot labels - Sizes are no longer added to metadata (there was always problems with this feature) - removed subsampling code (had bugs and is not really necessary) - fixed installer bug that prevented from tools/kegg from being populated with tools - Made "Apply Order to Viewers" more prominent - Added some missing tooltips - updated manual - fixed bug that caused metadata to be listed twice in sample viewer after Extract… command --- Release notes MEGAN6 V6_1_34beta: --- - fixed bug that prevented use of Cluster Analyzer in Community Edition - Check for Update now disables other commands while running --- Release notes MEGAN6 V6_1_33beta: --- - added tools for updating to latest KEGG version from KEGG ftp download for users that have a valid KEGG license - added mapping extension tool - fixed a number of minor bugs --- Release notes MEGAN6 V6_1_32beta: --- - fixed newly introduced bug that prevented Import from Blast from completing - changed default values for daa-meganizer, blast2rma and sam2rma: default min support percent is now 0.01 (not 0, as previously set) --- Release notes MEGAN6 V6_1_31beta: --- - fixed bug that prevented use of cluster viewer for functional analysis - fixed bug that prevented use of meganizer in some cases - improved log output of meganizer, and now also outputs total number of alignments --- Release notes MEGAN6 V6_1_30beta: --- - fixed bug that caused problems for RMA and DAA files in Sample Viewer - Extract to New Document… can now also be applied to meganized DAA files, not just RMA6 files --- Release notes MEGAN6 V6_1_29beta: --- - this is the first beta release, has no expiry date - fixed bug that occurs when an RMA or DAA file is renamed, causing the Sample Viewer to show the old name (or even multiple sample names) - updated NCBI taxonomy to Nov 2015 version - uploaded new GI to taxon-ID mapping file to MEGAN6 download page --- Release notes MEGAN6 V6_1_28alpha: --- - fixed bug that caused export using taxon paths to fail - extended expiry date to Jan 30, 2016 --- Release notes MEGAN6 V6_1_27alpha: --- - fixed serious bug in DAA parser that prevented import of DAA files - fixed serious bug in SampleViewer that caused loss of values entered by hand --- Release notes MEGAN6 V6_1_26alpha: --- - updated SEED hierarchy based on files downloaded from the SEED API in Nov 2015. This is a significant clean-up compared to the previous version. - Minor bug fixes --- Release notes MEGAN6 V6_1_25alpha: --- - Can how export assignment counts as percentages (of counts for all nodes selected) - In transposed chart, percentages are now based on percentages per sample (based on selected nodes), not percentage of reads assigned to a given class (which didn’t really make sense) - InterPro2GO is now recommended functional analyzer - COG analyzer has been updated - KEGG analyzer reflects early 2011 version of KEGG (before licensing changed) - Todo: update SEED analyzer --- Release notes MEGAN6 V6_1_24alpha: --- - Fixed bug the prevented use of "taxonomic profile" in command-line mode --- Release notes MEGAN6 V6_1_23alpha: --- - Added first version of 3D PCoA plot viewer to UE - Fixed fatal bug in DAA-parser and DAA-meganizer (UE) - Fixed recent bug that prevented opening of command input window (UE) - Worked on compatibility issues (windows) - fix minor bugs associated with remote browser - fixed minor bugs associate - added option to turn off notifications --- Release notes MEGAN6 V6_1_22alpha: --- - fixed serious bug in move column left or right in samples viewer - fixed bug that prevented use of sort by sample in samples viewer --- Release notes MEGAN6 V6_1_21alpha: --- - fixed bugs related to opening files in comparison window --- Release notes MEGAN6 V6_1_20alpha: --- - fixed issue that prevented import of additional metadata --- Release notes MEGAN6 V6_1_19alpha: --- - Modified Compare Window to allow comparison of unopened documents - Samples viewer now supports "Compare By Attribute" in which samples that have the same value for a given attribute are pooled and then compared against each other - Samples viewer now supports reordering of attributes and/or samples - Hide and unhide debugged - shape by attribute added - more work on selection color scheme --- Release notes MEGAN6 V6_1_18alpha: --- - fixed numerous "samples viewer" related bugs - changed selection color scheme --- Release notes MEGAN6 V6_1_17alpha: --- - fixed numerous "samples viewer" related bugs --- Release notes MEGAN6 V6_1_16alpha: --- - fixed bug that caused previous version not to start on some systems - fixed bug that caused previous version not to be able to save a file - first version of Excel-like metadata table aka "samples viewer" - more work toward integrating JavaFX --- Release notes MEGAN6 V6_1_15alpha: --- - added daa-meganizer to UE - added notifications - started working on JavaFX integration --- Release notes MEGAN6 V6_1_14alpha: --- - fixed newly introduced bug that caused MEGAN UE to freeze --- Release notes MEGAN6 V6_1_13alpha: --- - fixed java path problem in daa2rma --- Release notes MEGAN6 V6_1_12alpha: --- - added daa2rma script to tools directory - minor bug fixes --- Release notes MEGAN6 V6_1_11alpha: --- - first version of daa2rma parser, this can parse DAA files generated by DIAMOND --- Release notes MEGAN6 V6_1_9alpha: --- - fixed bug that prevented parsing of BlastTab format --- Release notes MEGAN6 V6_1_9alpha: --- - fixed Blast2LCA problem --- Release notes MEGAN6 V6_1_8alpha: --- - updated format produced by 'export blast' so that the output can be parsed by MEGAN - added option to paired reads dialog that explicitly allows reads not to differ by suffix - fixed paired reads related bug that caused 'change lca parameters' to fail - fixed bug that caused turning off of paired reads to be ignored in 'change lca parameters dialog' --- Release notes MEGAN6 V6_1_7alpha: --- - fixed a bug in enable/disable of some menu items in functional viewers - fixed a bug that sometimes caused a black box to appear in saved images in command line mode - updated blast2lca options and output format - some other minor bug fixes - fixed some problems in manual - fixed bug in export read-names to refSeq-ids - added export read-names to reference headers --- Release notes MEGAN6 V6_1_6alpha: --- - Speed up of SAM to RMA and BLAST to RMA computation (but more speed improvements necessary) - Fixed bug in computation of consensus sequence in alignment viewer - Simplified y axis in chart drawing --- Release notes MEGAN6 V6_1_5alpha: --- - fixed new bug that prevented creation of RMA files --- Release notes MEGAN6 V6_1_4alpha: --- - fixed bug introduced in previous version that prevented use of .map files in GI mapping --- Release notes MEGAN6 V6_1_3alpha: --- - more work on GI to ID mapping --- Release notes MEGAN6 V6_1_2alpha: --- - Major speedup of import from BLAST, sam2rma and blast2rma. Is now at least twice as fast. Turning off compression is now an option and gains an additional speed up of 20% (but without compression RMA files are about 4 times the size) --- Release notes MEGAN6 V6_1_1alpha: --- - added Open From URL… to File menu --- Release notes MEGAN6 V6_1_0alpha: --- - fixed bug caused by removal of taxon "Beta" - fixed some bugs associated with missing metadata - fixed bug that caused different copies of the same file to be considered one copy (and thus opened read-only) - added open from URL command in remote browser - updated registration code capture --- Release notes MEGAN6 V6_0_20alpha: --- - fixed two bugs in sam2rma - fixed bug that caused "uptodate" message even when not uptodate --- Release notes MEGAN6 V6_0_19alpha: --- - updated manual to MEGAN6 - fixed bug that prevented command line image generation for KEGG and other functional viewers - updated MeganServer access --- Release notes MEGAN6 V6_0_18alpha: --- - added min percent identity filter - fixed broken URL links - fixed minor bug in BIOM export - other small fixes --- Release notes MEGAN6 V6_0_17alpha: --- - more work on BIOM format - added Help menu --- Release notes MEGAN6 V6_0_16alpha: --- - More work on BIOM problems… - Fixed bug that caused read magnitudes to be ignored - Fixed bug associated with chart attributes command - Fixed progress bar bug in export assembly - Remote file browser displays descriptions as tool tips (if available) --- Release notes MEGAN6 V6_0_15alpha: --- - fixed bugs in BIOM import and export - more work on times series viewer - some work on remote file browser --- Release notes MEGAN6 V6_0_14alpha: --- - fixed a missing libraries issue (introduced in a very recent release) that broke a number of features --- Release notes MEGAN6 V6_0_13alpha: --- - another attempt to fix BIOM export --- Release notes MEGAN6 V6_0_12alpha: --- - fixed bug that prevented export BIOM - Added new group comparison and more work on time series viewer - modified remote file access to choose not to save credentials - remote file access does not display password --- Release notes MEGAN6 V6_0_11alpha: --- - assembly algorithm aims at path that maximizes total overlap of reads - minor bug fixes and clean up of export methods --- Release notes MEGAN6 V6_0_10alpha: --- - modified "List Paths" command so that it lists number of reads summarized at each path - Added blast2rma tool - Fixed bugs in sam2rma tool --- Release notes MEGAN6 V6_0_9alpha: --- - bug fix in Extract Reads… menu item - bug fix in Sample Viewer tables - added option to list command that allows one to list to a file - changed syntax of list commands - started work on Times Series Viewer (but not operating yet) --- Release notes MEGAN6 V6_0_8alpha: --- - fixed bug in Import CSV dialog - fixed bug in set context command (UE) --- Release notes MEGAN6 V6_0_7alpha: --- - Improved Export Tree command so that it uses the labels as displayed in the viewer and also work for the functional viewers - fixed bug that prevented the Set Context command from appearing (UE) --- Release notes MEGAN6 V6_0_6alpha: --- - fixed bug that prevented MEGAN from correctly accepting BLAST files that have no suffix - fixed bug that prevented parsing of BLAST files - fixed bug that broke some of the alignment context menu items --- Release notes MEGAN6 V6_0_5alpha: --- - set license to GPL3 - fixed minor bugs - updated Voronoi tree map (UE) --- Release notes MEGAN6 V6_0_4alpha: --- - some bug fixes - updated default MeganServer URL - updated license to GPL --- Release notes MEGAN6 V6_0_3alpha: --- - fixed bug that prevented export of overlap graph on older datasets - modified find algorithm to also take node ids (when displayed) into account --- Release notes MEGAN6 V6_0_2alpha: --- - Updated license text - Fixed bug that prevented Voronoi tree from working (UE) - Fixed bug in Overlap Graph exporter - Other bug fixes - Added readName_to_taxonMatches CSV export option --- Release notes MEGAN6 V6_0_1alpha: --- - early alpha version of MEGAN6 - fixed numerous bugs - Export of overlap graph seems to work --- Release notes MEGAN6 V6_0_0alpha: --- - New file format RMA6. Much faster to construct and uses less space than previous RMA versions, this included rewriting all BLAST importers - Rewrote all functional viewers - Rewrote read and taxon show commands in inspector - RAPSearch2 alignments can now be loaded into Alignment Viewer - XML alignments are now correctly formatted and can be loaded into the Alignment Viewer - Dots in RAPSearch2 queries are replaced by Xs - Parsing of RDP and similar taxonomic paths improved, now maps path to lowest taxon that lies in an NCBI path that is consistent with the RDP path - Much faster Extract to New Document command