--- Release notes MALT V0_6_3 (Thu, 18 Jul 2024): --- - fixed bug that prevented finding files in input directory --- Release notes MALT V0_6_2 (Tue, 12 Sep 2023): --- - MALT-build now finds gzipped fasta files in an input directory --- Release notes MALT V0_6_1 (Tue, 25 Oct 2022): --- - fixed bug that prevented user from undoing choice of lcaPercent smaller than 100 --- Release notes MALT V0_6_0 (Tue, 25 Oct 2022): --- - fixed bug that prevented the LCA algorithm from being applied to taxonomic classifications - updated to Java17 --- Release notes MALT V0_5_3 (Wed, 4 Aug 2021): --- CRITICAL update - Recent versions of MaltBuild ignored the taxonomy mapping file, this has been fixed - MaltBuild checks for existence of all input mapping files before running - Exception in gene item accessor has been fixed --- Release notes MALT V0_5_2 (Thu, 28 Jan 2021): --- - MaltRun now first checks whether output files will be writeable and provides a more informative error message if it is not the case --- Release notes MALT V0_5_1 (Tue, 19 Jan 2021): --- - fixed bug that caused negative array size exception if FastA-record larger than 1073741823 --- Release notes MALT V0_5_0 (Wed, 5 Aug 2020): --- - worked on support of mapping db. --- Release notes MALT /V0_3_2: --- - fixed some mapping-related bugs --- Release notes MALT /V0_2_0: --- - replaced memoryMapping option by memoryMode option that takes three values: - load tells program to load all indices at startup - page tells program to load indices page by page as required (good for small query files) - map tells program use memory mapping (good when using dedicated SSD disk) --- Release notes MALT /V0_1_2: --- - fixed fatal error that overwrote query sequence with query quality values when queries over 1000 bp long - added non-memory-mapped mode --- Release notes MALT /V0_1_1: --- - Fixed a bug that caused last lines of reference database to be ignored - Added some verbose output to help track down bugs caused by ONP sequences --- Release notes MALT /V0_1_0: --- - hash table now implemented using memory-mapped files, great reduction of startup time for malt-run - modified SAM output so as to be compatible with sam-tools. Requires MEGAN5.10.0 for parsing - fixed bug in softclipping output - fixed other some other bugs --- Release notes MALT /V0_0_12: --- - Fixed bug introduced in previous version that prevented alignments from appearing in RMA file - Modified SAM MD string so that it contains 0 after every ^ insert --- Release notes MALT /V0_0_11: --- - Fixed bug that caused installer to ignore set memory requriement - Fixed bug that caused SAM alignments to be off by one when alignment started at second or second-to-last position in query - Fixed by in SAM @SQ string - If —minSupportPercent is set then any —minSupport value is overridden - Added option to produce soft-clipped SAM output - Modified malt-run options so that both RMA and alignments can be saved in same run --- Release notes MALT /V0_0_10: --- - Fixed bug that prevented MEGAN from recognizing which LCA parameters were used - Fixed bug that caused hard clip to be missing in SAM cigar - Added feature that puts quality values in SAM output when using BlastN and fastQ --- Release notes MALT /V0_0_9: --- - Fixed bug that caused malt-run to abort on many samples --- Release notes MALT /V0_0_8: --- - Major change to output options (see manual for details), including: - RMA is not a possible output format. This produces a complete RMA file that can be opened in MEGAN - MEGAN profile output no longer supported