--- 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