Release notes from lambda

Version 3.1.0 [2024/08/26]

2024-08-26T12:32:30Z

This includes the changes used in https://doi.org/10.1093/bioinformatics/btae097

Features

Two new profiles: pairs-default and pairs-sensitive that are useful in combination with higher --num-matches. 6cd1d33
Improvements to the core algorithm. 40b49a0

Notable bug fixes

In edge cases, the alignment coordinates may have been calculated wrongly. f1ebc9a
Proper exception handling. aad68eb
Accept .fna and .faa as extensions for FASTA files. 05262cd

Compatibility

The command line interface is compatible to 3.0.0.
The on-disk format is compatible to 3.0.0.
The output generated for most input files has changed slightly since 3.0.0.

Dependencies

same as for 3.0.0

Version 3.0.0 [2023/07/25]

2023-07-25T21:53:01Z

This is the first release of the new lambda3 branch. It is much faster, offers new features but is not compatible to previous versions.

Version 3.0.0 [2023/07/25]

Features

New program mode for searching bisulphite data.
The nucleotide mode has received much more testing and optimisation.
Huge overhaul of the algorithm; Lambda3 is up to 3x faster than Lambda2 and uses less memory.
Use --profile fast or --profile sensitive to select finetuned parameter combinations that are faster or more sensitive than the default.

Compatibility

The command line interface is very similar to Lambda2's, but some options have been added and some removed.
The on-disk format of the index has changed. You need to recreate your index files or download new ones from the wiki. Indexes are now single files and may be used in compressed state.
GCC-11 or later and -std=c++20 is required to build.
Requires 64bit Intel or AMD CPU with SSE4 and POPCNT instructions.

Dependencies

SeqAn 2.4.1; SeqAn3 is not used anymore
BioC++ Core 0.7.1
BioC++ IO
Cereal 1.3.2
ShargParser-1.0.0
fmindex-collection
all of these requirements are only required at build-time.

Version 2.0.1 [2023/07/18]

2023-07-18T16:50:05Z

features

use --bit-score in addition to or instead of --e-value

bug fixes

fix 32bit builds
bug in BLASTN e-value calculation (slightly changed values)
various typos and documentation fixes
fix dispatcher script on macOS

compatibility

the command line interface is identical to lambda >= 1.9.4
the on-disk index format is compatible to lambda >= 1.9.3
requires seqan >= 2.3.1; binary packages based on seqan-2.4.0
compatible with C++17 if used with seqan >= 2.4.0

Release 2.0.0 [2019/01/11]

2020-11-09T12:44:25Z

First stable release in the 2.x branch. It is identical to 1.9.5.

Pre-Release 1.9.5 [2018/05/30]

2018-05-30T14:59:39Z

bug fixes

BLASTN was broken (#115)
wrong escaping of " and ' in command line arguments (#116)
mixed lower-case / upper-case letters led to error on indexing (#117)
divide-by-zero with very small databases (#118)
lca-computation error with some certain sequences that have no taxonomy information (#119)

compatibility

the command line interface is identical to lambda >= 1.9.4
the on-disk index format is compatible to lambda >= 1.9.3
requires seqan >= 2.3.1; binary packages based on seqan-2.4.0
compatible with C++17 if used with seqan >= 2.4.0

Release 1.0.3 [2018/02/17]

2018-02-17T17:02:09Z

bug-fixes and minor changes

fix build with seqan-2.4.0 (#114)

compatibility

both the interface and the generated index files are fully compatible to the 0.9.* and 1.0.* series
requires seqan-2.2.0 or later

packages are due at a later point in time, if you want the stable branch, just use the binaries from 1.0.2

Pre-Release 1.9.4 [2018/02/05]

2018-02-05T16:55:10Z

features and usability improvements

all new single-executable interface with sub-commands (like git); see the LAMBDA → lambda2-guide (#88, #94)
- the executable is now called lambda2
- the subcommands mkindexp, mkindexn, searchp and searchn are currently supported
- the -p/--program parameter has disappeared, instead one chooses via the command between nucleotide and protein search (#96)
- many options are now auto-detected from the files, including all index-options and the source alphabets (DNA vs AminoAcid) (#6, #60)
- all short options are now single-letter, some short-options specifiers where removed (#108)
man-pages are now automatically generated and included in the packages
generic and optimised binaries are now shipped within the same package and automatically selected
index generation is now 30% – 50% faster (#112)

bug fixes

crash on empty query sequences, fix requires seqan >= 2.4.0 (#111)
crash if output file is placed given in non-existent or non-writable directory (#113)

compatibility

the command line interface has changed considerably, please see the LAMBDA → lambda2-guide
the on-disk index format is compatible to 1.9.3
requires seqan >= 2.3.1; binary packages based on seqan-2.4.0
compatible with C++17 if used with seqan >= 2.4.0

Pre-Release 1.9.3 [2017/06/29]

2017-06-29T16:20:01Z

everything from 1.0.2, including checks for updates

features and usability improvements

faster searches through
- two-step extensions for short reads (#36)
- use of SIMD for short reads (#89)
smaller indexes again, approx. the size before 1.9.2 (#93)
species annotation (#76):
- support for extracting RefSeq and UniParc accession IDs
- support for UniProt .dat mapping files in addition to NCBI's .accession2taxid
the expected memory usage is pre-calculated and checked against available (#86)

bug-fixes and minor changes

fixed subject position error in some matches in 1.9.0 - 1.9.2 (#87)
stricter parameter checking that prevents wrong usage with obscure errors (#92)
better exception handling (#100)
some fixes to BLASTN and TBLASTX modes (#95, #102, #104)
rare crash on FreeBSD
stack overflow on long exact matches (especially BLASTP, BLASTN)

compatibility

the on-disk index format has changed and is not compatible to any previous version
requires seqan >= 2.3.1 (packages built from seqan-2.3.2)

Release 1.0.2 [2017/06/29]

2017-06-29T15:27:23Z

features

lambda now informs you if updates are available, see Privacy for more details (#97)

bug-fixes and minor changes

various fixes from new SeqAn versions

compatibility

both the interface and the generated index files are fully compatible to the 0.9.* and 1.0.* series
requires seqan >= 2.2.0 (pre-built executables based on seqan-2.3.2)

Pre-release 1.9.2 [2017/01/10]

2017-01-10T13:59:47Z

everything from 1.0.1

features

SIMD parallelization for short query sequences, e.g. Illumina; not yet default (#58)
species annotation of subject sequences, see Taxonomic Workflows (#63)
compile time option that enables larger protein databases sequences (#70)
bi-directional indexes supported; not yet default (#74)
taxonomic binning, see Taxonomic Workflows (#77)

bug-fixes and minor changes

crash when encountering input sequences that are shorter than a seed (#66)

compatibility

the on-disk index format has changed and is not compatible to any previous version
some of the optional --sam-bam-tags were renamed, see the wiki (#79)
requires seqan-2.3.1