CHANGELOG.md

CHANGELOG

Version 0.4.7 [2014/12/12]

bug-fixes and minor changes

• fix build on Darwin / MacOS X

availability

• Linux Binaries 64Bit
• Linux Binaries Sandybridge
• Darwin Binaries 64Bit
• Source code

Version 0.4.5 [2014/12/05]

bug-fixes and minor changes

• lambda_indexer now has a different suffix array construction algorithm
• this works on larger files (where the old algorithm sometimes failed) and is fully parallelized
• there is also a rough progress indication when indexing

availability

• Linux Binaries 64Bit
• Linux Binaries Sandybridge
• Source code

Version 0.4.1 [2014/11/10]

bug-fixes and minor changes

• default index type was not set to FM in lambda_indexer

availability

• Linux Binaries 64Bit
• Linux Binaries Sandybridge
• Source code

Version 0.4.0 [2014/11/07]

performance changes in comparison to published version (0.2)

• new default mode with 30-80% speed gains and up to 75% memory reduction over published version
• double-indexing mode with speed gains > 100%
• sensitivity slightly increased at the same time (1-2%)

changes in command line interface

• renamed many parameters and changed some defaults
• please look at lambda --help to see all the changes!!
• better control of verbosity with -v parameter
• threads now controlled with -t instead of environment variable

new features

• BlastN mode now usable again and proper parameter-handling added for it
• added percent identity cutoff in addition to e-value cutoff (-id)
• added a limit for maximum number of matches per query sequence (-nm)
• added abundancy heuristic (-pa) and priorization of hits to not look at all hits if number of hits >> chosen limit
• single-indexing mode which has huge memory advantages (-qi none) [now default]
• FM-Index is now also default
• removed Lambda-Alphabets, since they currently provide little benefit over Murphy10

bug-fixes and minor changes

• indeces with different settings (index type, alphabet) can now be created on the same fasta file without conflicts between them
• changed pre-scoring heuristic to include region around match (-ps and -pt)
• fixed build issues with gcc-4.8.x
• FastQ support fixed

availability

• Linux Binaries 64Bit
• Linux Binaries Sandybridge
• Source code (tarball)
• Source code (git)

Version 0.3 [2014/09/06]

performance changes in comparison to published version (0.2)

• Speed increased by ~20%
• Suffix-Array index memory consumption reduced from 16x to 6x input database size
• experimental support for FM-index as index (instead of SA) [not widely tested, yet]

bug-fixes and minor changes

• small bugs in BLAST output formats corrected

availability

• source-code .tar.gz
• source-code git commit d41b4b58749282dbca838a7f8506c0b378767b1b)

Version 0.2 [2014/04/07] published version

• multiple optimizations
• added option to partition the query sequences
• added overlapping seeds capability

availability

• source-code .tar.gz
• source-code git commit b8ca36432d0530dd5d39560f8e2dc2cffb7c5d9d)

Version 0.1 [2014/01/15] initial release