Release 1.0.1 [2017/01/09]

features

• can use .sam and .bam also as sequence input (via seqan-2.3)

bug-fixes and minor changes

• minor spelling and documentation fixes (#65)
• make Lambda build on 32bit platforms (#68)
• make Release the default CMAKE_BUILD_TYPE again -- If you built Lambda yourself and you didn't set this, please rebuild (#71)

infrastructure

• Lambda is now available in Debian as lambda-align
• it is also built on many non-x86 platforms, including PowerPC and Sparc64

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-release 1.9.1 [2016/08/19]

bug-fixes and minor changes

• fix SAM and BAM output (#61)

Release 1.0.0 [2016/08/18]

bug-fixes and minor changes

• wrong handling of empty databases or such with empty sequences (#54)

infrastructure

• removed the git-subtree and retroactively replaced it with git submodule (#55)
  • much smaller repository to clone, if you still want SeqAn with Lambda, add --recursive
  • the 1.0.* series now depends on SeqAn-2.2.0 and not any longer on a development version
  • previous git clones have been invalidated and must be forced-pulled or newly cloned
• significant decrease in binary size (6.3MB vs 30MB) and compile time (1.5m vs 10m) (#49)
• improved continuous integration (#52)

compatibility

• both the interface and the generated index files are fully compatible to the 0.9.* series

Pre-release 1.9.0 [2016/08/18]

major changes

• variable length seeding and new seeding strategy, much faster (#17)
• new FM index with EPR dictionaries (faster, but bigger) (#57)
• early support for SIMD operations in extension phase (only faster for small reads) (#58)
• new database/index format, files now moved to sub-directory, better diagnostics (#7)

compatibility

• support for .seg files and masking was removed, it yielded poor results and is superseded by variable length seeding (#47)
• the new index format is incompatible to previous releases and it now uses the -i parameter (#7)
• both, the command line options and the index-format are subject to change during the 1.9.* cycle!

Release 0.9.4 [2016/04/08]

new features

• support for soft-clipping in SAM/BAM IO via --sam-bam-clip (#43)

bug-fixes and minor changes

• missing or redundant hard-clip indicators in SAM/BAM cigar strings (#51)

infrastructure

• LLVM/Clang compiler >= 3.8.0 now supported (#27)
• reduced build times on GCC via parallelization (#45)
• continuous integration for OS X (#46)
• OpenBSD is now supported as platform (although slower than other Unixes) (#48)
• Intel Compiler >= 16.0.2 now supported (#50)

Release 0.9.3 [2015/12/11]

infrastructure

• added app tests (#14)
• added continuous integration via travis (#39)

bug-fixes and minor changes

• using indexes that are read-only now works (#38)
• fixed a crash in TBlastN-mode (#40)
• fixed a crash in BlastN-mode in combination with suffix array index type (#41)

Release 0.9.2 [2015/11/27]

new features of lambda

• support for SAM and BAM output formats (#15), see also Output-Formats

new features of lambda_indexer

• truncate subject IDs by default to save lots of space (can be deactivated) (#37)

bug-fixes and minor changes

• using SEG files works again (#33)
• compiler specific parts linked statically on Mac OS X (#34)
• BLASTN indexes were incorrectly classified as old format (#35)
• if an outdated index was detected the value 200 is returned by lambda, so scripts can automatically recreate indexes if using them fails (#35)

Release 0.9.1 [2015/10/23]

new features of lambda

• mmapped IO for the database enabling faster startup and memory sharing between instances (#3)

new features of lambda_indexer

• radixsort suffix array creation (originally by @meiers) resulting in over 30% less RAM and up to 30% speed-up (#11)

changes in command line interface of lambda_indexer

• all previous algorithms based on sorting superseded by radixsort, please remove e.g. -a quicksort from your scripts

bug-fixes and minor changes

• build in release mode by default (#29)
• improved progress reporting during indexing (#31)
• detect most cases where the index is incompatible (#32)

Release 0.9.0 [2015/09/14]

new features

• ported to SeqAn 2.0 bringing in lots of smaller changes (#1)
• support for column reordering and more columns in tabular output (#2)
• gzipped and bzipped input and output files supported (#19)
• some checks are performed on input data to detect wrong alphabets (#21)

compatibility

• previously generated indexes are unfortunately not compatible with 0.9.*

changes in command line interface

• hide most options by default (visible again with --full-help)

bug-fixes and minor changes

• error in man-page (#5)
• erroneously report "unexpected extension failure" (#9)
• crash in TBlastX mode (#10)
• parameter for number of matches not working (#13)
• crash when putative duplicates heuristic is turned off (#22)
• many small improvements to BlastIO