Releases | Open Source Science

btllib - btllib v1.7.5

Compiled python wrappers with SWIG 4.2.1

Scientific Software - Peer-reviewed - C++
Published by jwcodee about 1 year ago

btllib - btllib v1.7.4

Fixed Phred average calculation

Scientific Software - Peer-reviewed - C++
Published by jwcodee about 1 year ago

btllib - btllib v1.7.3

Fixed latest macOS compilation errors

Scientific Software - Peer-reviewed - C++
Published by parham-k over 1 year ago

btllib - btllib v1.7.2

Added an increment value parameter to the insert functions in counting Bloom filters

Scientific Software - Peer-reviewed - C++
Published by parham-k almost 2 years ago

btllib - btllib v1.7.1

Fixed segfault when hashing a sequence ending in a masked k-mer

Scientific Software - Peer-reviewed - C++
Published by parham-k almost 2 years ago

btllib - btllib v1.7.0

Converted ntHash to a header-only library
Improved ntHash's performance
Added base substitution functionality to ntHash
Added aaHash citation to README

Scientific Software - Peer-reviewed - C++
Published by parham-k about 2 years ago

btllib - btllib v1.6.2

Fixed issues related to coverage tests being included in release
Added a utility function to calculate the Phred average given a string
Enabled strict mode in bash scripts
Fixed const-related clang-tidy complaints

Scientific Software - Peer-reviewed - C++
Published by parham-k over 2 years ago

btllib - btllib v1.6.1

Added coverage tests
Fixed compilation issues when using GCC on macOS
ntHash: Fixed performance issues due to improper function inlining
ntHash: Fixed SeedNtHash's copy constructor
aaHash: Added ambiguous amino acid IUPAC code
RandSeq: Added option for seed value in the pseudo-random number generator

Scientific Software - Peer-reviewed - C++
Published by parham-k over 2 years ago

btllib - btllib v1.6.0

Added aaHash, a rolling hash algorithm for amino acid sequences
Added more tests for the Python wrappers
Fixed a thread-safety issue in miBF

Scientific Software - Peer-reviewed - C++
Published by parham-k almost 3 years ago

btllib - btllib v1.5.1

Updated the wrap script to generate more consistent wrappers
Fixed segmentation fault when using SeqReader in Python
Add basic unit tests for the Python wrappers

Scientific Software - Peer-reviewed - C++
Published by parham-k almost 3 years ago

btllib - btllib v1.5.0

Added a RandomSequenceGenerator API for generating random nucleotide or amino acid sequences
Added seqgen recipe, a tool for creating random DNA/RNA data
Added quality-based filtering to indexlr
Added minimizer quality to indexlr output
Added deletion support to counting Bloom filters
Fixed issue with outputting barcode (without ID) for stLFR reads in indexlr
Fixed CBF contains function

Scientific Software - Peer-reviewed - C++
Published by parham-k almost 3 years ago

btllib - btllib v1.4.10

Fixed a multithreading issue in SeqReader SAM module.

Scientific Software - Peer-reviewed - C++
Published by vlad0x00 about 3 years ago

btllib - btllib v1.4.9

Preferably make pipes in /dev/shm to reduce the chance of a filesystem not supporting pipes.

Scientific Software - Peer-reviewed - C++
Published by vlad0x00 over 3 years ago

btllib - btllib v1.4.8

Fixed the issue where some files (submodules) were not included in the release.

Scientific Software - Peer-reviewed - C++
Published by vlad0x00 over 3 years ago

btllib - btllib v1.4.7

Check whether Link Time Optimization is supported in compile script.

Scientific Software - Peer-reviewed - C++
Published by vlad0x00 over 3 years ago

btllib - btllib v1.4.6

Enabled Link Time Optimization and removal of assertions in code in the compile script.

Scientific Software - Peer-reviewed - C++
Published by vlad0x00 over 3 years ago

btllib - btllib v1.4.5

Fixed the issue where (Kmer)CountingBloomFilter and SeqReader and SeqWriter Format class were not provided by the Python interface.

Scientific Software - Peer-reviewed - C++
Published by vlad0x00 over 3 years ago

btllib - btllib v1.4.4

Fixed an issue where calling the compile script outside of btllib dir didn't work.
By default, btllib now preferentially builds at /tmp instead of $TMPDIR, as $TMPDIR is not necessarily removed on reboot.
Updated documentation.
Added threshold parameter to get_fpr() for Counting Bloom filters, giving you the false positive rate for a given threshold.
Fixed an OpenMP compile error.
Added a check for whether the Bloom filter exists when loading from a file.

Scientific Software - Peer-reviewed - C++
Published by vlad0x00 almost 4 years ago

btllib - btllib v1.4.3

Added a setup.py file in btllib/install/lib/btllib/python/ dir that allows installing the wrappers as a Python package.
Fixed an issue with compile script where it didn't detect missing temporary dependencies.

Scientific Software - Peer-reviewed - C++
Published by vlad0x00 almost 4 years ago

btllib - btllib v1.4.2

btllib building is now done in a temporary dir in order not to change the source dir (relevant for some build systems like automake)
compile script rewritten in Python
Python wrappers are now installed to lib/btllib/python/

Scientific Software - Peer-reviewed - C++
Published by vlad0x00 almost 4 years ago

btllib - btllib v1.4.1

Fixed installation of header files of included subprojects.

Scientific Software - Peer-reviewed - C++
Published by vlad0x00 almost 4 years ago

btllib - btllib v1.4.0

Fixed a bug when checking the validity of SeqReader and Indexlr records by converting them to bools.
Moved more code from include/ into src/.
The helper spawner process now belongs to a different process groups, ignoring signals like keyboard interrupt. In past versions this caused the helper process to crash with an error message if the main process was interrupted.
Added more insertion/querying methods to the counting bloom filters
Added a threadsafe get_basename utility function
Improved error printing for SeqWriter
sdsl is now a submodule and a meson subproject. This approach helped made meson dist work, allowing us to standardize packaging self contained btllib
NtHash has been updated to NtHash2. The new hash function has different, incompatible output compared to the old version. Canonical hash value is now calculated by adding the forward and the reverse, instead of picking the lower one in order to remove the bias towards lower values.
A number of optimizations have been done to NtHash code.
Fixed a bug where SeedNtHash produced wrong hash values if a seed has 0s at its ends.

Scientific Software - Peer-reviewed - C++
Published by vlad0x00 almost 4 years ago

btllib - btllib v1.3.0

btllib is now a compiled static library. From now on, C++ code requires running btllib/compile and -L btllib/lib -l btllib compiler flags. The rationale for this change was that header-only code can become ugly easily, doesn't allow one definition for project-global objects, and makes compile time longer.
Fixed a bug with SeqWriter where it didn't overwrite an existing file.
btllib/compile script again accepts environment variables: CFLAGS, CXXFLAGS, LDFLAGS

Scientific Software - Peer-reviewed - C++
Published by vlad0x00 almost 4 years ago

btllib - btllib v1.2.0

Updated ntHash with new spaced seed algorithm that makes them much faster if they have long streches of 1s or 0s.
Added BlindNtHash, which is manually fed characters in order to be able to implement implicit de Bruijn Graph.
Added roll_back() to ntHash to allow rolling backwards.
Added peek() and peek_back() to ntHash to peek the next character as if the roll was called.
SeqWriter can now use the with construct in Python.
Fixed a big with SeqReader when reading SAM files that disallowed tlen column to be negative.
Java wrappers removed, as they require maintenance but we were not using them.
Renamed compile-wrappers to compile as a preparation for a compiled library.
Compile script now ignores environment CFLAGS, CXXFLAGS, and LDFLAGS since it uses its own internally.

Scientific Software - Peer-reviewed - C++
Published by vlad0x00 almost 4 years ago

btllib - btllib v1.1.9

Fixed a deadlock in indexlr when processing an empty file.
Fixed a few data races thanks to thread sanitization.

Scientific Software - Peer-reviewed - C++
Published by vlad0x00 about 4 years ago

btllib - btllib v1.1.8

Optimizations for Bloom filters, SeqReader, and Indexlr.
SeedNtHash Python wrappers fixed.
Added more tests.

Scientific Software - Peer-reviewed - C++
Published by vlad0x00 about 4 years ago