Jillion 5.1 Released
2015-12-10 : Jillion 5.1 is now released. Download Jillion 5.1
- Support for reading and writing Samtools fasta index files (.fai).
- NucleotideFastaDataStore and ProteinFastaDataStores will now utilize a fasta index file if one is present for faster random access lookups.
- Added new getSequence() and getSubSequence() methods to FastaDataStore to quickly get the sequence from a fasta file or a part of the sequence from a fasta file.
- A few bug Fixes
See the Jillion 5.1 Release Notes for more details
Jillion 5 Released
2015-10-26 : Jillion 5.0 is now released. Download Jillion 5
Over 300 commits were made by a single developer and include many new features. Jillion 5 now requires Java 8 since it leverages Java 8 Lambda expressions for a more concise and simpler API.
- Java 8 Lambda support
- Simplified syntax for filtering using lambdas
- Improved SAM and BAM parsing and writing which uses bam indexes for improved parsing performance.
- New GenomeStatistics class that can compute N50 and similar computations
- Performance improvements; especially to Fastq file reading and writing.
- Bug fixes
- OSGI compliant jar
See the Jillion 5 Release Notes for more details
Jillion 4.2 Released
2015-09-08 Jillion 4.2 has been released. Download Jillion 4.2
- FastaFileParser and all Fasta Datastore implementations supports non-redundant text fasta files like the ones described in BLAST's README. If non-redundant records are encountered, then the visitXXX methods will be called in a way such that it will appear as if they were redundantly listed. The non-redundant defline will be split and each identical sequence will be visited separately with each of the many ids for it. Creating FastaVisitorMemento are also non-redundant aware and will correctly only visit the subset of non-redundant records according to when the memento was created.
- AminoAcid - Added Pyrrolysine 'O' to AminoAcid class and AminoAcidSequence as well as Blosum matrices.
- AlnFileParser - added lowercase basecall support which is used in MAFFT output. Jillion can now successfully parse .aln files produced by MAFFT.
- XMLBlastParser - If accession in subject is "No definition line found" will use subjectDefline instead.
- PrimerDetector - Added guard clause if input sequence is empty, then empty collection of hits is returned.