Release Notes

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Release Notes

Jillion 5.1 Released

2015-12-10 : Jillion 5.1 is now released. Download Jillion 5.1

New Features

  • 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.

New Features

  • 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

New Features

  1. 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.
  2. AminoAcid - Added Pyrrolysine 'O' to AminoAcid class and AminoAcidSequence as well as Blosum matrices.

Bug Fixes

  1. AlnFileParser - added lowercase basecall support which is used in MAFFT output. Jillion can now successfully parse .aln files produced by MAFFT.
  2. XMLBlastParser - If accession in subject is "No definition line found" will use subjectDefline instead.
  3. PrimerDetector - Added guard clause if input sequence is empty, then empty collection of hits is returned.
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