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Release 0.8.0
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@tfenne tfenne released this 14 Feb 00:14
0.8.0
9b073ef

Major release with the following changes:

  • Major improvements to the pairwise Aligner class:
    • Significant performance improvements in the Aligner class for pairwise alignments
    • When aligning DNA sequences aligner will produce matches in CIGAR for matches between compatible IUPAC codes (e.g. R paired with A or G)
    • New method to produce all alignments above a score threshold from a pair of sequences
    • New interface to allow for custom gap scoring
  • Added Sequences.revcomp() function that correctly reverse complements all IUPAC DNA/RNA codes
  • Added method to Metric class to return an Iterator over a metrics file instead of reading the whole file into memory
  • Io object now automatically supports bgzipped files with .bgz or .bgzip extensions
  • Fixed bug in SamReader that would occasionally cause exceptions with overlapping query regions
  • Updated to latest scala point version to create classes/JARs compatible with JDK 9 and 10 at runtime
  • Added method to ExtractBasecallingParamsForPicard to enable easy access to unmatched BAM file path
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