File: CHANGELOG

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pbgenomicconsensus 2.1.0-1
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Version 2.1.0
  * Major fixes for arrow
  * Documentation for arrow
  * Update for substantially-refactored ConsensusCore2
  * --dumpEvidence support for Arrow

Version 2.0.0
  * Working support for Arrow and POA-only consensus models

Version 1.1.0
  * Working support for DataSet read and reference files

Version 1.0.0
  * Working support for BAM files adhering to our BAM spec (version 3.0b6)

Version 0.9.2 (bugfix release, issued with SMRTanalysis 2.3.0p2)
  * Fix bug where output contained truncated contig names

Version 0.9.1 (released with SMRTanalysis 2.3.0p1)
  * Preliminary support for BAM file in quiver

Version 0.9.0 (released with SMRTanalysis 2.3)
  * Support for P6-C4 chemistry
  * Rate of MLE convergences failures reduced drastically
  * quiver will now abort if it is provided data lacking the full
    complement of QV tracks (except the MergeQV, which is allowed to
    be absent, as is the case in data from old basecaller versions)
  * Use the new chemistry information decoding spec---expects barcode
    information in the cmp.h5 but will fall back to the old
    "SequencingChemistry" tag if the barcodes are absent.

Version 0.8.0 (released with SMRTanalysis 2.2)
  * Improved consensus calling at edges of contigs and amplicons
  * Fixes to reduce algorithmic convergence failures
  * Improved support for chemistry mixtures
  * Faster analysis of P5-C3 chemistry
  * Improved robustness using P5-C3 chemistry
  * Faster startup time for large references

Version 0.7.0 (released with SMRTanalysis 2.1)
  * Support for diploid variant calling in plurality and quiver algorithms
  * Auto-windowing to skip coverage deserts, drastically improving user experience
    for amplicon workflows.
  * Command line support for operating on a chosen barcode
  * Fix bug in dinucleotide repeat refinement
  * Modification to variants.gff schema to support diploid variant reporting
  * Fix for memory leak affecting jobs with many reference contigs
    (large assemblies, for example)
  * Improved support for P5-C3 chemistry
  * Improved support for P4-C2 chemistry (was included in 2.0.1 release)

Version 0.6.0 (released with SMRTanalysis 2.0)
  * Improved Quiver accuracy, reducing errors in dinucleotide repeat regions
  * Improved, extensible support for existing and forthcoming sequencing chemistries