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Version 2.0

  • Python 3.7 port, removed support for Python 2.x

Version 1.4.0

  • Support for Vcf4Records and merging VCF files

Version 1.3.0

  • Better handling of h5py
  • Support 4.0 basecaller and chemistry
  • Misc fixes

Version 1.2.11

  • Support for 3.2 basecaller and chemistry
  • GFF bug fixes
  • Misc fixes and enhancements

Version 1.2.10 (> SMRTanalysis 3.1)

  • Update to pysam 0.9.0
  • Recognize new and prospective future partnumbers for the 3.1 timeframe
  • Misc fixes for speeding up dataset and cmp.h5 access

Version 1.2.9

  • Rename pulseFeature accessors to “baseFeature…”, since they reflect features accompanying basecalls as opposed to pulse calls; add “pulseFeature…” accessors that actually get the pulse features (from an internal-mode BAM)
  • Improve FastaWriter performance with IndexedFastaRecords
  • Improve DataSet chunking, filtration, consolidation

Version 1.2.8

  • Dataset improvements
  • Dataset CLI moved to pbcoretools
  • Support for context flag filtering
  • Misc fixes

Version 1.2.7…

  • Improved IPython tab completion
  • Can now use .open on Dataset XML files
  • Update to pysam 0.8.4
  • Miscellaneous bugfixes

Version 1.2.6

  • Recognize sequencing kit C4v2
  • Support for multipart bas files with the new Sequel holenumber format
  • Add readsByHoleNumber to aln file classes

Version 1.2.5

  • Accessors for SNR from BAM reads; needed for Arrow access

Version 1.2.4

  • add GFF gather functionality
  • support for 3.0.1 BAM format spec

Version 1.2.3

  • Updated for newer dataset schema
  • BAM access speed improvements
  • BGZF fixed for large bam.pbi files
  • readsInRange iteration order parity between different dataset sources

Version 1.2.2

  • Bug fixes and speed improvements to the
  • Dataset constructor APIs enhanced

Version 1.2.1

  • Same as 1.2.0; first version on PyPI

Version 1.2.0

  • Support for the new BGZF-based bam.pbi file format
  • Support for PacBio BAM spec version 3.0b7; previous versions are rejected

Version 1.1.0

  • Added dataset functionality to pbcore.io
  • Added dataset.py tools for CLI manipulation of DataSet XML files

Version 1.0.0

  • BAM fixes
  • Better FOFN handling
  • Recognize additional part numbers for P6 chemistry
  • Better –debug in ToolRunner

Version 0.9.5

  • BAM fixes
  • Adopt aStart, aEnd conventions from BAM spec, replacing rStart, rEnd
  • AlnIndex sharing among CmpH5Reader objects

Version 0.9.4

  • BAM support moved to 3.0 spec; support for earlier PacBio BAMs dropped
  • Deprecation warning decorators added
  • BAM-incompatible cmp.h5 accessors deprecated
  • Moved to support 3.0 FASTA conventions in Fasta readers
  • Rename FastaTable to IndexedFastaReader

Version 0.9.3

  • “.open” script added for convenience
  • openers added (factory methods invoking the appropriate Reader class; useful for applications that want to transparently use either BAM or cmp.h5)

Version 0.9.2

  • BAM support: Addition of BamReader, IndexedBamReader, and BamAlignment
  • Minor CmpH5Reader API changes for greater compatibility with BamReader (deprecation of movieInfo in favor of readGroupInfo)
  • Removed unused components from CmpH5Reader API
  • Add example BAM file
  • Length accessors for FAST[AQ] record types

Version 0.9.1 (SMRTanalysis 2.3.0p1)

  • FASTA header parsing into “id” and “metadata” now available in the FastaRecord types

Version 0.9.0 (SMRTanalysis 2.3.0)

  • pbcore.chemistry: a new subpackage for decoding barcode information to the human-readable chemistry name
  • BasH5Reader: more robust handling of broken region tables
  • CmpH5Reader: loading an empty cmp.h5 will raise an EmptyCmpH5Error. This is because the semantics of an empty cmp.h5 were never defined, and for example it is not defined whether or not a cmp.h5 lacking a movie table is compliant.