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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.
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