Google Nucleus Versions Save

New in 0.5.0:

Fixed bug preventing Nucleus to work with TensorFlow 2.0. Added util.vis routines for visualizing DeepVariant pileup examples. FASTA reader now supports keep_true_case option for keeping the original casing. VCF writer now supports writing headerless VCF files. SAM reader now supports optional fields of type 'B'. variant_utils now supports gVCF files. Numerous minor bug fixes.

New in 0.4.1:

• The pip package is slightly more robust.

New in 0.4.0:

The Nucleus pip package now works with Python 3.

New in 0.3.0:

Reading of VCF, SAM, and most other genomics files is now twice as fast. Read range and end calculations are now done in C++ for speed. VcfReader can now read "headerless" VCF files. variant_utils.major_allele_frequency now 5x faster. Memory leaks fixed in TFRecordReader/Writer and gfile_cc.

New in 0.2.3:

Nucleus no longer depends on any specific version of TensorFlow's python code. This should make it easier to use Nucleus with for example TensorFlow 2.0. Added BCF support to VcfWriter. Fixed memory leaks in VcfWriter::Write. Added print_tfrecord example program.

New in 0.2.2:

• Faster SAM file querying and read overlap calculations.
• Writing protocol buffers to files uses less memory.
• Smaller pip package.
• nucleus/util:io_utils refactored into nucleus/io:tfrecord and nucleus/io:sharded_file_utils.
• Alleles coming from VCF files are now always normalized as uppercase.

New in 0.2.1:

• Upgrades htslib dependency from 1.6 to 1.9.
• Minor VCF parsing fixes.
• Added new example program, apply_genotyping_prior.
• Slightly more robust pip package.

New in 0.2.0:

Support for reading and writing BedGraph files. Support for reading and writing GFF files. Support for reading and writing CRAM files. Support for writing SAM/BAM files. Support for reading unindexed FASTA files. Iteration support for indexed FASTA files. Ability to read VCF files from memory. Python API documentation. Python 3 compatibility. Added universal file converter example program.