├── .bazelrc ├── .github └── workflows │ └── test.yml ├── BUILD ├── CONTRIBUTING.md ├── Dockerfile.build_env ├── LICENSE ├── README.md ├── WORKSPACE ├── docs ├── examples.md ├── overview.md └── source │ ├── doc_index.md │ └── nucleus │ ├── examples │ ├── add_ad_to_vcf.md │ ├── apply_genotyping_prior.md │ ├── ascii_pileup.md │ ├── count_variants.md │ ├── filter_vcf.md │ ├── print_tfrecord.md │ └── validate_vcf.md │ ├── io │ ├── bed.md │ ├── bedgraph.md │ ├── clif_postproc.md │ ├── converter.md │ ├── fasta.md │ ├── fastq.md │ ├── genomics_reader.md │ ├── genomics_writer.md │ ├── gff.md │ ├── gfile.md │ ├── sam.md │ ├── sharded_file_utils.md │ ├── tabix.md │ ├── tfrecord.md │ └── vcf.md │ ├── pip_package │ └── setup.md │ ├── testing │ └── test_utils.md │ └── util │ ├── cigar.md │ ├── errors.md │ ├── genomics_math.md │ ├── proto_utils.md │ ├── ranges.md │ ├── sequence_utils.md │ ├── struct_utils.md │ ├── utils.md │ ├── variant_utils.md │ ├── variantcall_utils.md │ ├── vcf_constants.md │ └── vis.md ├── install.sh ├── nucleus ├── BUILD ├── __init__.py ├── examples │ ├── BUILD │ ├── __init__.py │ ├── add_ad_to_vcf.py │ ├── add_ad_to_vcf_test.py │ ├── apply_genotyping_prior.py │ ├── apply_genotyping_prior_test.py │ ├── ascii_pileup.py │ ├── ascii_pileup_test.py │ ├── count_variants.py │ ├── count_variants_test.py │ ├── dna_sequencing_error_correction.ipynb │ ├── filter_vcf.py │ ├── filter_vcf_test.py │ ├── images │ │ ├── consensus-approach-overview.jpg │ │ ├── consensus-input-and-output.jpg │ │ ├── model-architecture.jpg │ │ ├── raw-counts.jpg │ │ ├── read-pileup.jpg │ │ └── single-read-input-and-output.jpg │ ├── print_tfrecord.py │ ├── validate_vcf.py │ └── validate_vcf_test.py ├── io │ ├── BUILD │ ├── __init__.py │ ├── bed.py │ ├── bed_reader.cc │ ├── bed_reader.h │ ├── bed_reader_test.cc │ ├── bed_test.py │ ├── bed_writer.cc │ ├── bed_writer.h │ ├── bed_writer_test.cc │ ├── bedgraph.py │ ├── bedgraph_reader.cc │ ├── bedgraph_reader.h │ ├── bedgraph_reader_test.cc │ ├── bedgraph_test.py │ ├── bedgraph_writer.cc │ ├── bedgraph_writer.h │ ├── bedgraph_writer_test.cc │ ├── clif_postproc.py │ ├── converter.py │ ├── converter_test.py │ ├── fasta.py │ ├── fasta_test.py │ ├── fastq.py │ ├── fastq_reader.cc │ ├── fastq_reader.h │ ├── fastq_reader_test.cc │ ├── fastq_test.py │ ├── fastq_writer.cc │ ├── fastq_writer.h │ ├── fastq_writer_test.cc │ ├── genomics_io_noplugin_test.py │ ├── genomics_reader.py │ ├── genomics_reader_test.py │ ├── genomics_writer.py │ ├── gff.py │ ├── gff_reader.cc │ ├── gff_reader.h │ ├── gff_reader_test.cc │ ├── gff_test.py │ ├── gff_writer.cc │ ├── gff_writer.h │ ├── gff_writer_test.cc │ ├── gfile.cc │ ├── gfile.h │ ├── gfile.py │ ├── gfile_test.py │ ├── hts_path.cc │ ├── hts_path.h │ ├── hts_test.cc │ ├── hts_verbose.cc │ ├── hts_verbose.h │ ├── hts_verbose_test.cc │ ├── python │ │ ├── BUILD │ │ ├── __init__.py │ │ ├── bed_reader.clif │ │ ├── bed_reader_wrap_test.py │ │ ├── bed_writer.clif │ │ ├── bed_writer_wrap_test.py │ │ ├── bedgraph_reader.clif │ │ ├── bedgraph_writer.clif │ │ ├── fastq_reader.clif │ │ ├── fastq_reader_wrap_test.py │ │ ├── fastq_writer.clif │ │ ├── fastq_writer_wrap_test.py │ │ ├── gff_reader.clif │ │ ├── gff_reader_wrap_test.py │ │ ├── gff_writer.clif │ │ ├── gff_writer_wrap_test.py │ │ ├── gfile.clif │ │ ├── hts_verbose.clif │ │ ├── hts_verbose_test.py │ │ ├── reference.clif │ │ ├── reference_wrap_test.py │ │ ├── sam_reader.clif │ │ ├── sam_reader_wrap_test.py │ │ ├── sam_writer.clif │ │ ├── tabix_indexer.clif │ │ ├── tfrecord_reader.clif │ │ ├── tfrecord_writer.clif │ │ ├── vcf_reader.clif │ │ ├── vcf_reader_wrap_test.py │ │ ├── vcf_writer.clif │ │ └── vcf_writer_wrap_test.py │ ├── reader_base.cc │ ├── reader_base.h │ ├── reader_base_test.cc │ ├── reference.cc │ ├── reference.h │ ├── reference_test.cc │ ├── sam.py │ ├── sam_reader.cc │ ├── sam_reader.h │ ├── sam_reader_test.cc │ ├── sam_test.py │ ├── sam_utils.cc │ ├── sam_utils.h │ ├── sam_utils_test.cc │ ├── sam_writer.cc │ ├── sam_writer.h │ ├── sam_writer_test.cc │ ├── sharded_file_utils.py │ ├── sharded_file_utils_test.py │ ├── tabix.py │ ├── tabix_indexer.cc │ ├── tabix_indexer.h │ ├── tabix_indexer_test.cc │ ├── tabix_test.py │ ├── text_io_test.cc │ ├── text_reader.cc │ ├── text_reader.h │ ├── text_writer.cc │ ├── text_writer.h │ ├── tfrecord.py │ ├── tfrecord_reader.cc │ ├── tfrecord_reader.h │ ├── tfrecord_reader_test.cc │ ├── tfrecord_test.py │ ├── tfrecord_writer.cc │ ├── tfrecord_writer.h │ ├── vcf.py │ ├── vcf_conversion.cc │ ├── vcf_conversion.h │ ├── vcf_reader.cc │ ├── vcf_reader.h │ ├── vcf_reader_test.cc │ ├── vcf_roundtrip_test.cc │ ├── vcf_test.py │ ├── vcf_writer.cc │ ├── vcf_writer.h │ └── vcf_writer_test.cc ├── pip_package │ ├── BUILD │ ├── MANIFEST.in │ ├── build_pip_package.sh │ ├── egg_files │ │ ├── PKG-INFO │ │ ├── dependency_links.txt │ │ ├── namespace_packages.txt │ │ ├── not-zip-safe │ │ ├── requires.txt │ │ └── top_level.txt │ ├── setup.cfg │ └── setup.py ├── platform │ ├── BUILD │ └── types.h ├── protos │ ├── BUILD │ ├── __init__.py │ ├── bed.proto │ ├── bedgraph.proto │ ├── cigar.proto │ ├── example.proto │ ├── fasta.proto │ ├── fastq.proto │ ├── feature.proto │ ├── gff.proto │ ├── position.proto │ ├── range.proto │ ├── reads.proto │ ├── reference.proto │ ├── struct.proto │ └── variants.proto ├── testdata │ ├── 5col.bed │ ├── BUILD │ ├── NA12878_small.bam │ ├── NA12878_small.bam.bai │ ├── header_format_mixed_order.vcf │ ├── headerless.sam │ ├── malformed.bed │ ├── malformed.fasta │ ├── malformed.fastq │ ├── malformed.sam │ ├── malformed.vcf │ ├── malformed2.bed │ ├── malformed2.fastq │ ├── test.bam │ ├── test.bam.bai │ ├── test.bed │ ├── test.bed.gz │ ├── test.fasta │ ├── test.fasta.fai │ ├── test.fasta.gz │ ├── test.fasta.gz.fai │ ├── test.fasta.gz.gzi │ ├── test.sam │ ├── test.sam.golden.tfrecord │ ├── test_allele_depth.vcf │ ├── test_allele_depth.vcf.golden.tfrecord │ ├── test_alternate_index.bai │ ├── test_alternate_index.bam │ ├── test_cram.embed_ref_0_version_3.0.cram │ ├── test_cram.embed_ref_0_version_3.0.cram.crai │ ├── test_cram.embed_ref_1_version_3.0.cram │ ├── test_cram.embed_ref_1_version_3.0.cram.crai │ ├── test_cram.sam │ ├── test_features.gff │ ├── test_features.gff.gz │ ├── test_features.gff.tfrecord │ ├── test_features.gff.tfrecord.gz │ ├── test_likelihoods.vcf.golden.tfrecord │ ├── test_likelihoods_input.vcf │ ├── test_likelihoods_output.vcf │ ├── test_nist.b37_chr20_100kbp_at_10mb.bed │ ├── test_nist.b37_chr20_100kbp_at_10mb.vcf.gz │ ├── test_nist.b37_chr20_100kbp_at_10mb.vcf.gz.tbi │ ├── test_oq.sam │ ├── test_phaseset.vcf │ ├── test_phaseset.vcf.golden.tfrecord │ ├── test_py_roundtrip.vcf │ ├── test_reads.bgzip.fastq.gz │ ├── test_reads.fastq │ ├── test_reads.fastq.gz │ ├── test_reads.fastq.tfrecord │ ├── test_reads.fastq.tfrecord.gz │ ├── test_redefined_formats.vcf │ ├── test_regions.bed │ ├── test_regions.bed.gz │ ├── test_regions.bed.tfrecord │ ├── test_regions.bed.tfrecord.gz │ ├── test_regions.bedgraph │ ├── test_regions.bedgraph.gz │ ├── test_samples.vcf │ ├── test_samples.vcf.golden.tfrecord │ ├── test_samples.vcf.gz │ ├── test_samples.vcf.gz.tbi │ ├── test_sites.vcf │ ├── test_sites.vcf.golden.tfrecord │ ├── test_vaf.vcf │ ├── test_vaf.vcf.golden.tfrecord │ ├── test_valid_vcf_header_parsing.vcf │ ├── ucsc.hg19.chr20.unittest.fasta.gz │ ├── ucsc.hg19.chr20.unittest.fasta.gz.fai │ ├── ucsc.hg19.chr20.unittest.fasta.gz.gzi │ ├── unindexed.bam │ ├── unindexed.fasta │ ├── unindexed_emptylines.fasta │ └── vcf_no_header.vcf ├── testing │ ├── BUILD │ ├── __init__.py │ ├── gunit_extras_test.cc │ ├── protobuf_implementation_test.py │ ├── protocol-buffer-matchers.cc │ ├── protocol-buffer-matchers.h │ ├── tensorflow_smoke_test.py │ ├── test_utils.cc │ ├── test_utils.h │ ├── test_utils.py │ └── test_utils_test.py ├── tools │ ├── BUILD │ ├── __init__.py │ ├── make_cram_testdata.sh │ ├── md_extract_cmd.sh │ └── zip_dir.bzl ├── util │ ├── BUILD │ ├── __init__.py │ ├── cigar.py │ ├── cigar_test.py │ ├── errors.py │ ├── errors_test.py │ ├── genomics_math.py │ ├── genomics_math_test.py │ ├── math.cc │ ├── math.h │ ├── math_test.cc │ ├── port.h │ ├── proto_clif_converter.cc │ ├── proto_clif_converter.h │ ├── proto_ptr.h │ ├── proto_utils.py │ ├── python │ │ ├── BUILD │ │ ├── __init__.py │ │ ├── math.clif │ │ ├── math_wrap_test.py │ │ └── utils.clif │ ├── ranges.py │ ├── ranges_test.py │ ├── samplers.h │ ├── samplers_test.cc │ ├── sequence_utils.py │ ├── sequence_utils_test.py │ ├── struct_utils.py │ ├── struct_utils_test.py │ ├── utils.cc │ ├── utils.h │ ├── utils.py │ ├── utils_test.cc │ ├── utils_test.py │ ├── variant_utils.py │ ├── variant_utils_test.py │ ├── variantcall_utils.py │ ├── variantcall_utils_test.py │ ├── vcf_constants.py │ ├── vcf_constants_test.py │ ├── vis.py │ └── vis_test.py └── vendor │ ├── BUILD │ ├── __init__.py │ ├── message_module.cc │ ├── python │ ├── BUILD │ ├── __init__.py │ ├── statusor_examples.clif │ └── 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