├── .circleci └── installHDF5.sh ├── .gitignore ├── .pylintrc ├── CHANGELOG.org ├── LICENSE ├── MANIFEST.in ├── Makefile ├── README.md ├── bamboo-specs └── bamboo.yml ├── bamboo_build.sh ├── bamboo_wheel.sh ├── circle.yml ├── constraint.lock ├── doc ├── Makefile ├── conf.py ├── index.rst ├── modules.rst ├── pacbio-theme │ ├── static │ │ ├── headerGradient.jpg │ │ ├── pacbio.css │ │ ├── pacbioLogo.png │ │ └── pygments.css │ └── theme.conf ├── pbcore.chemistry.rst ├── pbcore.data.rst ├── pbcore.io.dataset.rst ├── pbcore.io.rst ├── pbcore.model.rst ├── pbcore.rst └── pbcore.util.rst ├── pbcore ├── __init__.py ├── chemistry │ ├── __init__.py │ ├── chemistry.py │ └── resources │ │ └── mapping.xml ├── data │ ├── Fluidigm_human_amplicons.fasta │ ├── Fluidigm_human_amplicons.fasta.fai │ ├── Fluidigm_human_amplicons_tiny.fasta │ ├── __init__.py │ ├── barcodes-ed65-450.fasta │ ├── barcodes-ed65-450.fasta.fai │ ├── blasr-output.m4 │ ├── blasr-output.m5 │ ├── chemistry.xml │ ├── datasets │ │ ├── CollectionMetadata.xml │ │ ├── __init__.py │ │ ├── alignment.dataset.xml │ │ ├── barcode.dataset.xml │ │ ├── ccsaligned.dataset.xml │ │ ├── ccsread.dataset.xml │ │ ├── contig.dataset.xml │ │ ├── empty_lambda.aligned.bam │ │ ├── empty_lambda.aligned.bam.bai │ │ ├── empty_lambda.aligned.bam.pbi │ │ ├── fofn.fofn │ │ ├── lambda.alignmentset.xml │ │ ├── lambda.referenceset.xml │ │ ├── m140905_042212_sidney_c100564852550000001823085912221377_s1_X0.subreads.fake_bc.bam │ │ ├── m140905_042212_sidney_c100564852550000001823085912221377_s1_X0.subreads.fake_bc.bam.bai │ │ ├── m140905_042212_sidney_c100564852550000001823085912221377_s1_X0.subreads.fake_bc.bam.pbi │ │ ├── m150430_142051_Mon_p1_b25.sts.xml │ │ ├── m150616_053259_ethan_c100710482550000001823136404221563_s1_p0.sts.xml │ │ ├── pbalchemysim.alignmentset.xml │ │ ├── pbalchemysim0.alignmentset.chunk0contigs.xml │ │ ├── pbalchemysim0.alignmentset.chunk1contigs.xml │ │ ├── pbalchemysim0.alignmentset.xml │ │ ├── pbalchemysim0.pbalign.bam │ │ ├── pbalchemysim0.pbalign.bam.bai │ │ ├── pbalchemysim0.pbalign.bam.pbi │ │ ├── pbalchemysim0.reference.fasta │ │ ├── pbalchemysim0.reference.fasta.fai │ │ ├── pbalchemysim0.referenceset.xml │ │ ├── pbalchemysim0.subreads.bam │ │ ├── pbalchemysim0.subreads.bam.bai │ │ ├── pbalchemysim0.subreads.bam.pbi │ │ ├── pbalchemysim0.subreadset.xml │ │ ├── pbalchemysim1.alignmentset.xml │ │ ├── pbalchemysim1.pbalign.bam │ │ ├── pbalchemysim1.pbalign.bam.bai │ │ ├── pbalchemysim1.pbalign.bam.pbi │ │ ├── pbalchemysim1.subreads.bam │ │ ├── pbalchemysim1.subreads.bam.bai │ │ ├── pbalchemysim1.subreads.bam.pbi │ │ ├── pbalchemysim1.subreadset.xml │ │ ├── reference.dataset.xml │ │ ├── subread.dataset.xml │ │ └── subreadSetWithStats.xml │ ├── empty.aligned_subreads.bam │ ├── empty.aligned_subreads.bam.pbi │ ├── empty.ccs.bam │ ├── empty.ccs.bam.pbi │ ├── empty2.bam │ ├── empty2.bam.pbi │ ├── lambdaNEB.fa │ ├── lambdaNEB.fa.fai │ ├── m130727_114215_42211_c100569412550000001823090301191423_s1_p0.ccs.bam │ ├── m130727_114215_42211_c100569412550000001823090301191423_s1_p0.ccs.bam.bai │ ├── m130727_114215_42211_c100569412550000001823090301191423_s1_p0.ccs.bam.pbi │ ├── m140905_042212_sidney_c100564852550000001823085912221377_s1_X0.aligned_subreads.bam │ ├── m140905_042212_sidney_c100564852550000001823085912221377_s1_X0.aligned_subreads.bam.bai │ ├── m140905_042212_sidney_c100564852550000001823085912221377_s1_X0.aligned_subreads.bam.pbi │ ├── m140905_042212_sidney_c100564852550000001823085912221377_s1_X0.aligned_subreads.bam.pbi.v3 │ ├── m140905_042212_sidney_c100564852550000001823085912221377_s1_X0.scraps.bam │ ├── m140905_042212_sidney_c100564852550000001823085912221377_s1_X0.scraps.bam.pbi │ ├── m140905_042212_sidney_c100564852550000001823085912221377_s1_X0.subreads.bam │ ├── m140905_042212_sidney_c100564852550000001823085912221377_s1_X0.subreads.bam.pbi │ ├── variants.gff │ ├── weird.fa │ └── weird.fa.fai ├── io │ ├── FastaIO.py │ ├── FastqIO.py │ ├── FofnIO.py │ ├── GffIO.py │ ├── VcfIO.py │ ├── __init__.py │ ├── _utils.py │ ├── align │ │ ├── BamAlignment.py │ │ ├── BamIO.py │ │ ├── BlasrIO.py │ │ ├── PacBioBamIndex.py │ │ ├── _AlignmentMixin.py │ │ ├── _BamSupport.py │ │ └── __init__.py │ ├── base.py │ ├── bedfile.py │ ├── dataset │ │ ├── DataSetErrors.py │ │ ├── DataSetIO.py │ │ ├── DataSetMembers.py │ │ ├── DataSetMetaTypes.py │ │ ├── DataSetReader.py │ │ ├── DataSetUtils.py │ │ ├── DataSetValidator.py │ │ ├── DataSetWriter.py │ │ ├── __init__.py │ │ ├── run_split.py │ │ └── utils.py │ └── opener.py ├── model │ ├── __init__.py │ └── baseRegions.py ├── sequence.py └── util │ ├── ToolRunner.py │ ├── __init__.py │ ├── decorators.py │ └── statistics.py ├── pytest.ini ├── setup.cfg ├── setup.py └── tests ├── conftest.py ├── data ├── report.txt ├── report2.txt ├── supplemental_resources.consensusreadset.xml ├── supplemental_resources2.consensusreadset.xml └── test_dataset_run_split │ └── filt.xml ├── test_dataset_run_split.py ├── test_mapped_sequence_identity.py 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