CHANGELOG.org
LICENSES.txt
MANIFEST.in
Makefile
README.md
circle.yml
requirements-dev.txt
requirements.txt
setup.cfg
setup.py
./pbcore/__init__.py
./pbcore/sequence.py
./pbcore/chemistry/__init__.py
./pbcore/chemistry/chemistry.py
./pbcore/chemistry/resources/mapping.xml
./pbcore/data/1.4_bas_files.fofn
./pbcore/data/2.0_bax_files.fofn
./pbcore/data/2.1_bax_files.fofn
./pbcore/data/2.1_ccs_files.fofn
./pbcore/data/2.3_bax_files.fofn
./pbcore/data/Fluidigm_human_amplicons.fasta
./pbcore/data/Fluidigm_human_amplicons.fasta.fai
./pbcore/data/Fluidigm_human_amplicons_tiny.fasta
./pbcore/data/__init__.py
./pbcore/data/aligned_reads_1.cmp.h5
./pbcore/data/barcodes-ed65-450.fasta
./pbcore/data/barcodes-ed65-450.fasta.fai
./pbcore/data/bc_files.fofn
./pbcore/data/blasr-output.m4
./pbcore/data/blasr-output.m5
./pbcore/data/chemistry.xml
./pbcore/data/empty.aligned_subreads.bam
./pbcore/data/empty.aligned_subreads.bam.pbi
./pbcore/data/empty.ccs.bam
./pbcore/data/empty.ccs.bam.pbi
./pbcore/data/lambdaNEB.fa
./pbcore/data/lambdaNEB.fa.fai
./pbcore/data/m110818_075520_42141_c100129202555500000315043109121112_s1_p0.bas.h5
./pbcore/data/m110818_075520_42141_c100129202555500000315043109121112_s2_p0.bas.h5
./pbcore/data/m130522_092457_42208_c100497142550000001823078008081323_s1_p0.1.bax.h5
./pbcore/data/m130522_092457_42208_c100497142550000001823078008081323_s1_p0.2.bax.h5
./pbcore/data/m130522_092457_42208_c100497142550000001823078008081323_s1_p0.3.bax.h5
./pbcore/data/m130522_092457_42208_c100497142550000001823078008081323_s1_p0.bas.h5
./pbcore/data/m130727_114215_42211_c100569412550000001823090301191423_s1_p0.1.ccs.h5
./pbcore/data/m130727_114215_42211_c100569412550000001823090301191423_s1_p0.ccs.bam
./pbcore/data/m130727_114215_42211_c100569412550000001823090301191423_s1_p0.ccs.bam.bai
./pbcore/data/m130727_114215_42211_c100569412550000001823090301191423_s1_p0.ccs.bam.pbi
./pbcore/data/m130731_192718_42129_c100564662550000001823085912221321_s1_p0.1.bax.h5
./pbcore/data/m130731_192718_42129_c100564662550000001823085912221321_s1_p0.1.rgn.h5
./pbcore/data/m130731_192718_42129_c100564662550000001823085912221321_s1_p0.2.bax.h5
./pbcore/data/m130731_192718_42129_c100564662550000001823085912221321_s1_p0.2.rgn.h5
./pbcore/data/m130731_192718_42129_c100564662550000001823085912221321_s1_p0.3.bax.h5
./pbcore/data/m130731_192718_42129_c100564662550000001823085912221321_s1_p0.3.rgn.h5
./pbcore/data/m130731_192718_42129_c100564662550000001823085912221321_s1_p0.bas.h5
./pbcore/data/m140307_221913_42203_c100626172550000001823119008061414_s1_p0.1.bc.h5
./pbcore/data/m140307_221913_42203_c100626172550000001823119008061414_s1_p0.2.bc.h5
./pbcore/data/m140307_221913_42203_c100626172550000001823119008061414_s1_p0.3.bc.h5
./pbcore/data/m140905_042212_sidney_c100564852550000001823085912221377_s1_X0.1.bax.h5
./pbcore/data/m140905_042212_sidney_c100564852550000001823085912221377_s1_X0.aligned_subreads.bam
./pbcore/data/m140905_042212_sidney_c100564852550000001823085912221377_s1_X0.aligned_subreads.bam.bai
./pbcore/data/m140905_042212_sidney_c100564852550000001823085912221377_s1_X0.aligned_subreads.bam.pbi
./pbcore/data/m140905_042212_sidney_c100564852550000001823085912221377_s1_X0.aligned_subreads.cmp.h5
./pbcore/data/m140905_042212_sidney_c100564852550000001823085912221377_s1_X0.scraps.bam
./pbcore/data/m140905_042212_sidney_c100564852550000001823085912221377_s1_X0.scraps.bam.pbi
./pbcore/data/m140905_042212_sidney_c100564852550000001823085912221377_s1_X0.subreads.bam
./pbcore/data/m140905_042212_sidney_c100564852550000001823085912221377_s1_X0.subreads.bam.pbi
./pbcore/data/m140912_020930_00114_c100702482550000001823141103261590_s1_p0.1.bax.h5
./pbcore/data/m140912_020930_00114_c100702482550000001823141103261590_s1_p0.2.bax.h5
./pbcore/data/m140912_020930_00114_c100702482550000001823141103261590_s1_p0.3.bax.h5
./pbcore/data/m140912_020930_00114_c100702482550000001823141103261590_s1_p0.bas.h5
./pbcore/data/variants.gff
./pbcore/data/weird.fa
./pbcore/data/weird.fa.fai
./pbcore/data/datasets/__init__.py
./pbcore/data/datasets/alignment.dataset.xml
./pbcore/data/datasets/barcode.dataset.xml
./pbcore/data/datasets/ccsaligned.dataset.xml
./pbcore/data/datasets/ccsread.dataset.xml
./pbcore/data/datasets/contig.dataset.xml
./pbcore/data/datasets/empty_lambda.aligned.bam
./pbcore/data/datasets/empty_lambda.aligned.bam.bai
./pbcore/data/datasets/empty_lambda.aligned.bam.pbi
./pbcore/data/datasets/fofn.fofn
./pbcore/data/datasets/hdfsubread_dataset.xml
./pbcore/data/datasets/lambda.alignmentset.xml
./pbcore/data/datasets/lambda.referenceset.xml
./pbcore/data/datasets/m140905_042212_sidney_c100564852550000001823085912221377_s1_X0.subreads.fake_bc.bam
./pbcore/data/datasets/m140905_042212_sidney_c100564852550000001823085912221377_s1_X0.subreads.fake_bc.bam.bai
./pbcore/data/datasets/m140905_042212_sidney_c100564852550000001823085912221377_s1_X0.subreads.fake_bc.bam.pbi
./pbcore/data/datasets/m150430_142051_Mon_p1_b25.sts.xml
./pbcore/data/datasets/m150616_053259_ethan_c100710482550000001823136404221563_s1_p0.sts.xml
./pbcore/data/datasets/pbalchemysim.alignmentset.xml
./pbcore/data/datasets/pbalchemysim.hdfsubreadset.xml
./pbcore/data/datasets/pbalchemysim0.alignmentset.chunk0contigs.xml
./pbcore/data/datasets/pbalchemysim0.alignmentset.chunk1contigs.xml
./pbcore/data/datasets/pbalchemysim0.alignmentset.xml
./pbcore/data/datasets/pbalchemysim0.bas.h5
./pbcore/data/datasets/pbalchemysim0.hdfsubreadset.xml
./pbcore/data/datasets/pbalchemysim0.pbalign.bam
./pbcore/data/datasets/pbalchemysim0.pbalign.bam.bai
./pbcore/data/datasets/pbalchemysim0.pbalign.bam.pbi
./pbcore/data/datasets/pbalchemysim0.reference.fasta
./pbcore/data/datasets/pbalchemysim0.reference.fasta.fai
./pbcore/data/datasets/pbalchemysim0.referenceset.xml
./pbcore/data/datasets/pbalchemysim0.subreads.bam
./pbcore/data/datasets/pbalchemysim0.subreads.bam.bai
./pbcore/data/datasets/pbalchemysim0.subreads.bam.pbi
./pbcore/data/datasets/pbalchemysim0.subreadset.xml
./pbcore/data/datasets/pbalchemysim1.alignmentset.xml
./pbcore/data/datasets/pbalchemysim1.bas.h5
./pbcore/data/datasets/pbalchemysim1.hdfsubreadset.xml
./pbcore/data/datasets/pbalchemysim1.pbalign.bam
./pbcore/data/datasets/pbalchemysim1.pbalign.bam.bai
./pbcore/data/datasets/pbalchemysim1.pbalign.bam.pbi
./pbcore/data/datasets/pbalchemysim1.subreads.bam
./pbcore/data/datasets/pbalchemysim1.subreads.bam.bai
./pbcore/data/datasets/pbalchemysim1.subreads.bam.pbi
./pbcore/data/datasets/pbalchemysim1.subreadset.xml
./pbcore/data/datasets/reference.dataset.xml
./pbcore/data/datasets/subread.dataset.xml
./pbcore/data/datasets/subreadSetWithStats.xml
./pbcore/data/datasets/transformed_rs_subread.dataset.xml
./pbcore/io/BarcodeH5Reader.py
./pbcore/io/BasH5IO.py
./pbcore/io/FastaIO.py
./pbcore/io/FastqIO.py
./pbcore/io/FofnIO.py
./pbcore/io/GffIO.py
./pbcore/io/VcfIO.py
./pbcore/io/__init__.py
./pbcore/io/_utils.py
./pbcore/io/base.py
./pbcore/io/opener.py
./pbcore/io/rangeQueries.py
./pbcore/io/align/BamAlignment.py
./pbcore/io/align/BamIO.py
./pbcore/io/align/BlasrIO.py
./pbcore/io/align/CmpH5IO.py
./pbcore/io/align/PacBioBamIndex.py
./pbcore/io/align/_AlignmentMixin.py
./pbcore/io/align/_BamSupport.py
./pbcore/io/align/__init__.py
./pbcore/io/align/_bgzf.py
./pbcore/io/dataset/DataSetErrors.py
./pbcore/io/dataset/DataSetIO.py
./pbcore/io/dataset/DataSetMembers.py
./pbcore/io/dataset/DataSetMetaTypes.py
./pbcore/io/dataset/DataSetReader.py
./pbcore/io/dataset/DataSetUtils.py
./pbcore/io/dataset/DataSetValidator.py
./pbcore/io/dataset/DataSetWriter.py
./pbcore/io/dataset/__init__.py
./pbcore/io/dataset/utils.py
./pbcore/io/dataset/pyxb/DataSetXsd.py
./pbcore/io/dataset/pyxb/__init__.py
./pbcore/io/dataset/pyxb/_pbbase.py
./pbcore/io/dataset/pyxb/_pbmeta.py
./pbcore/io/dataset/pyxb/_pbrk.py
./pbcore/io/dataset/pyxb/_pbsample.py
./pbcore/model/__init__.py
./pbcore/model/baseRegions.py
./pbcore/util/Process.py
./pbcore/util/ToolRunner.py
./pbcore/util/__init__.py
./pbcore/util/decorators.py
bin/updateXSDs.py
doc/Makefile
doc/conf.py
doc/index.rst
doc/modules.rst
doc/pbcore.chemistry.rst
doc/pbcore.data.rst
doc/pbcore.io.dataset.rst
doc/pbcore.io.rst
doc/pbcore.model.rst
doc/pbcore.rst
doc/pbcore.util.rst
doc/pacbio-theme/theme.conf
doc/pacbio-theme/static/headerGradient.jpg
doc/pacbio-theme/static/pacbio.css
doc/pacbio-theme/static/pacbioLogo.png
doc/pacbio-theme/static/pygments.css
pbcore.egg-info/PKG-INFO
pbcore.egg-info/SOURCES.txt
pbcore.egg-info/dependency_links.txt
pbcore.egg-info/entry_points.txt
pbcore.egg-info/not-zip-safe
pbcore.egg-info/requires.txt
pbcore.egg-info/top_level.txt
pbcore/data/Makefile
tests/test_pbcore_data.py
tests/test_pbcore_extract_bam_sequence.py
tests/test_pbcore_io_AlnFileReaders.py
tests/test_pbcore_io_BarcodeH5Reader.py
tests/test_pbcore_io_BasH5Collection.py
tests/test_pbcore_io_BasH5Reader.py
tests/test_pbcore_io_BlasrIO.py
tests/test_pbcore_io_FastaIO.py
tests/test_pbcore_io_FastaTable.py
tests/test_pbcore_io_FastqIO.py
tests/test_pbcore_io_FofnIO.py
tests/test_pbcore_io_GffIO.py
tests/test_pbcore_io_VcfIO.py
tests/test_pbcore_io_bgzf.py
tests/test_pbcore_io_lossless_bam.py
tests/test_pbcore_io_rangeQueries.py
tests/test_pbcore_io_unaligned_bam.py
tests/test_pbcore_util_sequences.py
tests/test_pbdataset.py
tests/test_pbdataset_filters.py
tests/test_pbdataset_metadata.py
tests/test_pbdataset_split.py
tests/test_pbdataset_subtypes.py
tests/test_pbdataset_utils.py
tests/utils.py