LICENSE
MANIFEST.in
README.md
setup.py
src/swigpyrun.h
src/cgatools/core.hpp
src/cgatools/reference/ChromosomeIdField.cpp
src/cgatools/reference/ChromosomeIdField.hpp
src/cgatools/reference/CompactDnaSequence.cpp
src/cgatools/reference/CompactDnaSequence.hpp
src/cgatools/reference/CrrFile.cpp
src/cgatools/reference/CrrFile.hpp
src/cgatools/reference/CrrFileWriter.cpp
src/cgatools/reference/CrrFileWriter.hpp
src/cgatools/reference/GeneDataStore.cpp
src/cgatools/reference/GeneDataStore.hpp
src/cgatools/reference/RangeAnnotationStore.hpp
src/cgatools/reference/RepeatMaskerStore.hpp
src/cgatools/reference/range.hpp
src/cgatools/util/BaseUtil.cpp
src/cgatools/util/BaseUtil.hpp
src/cgatools/util/DelimitedFile.cpp
src/cgatools/util/DelimitedFile.hpp
src/cgatools/util/DelimitedLineParser.cpp
src/cgatools/util/DelimitedLineParser.hpp
src/cgatools/util/Exception.cpp
src/cgatools/util/Exception.hpp
src/cgatools/util/GenericHistogram.cpp
src/cgatools/util/GenericHistogram.hpp
src/cgatools/util/IndirectComparator.hpp
src/cgatools/util/Md5.cpp
src/cgatools/util/Md5.hpp
src/cgatools/util/RangeIntersector.hpp
src/cgatools/util/RangeSet.cpp
src/cgatools/util/RangeSet.hpp
src/cgatools/util/Streams.cpp
src/cgatools/util/Streams.hpp
src/cgatools/util/StringSet.cpp
src/cgatools/util/StringSet.hpp
src/cgatools/util/parse.cpp
src/cgatools/util/parse.hpp
src/hdf5-blosc/blosc_filter.c
src/hdf5-blosc/blosc_filter.h
src/hdf5-blosc/blosc_plugin.c
src/hdf5-blosc/blosc_plugin.h
src/libplinkio/bed.c
src/libplinkio/bed.h
src/libplinkio/bed_header.c
src/libplinkio/bed_header.h
src/libplinkio/bim.c
src/libplinkio/bim.h
src/libplinkio/bim_parse.c
src/libplinkio/bim_parse.h
src/libplinkio/common.h
src/libplinkio/cplinkio.c
src/libplinkio/csv.h
src/libplinkio/fam.c
src/libplinkio/fam.h
src/libplinkio/fam_parse.c
src/libplinkio/fam_parse.h
src/libplinkio/file.c
src/libplinkio/file.h
src/libplinkio/libcsv.c
src/libplinkio/plinkio.c
src/libplinkio/plinkio.h
src/libplinkio/snp_lookup.h
src/libplinkio/snp_lookup_big.h
src/libplinkio/snp_lookup_little.h
src/libplinkio/snparray.c
src/libplinkio/snparray.h
src/libplinkio/status.h
src/libplinkio/utarray.h
src/sqlite/shell.c
src/sqlite/sqlite3.c
src/sqlite/sqlite3.h
src/sqlite/sqlite3ext.h
src/sqlite/vt_sqlite3_ext.cpp
src/sqlite/py2/cache.c
src/sqlite/py2/cache.h
src/sqlite/py2/connection.c
src/sqlite/py2/connection.h
src/sqlite/py2/cursor.c
src/sqlite/py2/cursor.h
src/sqlite/py2/microprotocols.c
src/sqlite/py2/microprotocols.h
src/sqlite/py2/module.c
src/sqlite/py2/module.h
src/sqlite/py2/prepare_protocol.c
src/sqlite/py2/prepare_protocol.h
src/sqlite/py2/row.c
src/sqlite/py2/row.h
src/sqlite/py2/sqlitecompat.h
src/sqlite/py2/statement.c
src/sqlite/py2/statement.h
src/sqlite/py2/util.c
src/sqlite/py2/util.h
src/sqlite/py3/cache.c
src/sqlite/py3/cache.h
src/sqlite/py3/connection.c
src/sqlite/py3/connection.h
src/sqlite/py3/cursor.c
src/sqlite/py3/cursor.h
src/sqlite/py3/microprotocols.c
src/sqlite/py3/microprotocols.h
src/sqlite/py3/module.c
src/sqlite/py3/module.h
src/sqlite/py3/prepare_protocol.c
src/sqlite/py3/prepare_protocol.h
src/sqlite/py3/row.c
src/sqlite/py3/row.h
src/sqlite/py3/sqlitecompat.h
src/sqlite/py3/statement.c
src/sqlite/py3/statement.h
src/sqlite/py3/util.c
src/sqlite/py3/util.h
src/ucsc/inc/aliType.h
src/ucsc/inc/asParse.h
src/ucsc/inc/bPlusTree.h
src/ucsc/inc/bamFile.h
src/ucsc/inc/base64.h
src/ucsc/inc/basicBed.h
src/ucsc/inc/bbiFile.h
src/ucsc/inc/bigBed.h
src/ucsc/inc/bigWig.h
src/ucsc/inc/binRange.h
src/ucsc/inc/bits.h
src/ucsc/inc/bwgInternal.h
src/ucsc/inc/cheapcgi.h
src/ucsc/inc/cirTree.h
src/ucsc/inc/common.h
src/ucsc/inc/dlist.h
src/ucsc/inc/dnaseq.h
src/ucsc/inc/dnautil.h
src/ucsc/inc/dystring.h
src/ucsc/inc/errabort.h
src/ucsc/inc/filePath.h
src/ucsc/inc/fuzzyFind.h
src/ucsc/inc/gfxPoly.h
src/ucsc/inc/hash.h
src/ucsc/inc/hmmstats.h
src/ucsc/inc/htmshell.h
src/ucsc/inc/https.h
src/ucsc/inc/internet.h
src/ucsc/inc/kxTok.h
src/ucsc/inc/linefile.h
src/ucsc/inc/localmem.h
src/ucsc/inc/memalloc.h
src/ucsc/inc/memgfx.h
src/ucsc/inc/mime.h
src/ucsc/inc/net.h
src/ucsc/inc/obscure.h
src/ucsc/inc/options.h
src/ucsc/inc/pipeline.h
src/ucsc/inc/portable.h
src/ucsc/inc/psl.h
src/ucsc/inc/rangeTree.h
src/ucsc/inc/rbTree.h
src/ucsc/inc/regexHelper.h
src/ucsc/inc/sig.h
src/ucsc/inc/sqlList.h
src/ucsc/inc/sqlNum.h
src/ucsc/inc/tokenizer.h
src/ucsc/inc/udc.h
src/ucsc/inc/vcf.h
src/ucsc/inc/verbose.h
src/ucsc/inc/zlibFace.h
src/ucsc/lib/aliType.c
src/ucsc/lib/asParse.c
src/ucsc/lib/bPlusTree.c
src/ucsc/lib/bamFile.c
src/ucsc/lib/base64.c
src/ucsc/lib/basicBed.c
src/ucsc/lib/bbiRead.c
src/ucsc/lib/bigBed.c
src/ucsc/lib/binRange.c
src/ucsc/lib/bits.c
src/ucsc/lib/bwgQuery.c
src/ucsc/lib/cheapcgi.c
src/ucsc/lib/cirTree.c
src/ucsc/lib/common.c
src/ucsc/lib/dlist.c
src/ucsc/lib/dnautil.c
src/ucsc/lib/dystring.c
src/ucsc/lib/errabort.c
src/ucsc/lib/ffAli.c
src/ucsc/lib/filePath.c
src/ucsc/lib/hash.c
src/ucsc/lib/hmmstats.c
src/ucsc/lib/htmshell.c
src/ucsc/lib/https.c
src/ucsc/lib/intExp.c
src/ucsc/lib/internet.c
src/ucsc/lib/kxTok.c
src/ucsc/lib/linefile.c
src/ucsc/lib/localmem.c
src/ucsc/lib/memalloc.c
src/ucsc/lib/mime.c
src/ucsc/lib/net.c
src/ucsc/lib/obscure.c
src/ucsc/lib/osunix.c
src/ucsc/lib/pipeline.c
src/ucsc/lib/portimpl.c
src/ucsc/lib/portimpl.h
src/ucsc/lib/psl.c
src/ucsc/lib/rangeTree.c
src/ucsc/lib/rbTree.c
src/ucsc/lib/regexHelper.c
src/ucsc/lib/servBrcMcw.c
src/ucsc/lib/servCrunx.c
src/ucsc/lib/servcis.c
src/ucsc/lib/servcl.c
src/ucsc/lib/servmsII.c
src/ucsc/lib/servpws.c
src/ucsc/lib/sqlList.c
src/ucsc/lib/sqlNum.c
src/ucsc/lib/tokenizer.c
src/ucsc/lib/udc.c
src/ucsc/lib/vcf.c
src/ucsc/lib/verbose.c
src/ucsc/lib/wildcmp.c
src/ucsc/lib/zlibFace.c
src/ucsc/samtools/bam.c
src/ucsc/samtools/bam.h
src/ucsc/samtools/bam_aux.c
src/ucsc/samtools/bam_import.c
src/ucsc/samtools/bam_index.c
src/ucsc/samtools/bam_pileup.c
src/ucsc/samtools/bgzf.c
src/ucsc/samtools/bgzf.h
src/ucsc/samtools/faidx.c
src/ucsc/samtools/faidx.h
src/ucsc/samtools/kstring.h
src/ucsc/samtools/razf.c
src/ucsc/samtools/razf.h
src/ucsc/samtools/sam.c
src/ucsc/samtools/sam.h
src/ucsc/samtools/sam_header.c
src/ucsc/samtools/sam_header.h
src/ucsc/tabix/bam_endian.h
src/ucsc/tabix/bedidx.c
src/ucsc/tabix/index.c
src/ucsc/tabix/khash.h
src/ucsc/tabix/knetfile.c
src/ucsc/tabix/knetfile.h
src/ucsc/tabix/kseq.h
src/ucsc/tabix/ksort.h
src/ucsc/tabix/kstring.c
src/ucsc/tabix/kstring.h
src/ucsc/tabix/tabix.h
src/variant_tools/__init__.py
src/variant_tools/_version.py
src/variant_tools/accessor.py
src/variant_tools/action.cpp
src/variant_tools/action.h
src/variant_tools/annotation.py
src/variant_tools/assoData.cpp
src/variant_tools/assoData.h
src/variant_tools/assoTests.h
src/variant_tools/assoTests.i
src/variant_tools/assoTests.py
src/variant_tools/assoTests_wrap.cpp
src/variant_tools/association.py
src/variant_tools/association_hdf5.py
src/variant_tools/cgatools.i
src/variant_tools/cgatools.py
src/variant_tools/cgatools_wrap.cpp
src/variant_tools/checking_asso_result.py
src/variant_tools/compare.py
src/variant_tools/exporter.py
src/variant_tools/exporter_reader.py
src/variant_tools/fisher2.c
src/variant_tools/fisher2.h
src/variant_tools/geno_store.py
src/variant_tools/genotypes.c
src/variant_tools/genotypes.h
src/variant_tools/importer.py
src/variant_tools/importer_allele_hdf5.py
src/variant_tools/io_vcf_read.c
src/variant_tools/io_vcf_read.pyx
src/variant_tools/liftOver.py
src/variant_tools/lm.cpp
src/variant_tools/lm.h
src/variant_tools/merge_sort_parallel.py
src/variant_tools/meta.py
src/variant_tools/phenotype.py
src/variant_tools/pipeline.py
src/variant_tools/plinkfile.py
src/variant_tools/plot.py
src/variant_tools/preprocessor.py
src/variant_tools/project.py
src/variant_tools/rtester.py
src/variant_tools/simulation.py
src/variant_tools/site_options.py
src/variant_tools/tester.py
src/variant_tools/text_reader.py
src/variant_tools/ucsctools.i
src/variant_tools/ucsctools.py
src/variant_tools/ucsctools_wrap.cpp
src/variant_tools/update.py
src/variant_tools/utils.cpp
src/variant_tools/utils.h
src/variant_tools/utils.py
src/variant_tools/variant.py
src/variant_tools/vt_sqlite3.py
src/variant_tools/vtools.py
src/variant_tools/vtools_report.py
src/variant_tools/worker_zmq.py
src/variant_tools.egg-info/PKG-INFO
src/variant_tools.egg-info/SOURCES.txt
src/variant_tools.egg-info/dependency_links.txt
src/variant_tools.egg-info/entry_points.txt
src/variant_tools.egg-info/requires.txt
src/variant_tools.egg-info/top_level.txt
test/run_tests.py
test/temp_test_import_hdf5.py
test/testUtils.py
test/test_admin.py
test/test_associate.py
test/test_avg_depth.py
test/test_compare.py
test/test_exclude.py
test/test_execute.py
test/test_export.py
test/test_func.py
test/test_import.py
test/test_init.py
test/test_liftover.py
test/test_output.py
test/test_phenotype.py
test/test_pipeline.py
test/test_remove.py
test/test_select.py
test/test_show.py
test/test_trans_ratio.py
test/test_update.py
test/test_use.py