├── .gitignore ├── .gitmodules ├── CHANGES ├── LICENSE ├── Makefile ├── README.md ├── Singularity ├── bin └── .gitignore ├── samples ├── 20_011976121_012173018.bin.onlyThree.bcf.gz ├── 20_011976121_012173018.bin.onlyThree.bcf.gz.csi ├── 20_011976121_012173018.bin.onlyThree.bin ├── 20_011976121_012173018.bin.onlyThree.bin.txt ├── 20_011976121_012173018.bin.onlyThree.gls ├── 20_011976121_012173018.bin.onlyThree.hap ├── 20_011976121_012173018.bin.onlyThree.haps ├── 20_011976121_012173018.bin.onlyThree.legend ├── 20_011976121_012173018.bin.onlyThree.scaffold50.hap ├── 20_011976121_012173018.bin.onlyThree.scaffold50.haps ├── 20_011976121_012173018.bin.onlyThree.scaffold50.legend ├── 20_011976121_012173018.bin.onlyThree.scaffold50.sorted.haps ├── 20_011976121_012173018.bin.onlyThree.scaffold50.sorted.tabhaps.gz ├── 20_011976121_012173018.bin.onlyThree.scaffold50.sorted.tabhaps.gz.tbi ├── 20_011976121_012173018.bin.onlyThree.scaffold50.sorted.unordered.haps ├── 20_011976121_012173018.bin.onlyThree.scaffold50.sorted.unordered.vcf.gz ├── 20_011976121_012173018.bin.onlyThree.scaffold50.sorted.unordered.vcf.gz.tbi ├── 20_011976121_012173018.bin.onlyThree.scaffold50.sorted.vcf.gz ├── 20_011976121_012173018.bin.onlyThree.scaffold50.sorted.vcf.gz.tbi ├── 20_011976121_012173018.bin.onlyThree.scaffold50.sorted.withMultiall.haps ├── 20_011976121_012173018.bin.onlyThree.scaffold50.sorted.withMultiall.multiSwapped.haps ├── 20_011976121_012173018.bin.onlyThree.scaffold50.sorted.wrongRegion.haps ├── 20_011976121_012173018.bin.onlyThree.vcf.gz ├── 20_011976121_012173018.bin.onlyThree.vcf.gz.csi ├── 20_011976121_012173018.bin.onlyThree.withMultiall.bin ├── 20_011976121_012173018.bin.onlyThree.withMultiall.bin.txt ├── 20_0_62000000.011976121_012173018.paste.onlyThree.hap ├── 20_0_62000000.011976121_012173018.paste.onlyThree.haps ├── 20_0_62000000.011976121_012173018.paste.onlyThree.legend ├── 20_0_62000000.011976121_012173018.paste.onlyThree.unsorted.haps ├── 20_0_62000000.011976121_012173018.paste.onlyThree.vcf.gz ├── 20_0_62000000.011976121_012173018.paste.onlyThree.vcf.gz.tbi ├── 20_0_62000000.bin.onlyThree.hap ├── 20_0_62000000.bin.onlyThree.legend ├── README.sh ├── brokenFiles │ ├── onlyThree.hapLegSamp.extraLine.sample │ └── onlyThree.hapsSample.extraLine.sample ├── geneticMap │ └── genetic_map_chr20_combined_b37.txt.gz ├── glReader │ ├── 20_011976121_012173018.bin.onlyThree.bcf │ ├── 20_011976121_012173018.bin.onlyThree.bcf.gz │ ├── 20_011976121_012173018.bin.onlyThree.bcf.gz.csi │ ├── 20_011976121_012173018.bin.onlyThree.vcf │ ├── 20_011976121_012173018.bin.onlyThree.vcf.gz │ └── 20_011976121_012173018.bin.onlyThree.vcf.gz.csi ├── hapGen │ ├── ex.almost_multi.vcf.gz │ ├── ex.almost_multi.vcf.gz.csi │ ├── ex.bgl.log │ ├── ex.bgl.vcf.gz │ ├── ex.bgl.vcf.gz.csi │ ├── ex.bin │ ├── ex.bt.leg │ ├── ex.forBT.gen.gz │ ├── ex.gen.gz │ ├── ex.gls.almost_multi.vcf.gz │ ├── ex.gls.almost_multi.vcf.gz.csi │ ├── ex.gls.multi.vcf.gz │ ├── ex.gls.multi.vcf.gz.csi │ ├── ex.gls.vcf.gz │ ├── ex.gls.vcf.gz.csi │ ├── ex.haps.gz │ ├── ex.leg │ ├── ex.map │ ├── ex.multi.bgl.vcf.gz │ ├── ex.multi.bgl.vcf.gz.csi │ ├── ex.multi.bin │ ├── ex.multi.vcf.gz │ ├── ex.multi.vcf.gz.csi │ ├── ex.sample │ ├── ex.vcf.gz │ ├── ex.vcf.gz.csi │ ├── ex.wtccc.haps.gz │ ├── ex.wtccc.sample │ └── generateGLs.R ├── multi_gls │ ├── 20.5335724-5861377.1024_site_subset.union.filteredAC5.onlyPhased.NM_HOMMAJORv3.inGLSamples.winni_filt_subset.with_multi.bcf.gz │ ├── 20.5335724-5861377.1024_site_subset.union.filteredAC5.onlyPhased.NM_HOMMAJORv3.inGLSamples.winni_filt_subset.with_multi.bcf.gz.csi │ ├── 20.5335724-5861377.1024_site_subset.union.filteredAC5.onlyPhased.NM_HOMMAJORv3.inGLSamples.winni_filt_subset.with_multi.ordered.bcf.gz │ ├── 20.5335724-5861377.1024_site_subset.union.filteredAC5.onlyPhased.NM_HOMMAJORv3.inGLSamples.winni_filt_subset.with_multi.ordered.hap.gz │ ├── 20.5335724-5861377.1024_site_subset.union.filteredAC5.onlyPhased.NM_HOMMAJORv3.inGLSamples.winni_filt_subset.with_multi.ordered.sample │ ├── 20.5335724-5861377.1024_site_subset.union.filteredAC5.onlyPhased.NM_HOMMAJORv3.inGLSamples.winni_filt_subset.with_multi.ordered.tabhaps.gz │ ├── 20.5335724-5861377.1024_site_subset.union.filteredAC5.onlyPhased.NM_HOMMAJORv3.inGLSamples.winni_filt_subset.with_multi.ordered.tabhaps.gz.tbi │ ├── 20.5335724-5861377.chip.omni_broad_sanger_combined.20140818.snps.genotypes.samples │ ├── 20.5335724-5861377.chip.omni_broad_sanger_combined.20140818.snps.genotypes.vcf.gz │ ├── 20.5335724-5861377.chip.omni_broad_sanger_combined.20140818.snps.genotypes.vcf.gz.csi │ ├── chr20.5335724-5861377.1024_site_subset.HRC.r1.AC5.TGPP3_samples.likelihoods.winniFilter.bcf.gz │ ├── chr20.5335724-5861377.1024_site_subset.HRC.r1.AC5.TGPP3_samples.likelihoods.winniFilter.bcf.gz.csi │ ├── chr20.5335724-5861377.1024_site_subset.HRC.r1.AC5.TGPP3_samples.likelihoods.winniFilter.bin │ ├── chr20.5335724-5861377.1024_site_subset.HRC.r1.AC5.TGPP3_samples.likelihoods.winniFilter.no_multi.bcf.gz │ ├── chr20.5335724-5861377.1024_site_subset.HRC.r1.AC5.TGPP3_samples.likelihoods.winniFilter.no_multi.bcf.gz.csi │ ├── chr20.5335724-5861377.1024_site_subset.HRC.r1.AC5.TGPP3_samples.likelihoods.winniFilter.sites.vcf.gz │ └── chr20.5335724-5861377.1024_site_subset.HRC.r1.AC5.TGPP3_samples.likelihoods.winniFilter.vcf.gz ├── onlyThree.hapLegSamp.sample ├── onlyThree.hapsSample.sample ├── onlyThree.hapsSample.unordered.sample └── simple_gls │ ├── simple.gls.bin │ ├── simple.gls.txt │ ├── simple.gls.v1.bin │ ├── simple.gls.v1.expected.bin.vcf │ ├── simple.gls.v1.noSamp1.expected.bin.vcf │ ├── simple.gls.v1.region.expected.bin.vcf │ ├── simple.gls.v1.samePos.bin │ ├── simple.gls.v1.samePos.expected.bin.vcf │ ├── simple.gls.v1.samePos.txt │ ├── simple.gls.v1.txt │ ├── simple.gls.v2.samePos.err.bin │ └── simple.gls.v2.samePos.err.txt ├── scripts ├── bin2vcf.pl ├── reorder_multi.pl └── vcf2STbin.pl ├── src ├── MHSampler.hpp ├── Makefile ├── OUTLINE ├── bak │ ├── haplotypeCluster.cpp │ ├── haplotypeCluster.h │ ├── haplotypeCluster_kmeans.cpp │ ├── impute.cpp │ ├── impute.h │ └── main.cpp ├── bio.cpp ├── bio.hpp ├── emcchain.cpp ├── emcchain.hpp ├── geneticMap.cpp ├── geneticMap.hpp ├── glPack.cpp ├── glPack.hpp ├── glReader.cpp ├── glReader.hpp ├── glVQ.cpp ├── glVQ.hpp ├── globals.h ├── gtest-1.7.0 │ ├── CHANGES │ ├── CMakeLists.txt │ ├── CONTRIBUTORS │ ├── LICENSE │ ├── Makefile.am │ ├── Makefile.in │ ├── README │ ├── aclocal.m4 │ ├── build-aux │ │ ├── config.guess │ │ ├── config.h.in │ │ ├── config.sub │ │ ├── depcomp │ │ ├── install-sh │ │ ├── ltmain.sh │ │ └── missing │ ├── cmake │ │ └── internal_utils.cmake │ ├── codegear │ │ ├── gtest.cbproj │ │ ├── gtest.groupproj │ │ ├── gtest_all.cc │ │ ├── gtest_link.cc │ │ ├── gtest_main.cbproj │ │ └── gtest_unittest.cbproj │ ├── configure │ ├── configure.ac │ ├── fused-src │ │ └── gtest │ │ │ ├── gtest-all.cc │ │ │ ├── gtest.h │ │ │ └── gtest_main.cc │ ├── include │ │ └── gtest │ │ │ ├── gtest-death-test.h │ │ │ ├── gtest-message.h │ │ │ ├── gtest-param-test.h │ │ │ ├── gtest-param-test.h.pump │ │ │ ├── gtest-printers.h │ │ │ ├── gtest-spi.h │ │ │ ├── gtest-test-part.h │ │ │ ├── gtest-typed-test.h │ │ │ ├── gtest.h │ │ │ ├── gtest_pred_impl.h │ │ │ ├── gtest_prod.h │ │ │ └── internal │ │ │ ├── gtest-death-test-internal.h │ │ │ ├── gtest-filepath.h │ │ │ ├── gtest-internal.h │ │ │ ├── gtest-linked_ptr.h │ │ │ ├── gtest-param-util-generated.h │ │ │ ├── gtest-param-util-generated.h.pump │ │ │ ├── gtest-param-util.h │ │ │ ├── gtest-port.h │ │ │ ├── gtest-string.h │ │ │ ├── gtest-tuple.h │ │ │ ├── gtest-tuple.h.pump │ │ │ ├── gtest-type-util.h │ │ │ └── gtest-type-util.h.pump │ ├── m4 │ │ ├── acx_pthread.m4 │ │ ├── gtest.m4 │ │ ├── libtool.m4 │ │ ├── ltoptions.m4 │ │ ├── ltsugar.m4 │ │ ├── ltversion.m4 │ │ └── lt~obsolete.m4 │ ├── make │ │ └── Makefile │ ├── msvc │ │ ├── gtest-md.sln │ │ ├── gtest-md.vcproj │ │ ├── gtest.sln │ │ ├── gtest.vcproj │ │ ├── gtest_main-md.vcproj │ │ ├── gtest_main.vcproj │ │ ├── gtest_prod_test-md.vcproj │ │ ├── gtest_prod_test.vcproj │ │ ├── gtest_unittest-md.vcproj │ │ └── gtest_unittest.vcproj │ ├── samples │ │ ├── prime_tables.h │ │ ├── sample1.cc │ │ ├── sample1.h │ │ ├── sample10_unittest.cc │ │ ├── sample1_unittest.cc │ │ ├── sample2.cc │ │ ├── sample2.h │ │ ├── sample2_unittest.cc │ │ ├── sample3-inl.h │ │ ├── sample3_unittest.cc │ │ ├── sample4.cc │ │ ├── sample4.h │ │ ├── sample4_unittest.cc │ │ ├── sample5_unittest.cc │ │ ├── sample6_unittest.cc │ │ ├── sample7_unittest.cc │ │ ├── sample8_unittest.cc │ │ └── sample9_unittest.cc │ ├── scripts │ │ ├── fuse_gtest_files.py │ │ ├── gen_gtest_pred_impl.py │ │ ├── gtest-config.in │ │ ├── pump.py │ │ └── test │ │ │ └── Makefile │ ├── src │ │ ├── gtest-all.cc │ │ ├── gtest-death-test.cc │ │ ├── gtest-filepath.cc │ │ ├── gtest-internal-inl.h │ │ ├── gtest-port.cc │ │ ├── gtest-printers.cc │ │ ├── gtest-test-part.cc │ │ ├── gtest-typed-test.cc │ │ ├── gtest.cc │ │ └── gtest_main.cc │ ├── test │ │ ├── gtest-death-test_ex_test.cc │ │ ├── gtest-death-test_test.cc │ │ ├── gtest-filepath_test.cc │ │ ├── gtest-linked_ptr_test.cc │ │ ├── gtest-listener_test.cc │ │ ├── gtest-message_test.cc │ │ ├── gtest-options_test.cc │ │ ├── gtest-param-test2_test.cc │ │ ├── gtest-param-test_test.cc │ │ ├── gtest-param-test_test.h │ │ ├── gtest-port_test.cc │ │ ├── gtest-printers_test.cc │ │ ├── gtest-test-part_test.cc │ │ ├── gtest-tuple_test.cc │ │ ├── gtest-typed-test2_test.cc │ │ ├── gtest-typed-test_test.cc │ │ ├── gtest-typed-test_test.h │ │ ├── gtest-unittest-api_test.cc │ │ ├── gtest_all_test.cc │ │ ├── gtest_break_on_failure_unittest.py │ │ ├── gtest_break_on_failure_unittest_.cc │ │ ├── gtest_catch_exceptions_test.py │ │ ├── gtest_catch_exceptions_test_.cc │ │ ├── gtest_color_test.py │ │ ├── gtest_color_test_.cc │ │ ├── gtest_env_var_test.py │ │ ├── gtest_env_var_test_.cc │ │ ├── gtest_environment_test.cc │ │ ├── gtest_filter_unittest.py │ │ ├── gtest_filter_unittest_.cc │ │ ├── gtest_help_test.py │ │ ├── gtest_help_test_.cc │ │ ├── gtest_list_tests_unittest.py │ │ ├── gtest_list_tests_unittest_.cc │ │ ├── gtest_main_unittest.cc │ │ ├── gtest_no_test_unittest.cc │ │ ├── gtest_output_test.py │ │ ├── gtest_output_test_.cc │ │ ├── gtest_output_test_golden_lin.txt │ │ ├── gtest_pred_impl_unittest.cc │ │ ├── gtest_premature_exit_test.cc │ │ ├── gtest_prod_test.cc │ │ ├── gtest_repeat_test.cc │ │ ├── gtest_shuffle_test.py │ │ ├── gtest_shuffle_test_.cc │ │ ├── gtest_sole_header_test.cc │ │ ├── gtest_stress_test.cc │ │ ├── gtest_test_utils.py │ │ ├── gtest_throw_on_failure_ex_test.cc │ │ ├── gtest_throw_on_failure_test.py │ │ ├── gtest_throw_on_failure_test_.cc │ │ ├── gtest_uninitialized_test.py │ │ ├── gtest_uninitialized_test_.cc │ │ ├── gtest_unittest.cc │ │ ├── gtest_xml_outfile1_test_.cc │ │ ├── gtest_xml_outfile2_test_.cc │ │ ├── gtest_xml_outfiles_test.py │ │ ├── gtest_xml_output_unittest.py │ │ ├── gtest_xml_output_unittest_.cc │ │ ├── gtest_xml_test_utils.py │ │ ├── production.cc │ │ └── production.h │ └── xcode │ │ ├── Config │ │ ├── DebugProject.xcconfig │ │ ├── FrameworkTarget.xcconfig │ │ ├── General.xcconfig │ │ ├── ReleaseProject.xcconfig │ │ ├── StaticLibraryTarget.xcconfig │ │ └── TestTarget.xcconfig │ │ ├── Resources │ │ └── Info.plist │ │ ├── Samples │ │ └── FrameworkSample │ │ │ ├── Info.plist │ │ │ ├── WidgetFramework.xcodeproj │ │ │ └── project.pbxproj │ │ │ ├── runtests.sh │ │ │ ├── widget.cc │ │ │ ├── widget.h │ │ │ └── widget_test.cc │ │ ├── Scripts │ │ ├── runtests.sh │ │ └── versiongenerate.py │ │ └── gtest.xcodeproj │ │ └── project.pbxproj ├── hapPanel.cpp ├── hapPanel.hpp ├── haplotype.cpp ├── haplotype.hpp ├── hmmLike.cpp ├── hmmLike.cu ├── hmmLike.h ├── hmmLike.hcu ├── hmmLike.hpp ├── impute.cpp ├── impute.hpp ├── insti.cpp ├── insti.hpp ├── kMeans.hpp ├── kMedoids.cpp ├── kMedoids.hpp ├── kNN.cpp ├── kNN.hpp ├── main.cpp ├── olivier │ ├── utils.cpp │ └── utils.hpp ├── sampler.cpp ├── sampler.hpp ├── tabix.cpp ├── tabix.hpp ├── testing │ ├── Makefile │ ├── cuda_tests.cpp │ ├── cuda_tests.cu │ ├── glPack_unittests.cpp │ ├── glReader_tests.cpp │ ├── insti_unittests.cpp │ └── other_unittests.cpp └── version.hpp └── t ├── 10-phase_simple_gls.t ├── 15-phase_simple_gls_multiallelic.t ├── 90-phase_simulated_gls.t ├── 905-phase_simulated_gls_multi.t ├── 91-phase_simulated_gls_with_scaffold.t ├── 92-phase_real_gls_with_pre_haps_multi.t ├── VCFComp.pm └── regression_tests.pl /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/winni2k/GLPhase/HEAD/.gitignore -------------------------------------------------------------------------------- /.gitmodules: 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