├── .gitignore ├── .gitmodules ├── .travis.yml ├── LICENSE ├── Makefile ├── Makefile.default ├── README.md ├── ahmm.cpp ├── ahmm.h ├── align.cpp ├── align.h ├── allele.cpp ├── allele.h ├── annotate_1000g.cpp ├── annotate_1000g.h ├── annotate_dbsnp_rsid.cpp ├── annotate_dbsnp_rsid.h ├── annotate_indels.cpp ├── annotate_indels.h ├── annotate_indels2.cpp ├── annotate_indels2.h ├── annotate_indels3.cpp ├── annotate_regions.cpp ├── annotate_regions.h ├── annotate_variants.cpp ├── annotate_variants.h ├── annotate_vntrs.cpp ├── annotate_vntrs.h ├── augmented_bam_record.cpp ├── augmented_bam_record.h ├── bam_ordered_reader.cpp ├── bam_ordered_reader.h ├── bcf_genotyping_buffered_reader.cpp ├── bcf_genotyping_buffered_reader.h ├── bcf_ordered_reader.cpp ├── bcf_ordered_reader.h ├── bcf_ordered_writer.cpp ├── bcf_ordered_writer.h ├── bcf_single_genotyping_buffered_reader.cpp ├── bcf_single_genotyping_buffered_reader.h ├── bcf_synced_reader.cpp ├── bcf_synced_reader.h ├── bed.cpp ├── bed.h ├── candidate_motif_picker.cpp ├── candidate_motif_picker.h ├── candidate_region_extractor.cpp ├── candidate_region_extractor.h ├── cat.cpp ├── cat.h ├── chmm.cpp ├── chmm.h ├── circular_buffer.cpp ├── circular_buffer.h ├── complex_genotyping_record.cpp ├── complex_genotyping_record.h ├── compute_concordance.cpp ├── compute_concordance.h ├── compute_features.cpp ├── compute_features.h ├── compute_features2.cpp ├── compute_features2.h ├── compute_rl_dist.cpp ├── compute_rl_dist.h ├── config.cpp ├── config.h ├── consolidate.cpp ├── consolidate.h ├── consolidate_adjacent_vntrs.cpp ├── consolidate_adjacent_vntrs.h ├── consolidate_multiallelics.cpp ├── consolidate_multiallelics.h ├── consolidate_vntrs.cpp ├── consolidate_vntrs.h ├── construct_probes.cpp ├── construct_probes.h ├── decompose.cpp ├── decompose.h ├── decompose2.cpp ├── decompose2.h ├── decompose_blocksub.cpp ├── decompose_blocksub.h ├── discover.cpp ├── discover.h ├── duplicate.cpp ├── duplicate.h ├── estimate.cpp ├── estimate.h ├── estimator.cpp ├── estimator.h ├── extract_vntrs.cpp ├── extract_vntrs.h ├── filter.cpp ├── filter.h ├── filter_overlap.cpp ├── filter_overlap.h ├── flank_detector.cpp ├── flank_detector.h ├── fuzzy_aligner.cpp ├── fuzzy_aligner.h ├── fuzzy_partition.cpp ├── fuzzy_partition.h ├── gencode.cpp ├── gencode.h ├── genome_interval.cpp ├── genome_interval.h ├── genotype.cpp ├── genotype.h ├── genotyping_record.cpp ├── genotyping_record.h ├── ghmm.cpp ├── ghmm.h ├── hfilter.cpp ├── hfilter.h ├── hts_utils.cpp ├── hts_utils.h ├── indel_annotator.cpp ├── indel_annotator.h ├── indel_genotyping_record.cpp ├── indel_genotyping_record.h ├── index.cpp ├── index.h ├── info2tab.cpp ├── info2tab.h ├── interval.cpp ├── interval.h ├── interval_tree.cpp ├── interval_tree.h ├── large_motif_tree.cpp ├── large_motif_tree.h ├── lfhmm.cpp ├── lfhmm.h ├── lhmm.cpp ├── lhmm.h ├── lhmm1.cpp ├── lhmm1.h ├── lib ├── Rmath │ ├── Make.inc │ ├── Makefile │ ├── README.md │ ├── Rmath │ │ ├── R_ext │ │ │ ├── Arith.h │ │ │ ├── Boolean.h │ │ │ ├── Error.h │ │ │ ├── Print.h │ │ │ ├── RS.h │ │ │ ├── Random.h │ │ │ └── libextern.h │ │ ├── Rconfig.h │ │ ├── Rmath.h │ │ ├── Rmath.h0 │ │ └── config.h │ ├── bd0.c │ ├── bessel.h │ ├── bessel_i.c │ ├── bessel_j.c │ ├── bessel_k.c │ ├── bessel_y.c │ ├── beta.c │ ├── chebyshev.c │ ├── choose.c │ ├── d1mach.c │ ├── dbeta.c │ ├── dbinom.c │ ├── dcauchy.c │ ├── dchisq.c │ ├── dexp.c │ ├── df.c │ ├── dgamma.c │ ├── dgeom.c │ ├── dhyper.c │ ├── dlnorm.c │ ├── dlogis.c │ ├── dnbeta.c │ ├── dnbinom.c │ ├── dnchisq.c │ ├── dnf.c │ ├── dnorm.c │ ├── dnt.c │ ├── dpois.c │ ├── dpq.h │ ├── dt.c │ ├── dunif.c │ ├── dweibull.c │ ├── expm1.c │ ├── fmax2.c │ ├── fmin2.c │ ├── fprec.c │ ├── fround.c │ ├── fsign.c │ ├── ftrunc.c │ ├── gamma.c │ ├── gamma_cody.c │ ├── gammalims.c │ ├── i1mach.c │ ├── imax2.c │ ├── imin2.c │ ├── lbeta.c │ ├── lgamma.c │ ├── lgammacor.c │ ├── librandom.c │ ├── log1p.c │ ├── mlutils.c │ ├── nmath.h │ ├── pbeta.c │ ├── pbinom.c │ ├── pcauchy.c │ ├── pchisq.c │ ├── pexp.c │ ├── pf.c │ ├── pgamma.c │ ├── pgeom.c │ ├── phyper.c │ ├── plnorm.c │ ├── plogis.c │ ├── pnbeta.c │ ├── pnbinom.c │ ├── pnchisq.c │ ├── pnf.c │ ├── pnorm.c │ ├── pnt.c │ ├── polygamma.c │ ├── ppois.c │ ├── pt.c │ ├── ptukey.c │ ├── punif.c │ ├── pweibull.c │ ├── qbeta.c │ ├── qbinom.c │ ├── qcauchy.c │ ├── qchisq.c │ ├── qexp.c │ ├── qf.c │ ├── qgamma.c │ ├── qgeom.c │ ├── qhyper.c │ ├── qlnorm.c │ ├── qlogis.c │ ├── qnbeta.c │ ├── qnbinom.c │ ├── qnchisq.c │ ├── qnf.c │ ├── qnorm.c │ ├── qnt.c │ ├── qpois.c │ ├── qt.c │ ├── qtukey.c │ ├── qunif.c │ ├── qweibull.c │ ├── randmtzig.c │ ├── rbeta.c │ ├── rbinom.c │ ├── rcauchy.c │ ├── rchisq.c │ ├── rexp.c │ ├── rf.c │ ├── rgamma.c │ ├── rgeom.c │ ├── rhyper.c │ ├── rlnorm.c │ ├── rlogis.c │ ├── rmultinom.c │ ├── rnbinom.c │ ├── rnchisq.c │ ├── rnorm.c │ ├── rpois.c │ ├── rt.c │ ├── runif.c │ ├── rweibull.c │ ├── sexp.c │ ├── sign.c │ ├── signrank.c │ ├── snorm.c │ ├── stirlerr.c │ ├── sunif.c │ ├── toms708.c │ └── wilcox.c ├── libdeflate │ ├── .cirrus.yml │ ├── .github │ │ └── workflows │ │ │ └── ci.yml │ ├── .gitignore │ ├── COPYING │ ├── Makefile │ ├── Makefile.msc │ ├── NEWS │ ├── README.md │ ├── common │ │ ├── common_defs.h │ │ ├── compiler_gcc.h │ │ └── compiler_msc.h │ ├── lib │ │ ├── adler32.c │ │ ├── adler32_vec_template.h │ │ ├── arm │ │ │ ├── adler32_impl.h │ │ │ ├── cpu_features.c │ │ │ ├── cpu_features.h │ │ │ ├── crc32_impl.h │ │ │ └── matchfinder_impl.h │ │ ├── bt_matchfinder.h │ │ ├── cpu_features_common.h │ │ ├── crc32.c │ │ ├── crc32_table.h │ │ ├── crc32_vec_template.h │ │ ├── decompress_template.h │ │ ├── deflate_compress.c │ │ ├── deflate_compress.h │ │ ├── deflate_constants.h │ │ ├── deflate_decompress.c │ │ ├── gzip_compress.c │ │ ├── gzip_constants.h │ │ ├── gzip_decompress.c │ │ ├── hc_matchfinder.h │ │ ├── lib_common.h │ │ ├── matchfinder_common.h │ │ ├── unaligned.h │ │ ├── utils.c │ │ ├── x86 │ │ │ ├── adler32_impl.h │ │ │ ├── cpu_features.c │ │ │ ├── cpu_features.h │ │ │ ├── crc32_impl.h │ │ │ ├── crc32_pclmul_template.h │ │ │ ├── decompress_impl.h │ │ │ └── matchfinder_impl.h │ │ ├── zlib_compress.c │ │ ├── zlib_constants.h │ │ └── zlib_decompress.c │ ├── libdeflate.h │ ├── programs │ │ ├── benchmark.c │ │ ├── checksum.c │ │ ├── gzip.c │ │ ├── prog_util.c │ │ ├── prog_util.h │ │ ├── test_checksums.c │ │ ├── test_custom_malloc.c │ │ ├── test_incomplete_codes.c │ │ ├── test_litrunlen_overflow.c │ │ ├── test_slow_decompression.c │ │ ├── test_trailing_bytes.c │ │ ├── test_util.c │ │ ├── test_util.h │ │ └── tgetopt.c │ └── scripts │ │ ├── afl-fuzz │ │ ├── Makefile │ │ ├── deflate_compress │ │ │ ├── fuzz.c │ │ │ └── inputs │ │ │ │ └── 0 │ │ ├── deflate_decompress │ │ │ ├── fuzz.c │ │ │ └── inputs │ │ │ │ └── 0 │ │ ├── gzip_decompress │ │ │ ├── fuzz.c │ │ │ └── inputs │ │ │ │ └── 0 │ │ ├── prepare_for_fuzz.sh │ │ └── zlib_decompress │ │ │ ├── fuzz.c │ │ │ └── inputs │ │ │ └── 0 │ │ ├── android_build.sh │ │ ├── android_tests.sh │ │ ├── checksum_benchmarks.sh │ │ ├── detect.sh │ │ ├── exec_tests.sh │ │ ├── gen_crc32_multipliers.c │ │ ├── gen_crc32_table.c │ │ ├── gzip_tests.sh │ │ ├── make-windows-releases.sh │ │ ├── msc_test.bat │ │ ├── pgo_build.sh │ │ ├── produce_gzip_benchmark_table.sh │ │ └── run_tests.sh ├── libsvm │ ├── COPYRIGHT │ ├── Makefile │ ├── python │ │ └── commonutil.py │ ├── svm.cpp │ └── svm.h ├── pcre2 │ ├── Makefile │ ├── config.h │ ├── config.h.in │ ├── dftables.c │ ├── pcre2.h │ ├── pcre2.h.in │ ├── pcre2_auto_possess.c │ ├── pcre2_chartables.c │ ├── pcre2_compile.c │ ├── pcre2_config.c │ ├── pcre2_context.c │ ├── pcre2_dfa_match.c │ ├── pcre2_error.c │ ├── pcre2_internal.h │ ├── pcre2_intmodedep.h │ ├── pcre2_jit_compile.c │ ├── pcre2_jit_match.c │ ├── pcre2_jit_misc.c │ ├── pcre2_jit_test.c │ ├── pcre2_maketables.c │ ├── pcre2_match.c │ ├── pcre2_match_data.c │ ├── pcre2_newline.c │ ├── pcre2_ord2utf.c │ ├── pcre2_pattern_info.c │ ├── pcre2_printint.c │ ├── pcre2_string_utils.c │ ├── pcre2_study.c │ ├── pcre2_substitute.c │ ├── pcre2_substring.c │ ├── pcre2_tables.c │ ├── pcre2_ucd.c │ ├── pcre2_ucp.h │ ├── pcre2_valid_utf.c │ ├── pcre2_xclass.c │ ├── pcre2demo.c │ ├── pcre2grep.c │ ├── pcre2posix.c │ ├── pcre2posix.h │ ├── pcre2test.c │ └── sljit │ │ ├── sljitConfig.h │ │ ├── sljitConfigInternal.h │ │ ├── sljitExecAllocator.c │ │ ├── sljitLir.c │ │ ├── sljitLir.h │ │ ├── sljitNativeARM_32.c │ │ ├── sljitNativeARM_64.c │ │ ├── sljitNativeARM_T2_32.c │ │ ├── sljitNativeMIPS_32.c │ │ ├── sljitNativeMIPS_64.c │ │ ├── sljitNativeMIPS_common.c │ │ ├── sljitNativePPC_32.c │ │ ├── sljitNativePPC_64.c │ │ ├── sljitNativePPC_common.c │ │ ├── sljitNativeSPARC_32.c │ │ ├── sljitNativeSPARC_common.c │ │ ├── sljitNativeTILEGX-encoder.c │ │ ├── sljitNativeTILEGX_64.c │ │ ├── sljitNativeX86_32.c │ │ ├── sljitNativeX86_64.c │ │ ├── sljitNativeX86_common.c │ │ └── sljitUtils.c └── tclap │ ├── Arg.h │ ├── ArgException.h │ ├── ArgTraits.h │ ├── CmdLine.h │ ├── CmdLineInterface.h │ ├── CmdLineOutput.h │ ├── Constraint.h │ ├── DocBookOutput.h │ ├── HelpVisitor.h │ ├── IgnoreRestVisitor.h │ ├── MultiArg.h │ ├── MultiSwitchArg.h │ ├── OptionalUnlabeledTracker.h │ ├── README.md │ ├── StandardTraits.h │ ├── StdOutput.h │ ├── SwitchArg.h │ ├── UnlabeledMultiArg.h │ ├── UnlabeledValueArg.h │ ├── ValueArg.h │ ├── ValuesConstraint.h │ ├── VersionVisitor.h │ ├── Visitor.h │ ├── XorHandler.h │ └── ZshCompletionOutput.h ├── liftover.cpp ├── liftover.h ├── log_tool.cpp ├── log_tool.h ├── main.cpp ├── merge.cpp ├── merge.h ├── merge_candidate_variants.cpp ├── merge_candidate_variants.h ├── merge_genotypes.cpp ├── merge_genotypes.h ├── milk_filter.cpp ├── milk_filter.h ├── motif_map.cpp ├── motif_map.h ├── motif_tree.cpp ├── motif_tree.h ├── multi_partition.cpp ├── multi_partition.h ├── multiallelics_consolidator.cpp ├── multiallelics_consolidator.h ├── needle.cpp ├── needle.h ├── normalize.cpp ├── normalize.h ├── nuclear_pedigree.cpp ├── nuclear_pedigree.h ├── ordered_bcf_overlap_matcher.cpp ├── ordered_bcf_overlap_matcher.h ├── ordered_region_overlap_matcher.cpp ├── ordered_region_overlap_matcher.h ├── partition.cpp ├── partition.h ├── paste.cpp ├── paste.h ├── paste_and_compute_features_sequential.cpp ├── paste_and_compute_features_sequential.h ├── paste_genotypes.cpp ├── paste_genotypes.h ├── pedigree.cpp ├── pedigree.h ├── peek.cpp ├── peek.h ├── pileup.cpp ├── pileup.h ├── pregex.cpp ├── pregex.h ├── profile_afs.cpp ├── profile_afs.h ├── profile_chm1.cpp ├── profile_chm1.h ├── profile_chrom.cpp ├── profile_chrom.h ├── profile_fic_hwe.cpp ├── profile_fic_hwe.h ├── profile_hwe.cpp ├── profile_hwe.h ├── profile_indels.cpp ├── profile_indels.h ├── profile_len.cpp ├── profile_len.h ├── profile_mendelian.cpp ├── profile_mendelian.h ├── profile_na12878.cpp ├── profile_na12878.h ├── profile_snps.cpp ├── profile_snps.h ├── profile_vntrs.cpp ├── profile_vntrs.h ├── program.cpp ├── program.h ├── read_filter.cpp ├── read_filter.h ├── reference_sequence.cpp ├── reference_sequence.h ├── rfhmm.cpp ├── rfhmm.h ├── rfhmm_x.cpp ├── rfhmm_x.h ├── rminfo.cpp ├── rminfo.h ├── seq.cpp ├── seq.h ├── set_ref.cpp ├── set_ref.h ├── snp_genotyping_record.cpp ├── snp_genotyping_record.h ├── sort.cpp ├── sort.h ├── str_annotator.cpp ├── str_annotator.h ├── subset.cpp ├── subset.h ├── sv_tree.cpp ├── sv_tree.h ├── svm_predict.cpp ├── svm_predict.h ├── svm_train.cpp ├── svm_train.h ├── tbx_ordered_reader.cpp ├── tbx_ordered_reader.h ├── test.cpp ├── test.h ├── test ├── decompose │ ├── 01_IN_multi.vcf │ ├── 01_OUT_multi.stderr │ └── 01_OUT_multi.vcf ├── decompose_blocksub │ ├── 01_IN_even_length.vcf │ ├── 01_OUT_even_length.stderr │ ├── 01_OUT_even_length.vcf │ ├── 02_IN_uneven_length.vcf │ ├── 02_OUT_uneven_length.stderr │ ├── 02_OUT_uneven_length.vcf │ ├── 03_IN_phased_even_length.vcf │ ├── 03_OUT_phased_even_length.stderr │ ├── 03_OUT_phased_even_length.vcf │ └── mnv │ │ ├── 1bp_dist_mnv.vcf │ │ ├── 2bp_dist_mnv.vcf │ │ ├── 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