├── .github └── workflows │ └── test.yml ├── .gitignore ├── CMakeLists.txt ├── LICENSE ├── README.md ├── ext ├── htslib │ ├── .gitignore │ ├── .travis.yml │ ├── Makefile │ ├── README.md │ ├── bgzf.c │ ├── bgzip.c │ ├── config.h │ ├── cram │ │ ├── cram.h │ │ ├── cram_codecs.c │ │ ├── cram_codecs.h │ │ ├── cram_decode.c │ │ ├── cram_decode.h │ │ ├── cram_encode.c │ │ ├── cram_encode.h │ │ ├── cram_index.c │ │ ├── cram_index.h │ │ ├── cram_io.c │ │ ├── cram_io.h │ │ ├── cram_samtools.c │ │ ├── cram_samtools.h │ │ ├── cram_stats.c │ │ ├── cram_stats.h │ │ ├── cram_structs.h │ │ ├── files.c │ │ ├── mFILE.c │ │ ├── mFILE.h │ │ ├── md5.c │ │ ├── md5.h │ │ ├── misc.h │ │ ├── open_trace_file.c │ │ ├── open_trace_file.h │ │ ├── os.h │ │ ├── pooled_alloc.c │ │ ├── pooled_alloc.h │ │ ├── sam_header.c │ │ ├── sam_header.h │ │ ├── string_alloc.c │ │ ├── string_alloc.h │ │ ├── thread_pool.c │ │ ├── thread_pool.h │ │ ├── vlen.c │ │ ├── vlen.h │ │ ├── zfio.c │ │ └── zfio.h │ ├── faidx.5 │ ├── faidx.c │ ├── hfile.c │ ├── hfile_internal.h │ ├── hfile_net.c │ ├── hts.c │ ├── htslib.mk │ ├── htslib │ │ ├── bgzf.h │ │ ├── faidx.h │ │ ├── hfile.h │ │ ├── hts.h │ │ ├── hts_defs.h │ │ ├── kfunc.h │ │ ├── khash.h │ │ ├── khash_str2int.h │ │ ├── klist.h │ │ ├── knetfile.h │ │ ├── kseq.h │ │ ├── ksort.h │ │ ├── kstdint.h │ │ ├── kstring.h │ │ ├── sam.h │ │ ├── synced_bcf_reader.h │ │ ├── tbx.h │ │ ├── vcf.h │ │ ├── vcf_sweep.h │ │ └── vcfutils.h │ ├── htslib_vars.mk │ ├── kfunc.c │ ├── knetfile.c │ ├── kstring.c │ ├── sam.5 │ ├── sam.c │ ├── synced_bcf_reader.c │ ├── tabix.1 │ ├── tabix.c │ ├── tbx.c │ ├── vcf.5 │ ├── vcf.c │ ├── vcf_sweep.c │ └── vcfutils.c └── zlib-ng │ ├── .codecov.yaml │ ├── .gitattributes │ ├── .github │ └── workflows │ │ ├── analyze.yml │ │ ├── cmake.yml │ │ ├── configure.yml │ │ ├── fuzz.yml │ │ ├── libpng.yml │ │ ├── link.yml │ │ ├── nmake.yml │ │ ├── pigz.yml │ │ ├── pkgcheck.yml │ │ └── release.yml │ ├── .gitignore │ ├── .shellcheckrc │ ├── CMakeLists.txt │ ├── FAQ.zlib │ ├── INDEX.md │ ├── LICENSE.md │ ├── Makefile.in │ ├── PORTING.md │ ├── README.md │ ├── adler32.c │ ├── adler32_fold.c │ ├── adler32_fold.h │ ├── adler32_p.h │ ├── arch │ ├── .gitignore │ ├── arm │ │ ├── Makefile.in │ │ ├── adler32_neon.c │ │ ├── arm_features.c │ │ ├── arm_features.h │ │ ├── chunkset_neon.c │ │ ├── compare256_neon.c │ │ ├── crc32_acle.c │ │ ├── ctzl.h │ │ ├── insert_string_acle.c │ │ └── slide_hash_neon.c │ ├── generic │ │ ├── Makefile.in │ │ └── chunk_permute_table.h │ ├── power │ │ ├── Makefile.in │ │ ├── adler32_power8.c │ │ ├── adler32_vmx.c │ │ ├── chunkset_power8.c │ │ ├── compare256_power9.c │ │ ├── crc32_constants.h │ │ ├── crc32_power8.c │ │ ├── fallback_builtins.h │ │ ├── power_features.c │ │ ├── power_features.h │ │ ├── slide_hash_power8.c │ │ ├── slide_hash_vmx.c │ │ └── slide_ppc_tpl.h │ ├── s390 │ │ ├── Makefile.in │ │ ├── README.md │ │ ├── crc32-vx.c │ │ ├── dfltcc_common.c │ │ ├── dfltcc_common.h │ │ ├── dfltcc_deflate.c │ │ ├── dfltcc_deflate.h │ │ ├── dfltcc_detail.h │ │ ├── dfltcc_inflate.c │ │ ├── dfltcc_inflate.h │ │ ├── s390_features.c │ │ ├── s390_features.h │ │ └── self-hosted-builder │ │ │ ├── actions-runner.Dockerfile │ │ │ ├── actions-runner.service │ │ │ ├── fs │ │ │ └── usr │ │ │ │ └── bin │ │ │ │ ├── actions-runner │ │ │ │ └── entrypoint │ │ │ └── qemu-user-static.service │ └── x86 │ │ ├── Makefile.in │ │ ├── adler32_avx2.c │ │ ├── adler32_avx2_p.h │ │ ├── adler32_avx2_tpl.h │ │ ├── adler32_avx512.c │ │ ├── adler32_avx512_p.h │ │ ├── adler32_avx512_tpl.h │ │ ├── adler32_avx512_vnni.c │ │ ├── adler32_sse42.c │ │ ├── adler32_ssse3.c │ │ ├── adler32_ssse3_p.h │ │ ├── chunkset_avx.c │ │ ├── chunkset_sse2.c │ │ ├── chunkset_sse41.c │ │ ├── compare256_avx2.c │ │ ├── compare256_sse2.c │ │ ├── crc32_fold_pclmulqdq.c │ │ ├── crc32_fold_pclmulqdq_tpl.h │ │ ├── crc32_fold_vpclmulqdq.c │ │ ├── crc32_fold_vpclmulqdq_tpl.h │ │ ├── insert_string_sse42.c │ │ ├── slide_hash_avx2.c │ │ ├── slide_hash_sse2.c │ │ ├── x86_features.c │ │ └── x86_features.h │ ├── chunkset.c │ ├── chunkset_tpl.h │ ├── cmake │ ├── detect-arch.c │ ├── detect-arch.cmake │ ├── detect-coverage.cmake │ ├── detect-install-dirs.cmake │ ├── detect-intrinsics.cmake │ ├── detect-sanitizer.cmake │ ├── fallback-macros.cmake │ ├── toolchain-aarch64.cmake │ ├── toolchain-arm.cmake │ ├── toolchain-armhf.cmake │ ├── toolchain-mingw-i686.cmake │ ├── toolchain-mingw-x86_64.cmake │ ├── toolchain-powerpc.cmake │ ├── toolchain-powerpc64.cmake │ ├── toolchain-powerpc64le.cmake │ ├── toolchain-s390x.cmake │ └── toolchain-sparc64.cmake │ ├── compare256.c │ ├── compress.c │ ├── configure │ ├── cpu_features.c │ ├── cpu_features.h │ ├── crc32_braid.c │ ├── crc32_braid_comb.c │ ├── crc32_braid_comb_p.h │ ├── crc32_braid_p.h │ ├── crc32_braid_tbl.h │ ├── crc32_fold.c │ ├── crc32_fold.h │ ├── deflate.c │ ├── deflate.h │ ├── deflate_fast.c │ ├── deflate_huff.c │ ├── deflate_medium.c │ ├── deflate_p.h │ ├── deflate_quick.c │ ├── deflate_rle.c │ ├── deflate_slow.c │ ├── deflate_stored.c │ ├── doc │ ├── algorithm.txt │ ├── crc-doc.1.0.pdf │ ├── crc-pclmulqdq.pdf │ ├── rfc1950.txt │ ├── rfc1951.txt │ ├── rfc1952.txt │ └── txtvsbin.txt │ ├── fallback_builtins.h │ ├── functable.c │ ├── functable.h │ ├── gzguts.h │ ├── gzlib.c │ ├── gzread.c.in │ ├── gzwrite.c │ ├── infback.c │ ├── inffast.c │ ├── inffast.h │ ├── inffixed_tbl.h │ ├── inflate.c │ ├── inflate.h │ ├── inflate_p.h │ ├── inftrees.c │ ├── inftrees.h │ ├── insert_string.c │ ├── insert_string_roll.c │ ├── insert_string_tpl.h │ ├── match_tpl.h │ ├── slide_hash.c │ ├── test │ ├── .gitignore │ ├── CMakeLists.txt │ ├── CVE-2002-0059 │ │ └── test.gz │ ├── CVE-2004-0797 │ │ └── test.gz │ ├── CVE-2005-1849 │ │ └── test.gz │ ├── CVE-2005-2096 │ │ └── test.gz │ ├── CVE-2018-25032 │ │ ├── default.txt │ │ └── fixed.txt │ ├── GH-361 │ │ └── test.txt │ ├── GH-364 │ │ └── test.bin │ ├── GH-382 │ │ └── defneg3.dat │ ├── GH-751 │ │ └── test.txt │ ├── GH-979 │ │ └── pigz-2.6.tar.gz │ ├── Makefile.in │ ├── README.md │ ├── abi │ │ ├── ignore │ │ ├── zlib-ng-843c16c87afd53a20bf915661012b02acdd30281-x86_64-pc-linux-gnu.abi │ │ ├── zlib-v1.2.11-arm-linux-gnueabihf.abi │ │ ├── zlib-v1.2.11-x86_64-linux-gnu.abi │ │ └── zlib-v1.2.12-x86_64-pc-linux-gnu.abi │ ├── abicheck.md │ ├── abicheck.sh │ ├── add-subdirectory-project │ │ ├── CMakeLists.txt │ │ └── main.c │ ├── benchmarks │ │ ├── CMakeLists.txt │ │ ├── README.md │ │ ├── benchmark_adler32.cc │ │ ├── benchmark_adler32_copy.cc │ │ ├── benchmark_compare256.cc │ │ ├── benchmark_crc32.cc │ │ ├── benchmark_main.cc │ │ ├── benchmark_png_decode.cc │ │ ├── benchmark_png_encode.cc │ │ ├── benchmark_png_shared.h │ │ └── benchmark_slidehash.cc │ ├── cmake │ │ ├── compress-and-verify.cmake │ │ ├── run-and-compare.cmake │ │ ├── run-and-redirect.cmake │ │ ├── test-cves.cmake │ │ ├── test-data.cmake │ │ ├── test-issues.cmake │ │ └── test-tools.cmake │ ├── data │ │ ├── fireworks.jpg │ │ ├── lcet10.txt │ │ └── paper-100k.pdf │ ├── example.c │ ├── fuzz │ │ ├── CMakeLists.txt │ │ ├── fuzzer_checksum.c │ │ ├── fuzzer_compress.c │ │ ├── fuzzer_example_dict.c │ │ ├── fuzzer_example_flush.c │ │ ├── fuzzer_example_large.c │ │ ├── fuzzer_example_small.c │ │ ├── fuzzer_minigzip.c │ │ └── standalone_fuzz_target_runner.c │ ├── gh1235.c │ ├── infcover.c │ ├── minideflate.c │ ├── minigzip.c │ ├── pigz │ │ └── CMakeLists.txt │ ├── pkgcheck.sh │ ├── switchlevels.c │ ├── test_adler32.cc │ ├── test_aligned_alloc.cc │ ├── test_compare256.cc │ ├── test_compress.cc │ ├── test_compress_bound.cc │ ├── test_compress_dual.cc │ ├── test_crc32.cc │ ├── test_cve-2003-0107.cc │ ├── test_deflate_bound.cc │ ├── test_deflate_concurrency.cc │ ├── test_deflate_copy.cc │ ├── test_deflate_dict.cc │ ├── test_deflate_hash_head_0.cc │ ├── test_deflate_header.cc │ ├── test_deflate_params.cc │ ├── test_deflate_pending.cc │ ├── test_deflate_prime.cc │ ├── test_deflate_quick_bi_valid.cc │ ├── test_deflate_quick_block_open.cc │ ├── test_deflate_tune.cc │ ├── test_dict.cc │ ├── test_gzio.cc │ ├── test_inflate_adler32.cc │ ├── test_inflate_sync.cc │ ├── test_large_buffers.cc │ ├── test_main.cc │ ├── test_shared.h │ ├── test_small_buffers.cc │ └── test_version.cc │ ├── tools │ ├── config.sub │ ├── makecrct.c │ ├── makefixed.c │ └── maketrees.c │ ├── trees.c │ ├── trees.h │ ├── trees_emit.h │ ├── trees_tbl.h │ ├── uncompr.c │ ├── win32 │ ├── Makefile.a64 │ ├── Makefile.arm │ ├── Makefile.msc │ ├── replace.vbs │ ├── zlib-ng.def.in │ ├── zlib-ng1.rc │ ├── zlib.def.in │ ├── zlib1.rc │ └── zlibcompat.def.in │ ├── zbuild.h │ ├── zconf-ng.h.in │ ├── zconf.h.in │ ├── zendian.h │ ├── zlib-ng.h.in │ ├── zlib-ng.map │ ├── zlib.h.in │ ├── zlib.map │ ├── zlib.pc.cmakein │ ├── zlib.pc.in │ ├── zlib_name_mangling-ng.h.in │ ├── zlib_name_mangling.h.empty │ ├── zlib_name_mangling.h.in │ ├── zutil.c │ ├── zutil.h │ └── zutil_p.h ├── figures ├── splitcode_example.png ├── splitcode_figure.png └── splitcode_logo.png ├── func_tests ├── A_1.fastq.gz ├── A_2.fastq.gz ├── B_1.fastq.gz ├── B_2.fastq.gz ├── CMakeLists.txt ├── b.fastq ├── config.tsv ├── config_.tsv ├── config__.tsv ├── config___.tsv ├── config_fastassign.txt ├── config_fastassign_2.txt ├── config_sm.txt ├── configb.txt ├── even.txt ├── example.SJ.tab ├── from_name.fq ├── input.fastq ├── input_.fastq ├── input__.fastq ├── input___.fastq ├── nest.test.1.R1.fa ├── nest.test.1.R1.fq ├── nest.test.1.R2.fq ├── nest.test.2.R1.fq ├── nest.test.2.R2.fq ├── nest.test.3.R1.fq ├── nest.test.3.R2.fq ├── nest_config.txt ├── nest_config_2.txt ├── nest_config_3.txt ├── nest_config_4.txt ├── nest_config_5.txt ├── odd.txt ├── runtests.sh ├── smR1.fastq.gz ├── smR2.fastq.gz ├── splitcode_example_config.txt ├── splitcode_example_config_2.txt ├── splitcode_example_config_3.txt ├── splitcode_example_config_4.txt ├── test_1.vcf.gz ├── test_2.vcf.gz └── vcf_validation.fa.gz └── src ├── CMakeLists.txt ├── LiftWorkflow.h ├── ProcessReads.cpp ├── ProcessReads.h ├── SplitCode.h ├── common.h ├── 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