├── LICENSE ├── Makefile ├── README.md ├── SuperReads_RNA ├── LICENSE.txt ├── PkgConfig.pm ├── README.md ├── global-1 │ ├── LICENSE.txt │ ├── Makefile.am │ ├── SuperReadsR │ │ ├── AUTHORS │ │ ├── COPYING │ │ ├── ChangeLog │ │ ├── INSTALL │ │ ├── Makefile.am │ │ ├── NEWS │ │ ├── README │ │ ├── create_rna_sr.py │ │ ├── gtest.mk │ │ ├── include │ │ │ ├── binary_search_tree_iterator.hpp │ │ │ ├── charb.hpp │ │ │ ├── charbuf.hpp │ │ │ ├── exp_buffer.hpp │ │ │ ├── exp_vector.hpp │ │ │ ├── fork_exec.hpp │ │ │ ├── gcc_builtins.hpp │ │ │ ├── gzip_stream.hpp │ │ │ ├── heap.hpp │ │ │ ├── jflib │ │ │ │ ├── multiplexed_io.hpp │ │ │ │ ├── multiplexed_parser.hpp │ │ │ │ └── pool.hpp │ │ │ ├── misc.hpp │ │ │ ├── multi_thread_skip_list_map.hpp │ │ │ ├── multi_thread_skip_list_set.hpp │ │ │ ├── rb_node.hpp │ │ │ ├── rb_tree.hpp │ │ │ ├── reallocators.hpp │ │ │ ├── skip_list_common.hpp │ │ │ ├── skip_list_map.hpp │ │ │ ├── skip_list_set.hpp │ │ │ ├── thread_pool.hpp │ │ │ ├── timer.h │ │ │ └── tmpstream.hpp │ │ ├── lib │ │ │ └── fork_exec.cpp │ │ ├── src │ │ │ ├── MasurcaCommon.pm │ │ │ ├── MasurcaConf.pm │ │ │ ├── MasurcaPaths.pm.in │ │ │ ├── MasurcaSuperReads.pm │ │ │ ├── MurmurHash3.cpp │ │ │ ├── MurmurHash3.h │ │ │ ├── aligned_simple_array.hpp │ │ │ ├── assign_reads.cpp │ │ │ ├── bloom_counter2.hpp │ │ │ ├── bloom_filter.hpp │ │ │ ├── bloom_hash.hpp │ │ │ ├── bloom_query.cc │ │ │ ├── bloom_query_cmdline.hpp │ │ │ ├── createSuperReads_RNA │ │ │ ├── create_k_unitigs_common.hpp │ │ │ ├── create_k_unitigs_large_k.cc │ │ │ ├── create_k_unitigs_large_k2.cc │ │ │ ├── create_k_unitigs_large_k2_cmdline.hpp │ │ │ ├── create_k_unitigs_large_k_cmdline.hpp │ │ │ ├── diskBasedUnitigger.h │ │ │ ├── expand_fastq │ │ │ ├── extract_unjoined_pairs.pl │ │ │ ├── extractreads.pl │ │ │ ├── extractreads_not.pl │ │ │ ├── fibonacci_coding.cc │ │ │ ├── fibonacci_coding.hpp │ │ │ ├── gcc_builtins.cc │ │ │ ├── getNumBasesPerReadInFastaFile.perl │ │ │ ├── homo_trim.cc │ │ │ ├── mergeSuperReadsUniquely.pl │ │ │ ├── read_parser.cc │ │ │ ├── read_parser.hpp │ │ │ ├── reduce_sr.cc │ │ │ ├── reduce_sr_cmdline.hpp │ │ │ ├── rename_filter_fastq.cc │ │ │ ├── rename_filter_fastq_cmdline.hpp │ │ │ ├── reverse_complement.cc │ │ │ ├── semaphore.cc │ │ │ ├── semaphore_cmdline.hpp │ │ │ ├── sorted_merge.cc │ │ │ ├── sorted_merge_cmdline.hpp │ │ │ ├── sr_names.hpp │ │ │ ├── superread_index.cpp │ │ │ └── superread_index.hpp │ │ ├── src2 │ │ │ ├── add_missing_mates.pl │ │ │ ├── createFastaSuperReadSequences.cc │ │ │ ├── createKUnitigMaxOverlaps.cc │ │ │ ├── createSuperReadsForDirectory.perl │ │ │ ├── create_sr_frg.cc │ │ │ ├── eliminateBadSuperReadsUsingList.cc │ │ │ ├── findMatchesBetweenKUnitigsAndReads.cc │ │ │ ├── findMatchesBetweenKUnitigsAndReads_cmdline.hpp │ │ │ ├── getLengthStatisticsForKUnitigsFile.perl │ │ │ ├── getSuperReadInsertCountsFromReadPlacementFile.cc │ │ │ ├── getSuperReadInsertCountsFromReadPlacementFileTwoPasses.cc │ │ │ ├── getSuperReadInsertCountsFromReadPlacementFileTwoPasses_cmdline.hpp │ │ │ ├── getSuperReadInsertCountsFromReadPlacementFile_cmdline.hpp │ │ │ ├── joinKUnitigs_v3.cc │ │ │ ├── joinKUnitigs_v3_cmdline.hpp │ │ │ ├── outputAlekseysJellyfishReductionFile.perl │ │ │ ├── outputRecordsNotOnList.cc │ │ │ ├── splitFileAtNs.cc │ │ │ └── translateReduceFile.perl │ │ └── unittests │ │ │ ├── gtest │ │ │ ├── include │ │ │ │ └── gtest │ │ │ │ │ ├── gtest-death-test.h │ │ │ │ │ ├── gtest-message.h │ │ │ │ │ ├── gtest-param-test.h │ │ │ │ │ ├── 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.h │ │ │ │ │ ├── gtest-port.h │ │ │ │ │ ├── gtest-string.h │ │ │ │ │ ├── gtest-tuple.h │ │ │ │ │ └── gtest-type-util.h │ │ │ └── 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 │ │ │ ├── misc.cc │ │ │ ├── misc.hpp │ │ │ ├── test_bloom_counter2.cc │ │ │ ├── test_bloom_filter.cc │ │ │ ├── test_charb.cc │ │ │ ├── test_charbuf.cc │ │ │ ├── test_exp_buffer.cc │ │ │ ├── test_exp_vector.cc │ │ │ ├── test_fork_exec.cc │ │ │ ├── test_hash.cc │ │ │ ├── test_heap.cc │ │ │ ├── test_main.cc │ │ │ ├── test_main_cmdline.hpp │ │ │ ├── test_multi_thread_skip_list_map.cc │ │ │ ├── test_multi_thread_skip_list_set.cc │ │ │ ├── test_rbtree.cc │ │ │ ├── test_read_parser.cc │ │ │ ├── test_skip_list_map.cc │ │ │ ├── test_skip_list_set.cc │ │ │ ├── test_sr_names.cc │ │ │ └── test_thread_pool.cc │ ├── configure.ac │ ├── jellyfish │ │ ├── LICENSE │ │ ├── Makefile.am │ │ ├── README │ │ ├── doc │ │ │ ├── jellyfish.man │ │ │ └── jellyfish.pdf │ │ ├── gtest.mk │ │ ├── include │ │ │ └── jellyfish │ │ │ │ ├── allocators_mmap.hpp │ │ │ │ ├── atomic_bits_array.hpp │ │ │ │ ├── atomic_field.hpp │ │ │ │ ├── atomic_gcc.hpp │ │ │ │ ├── backtrace.hpp │ │ │ │ ├── binary_dumper.hpp │ │ │ │ ├── bloom_common.hpp │ │ │ │ ├── bloom_counter2.hpp │ │ │ │ ├── bloom_filter.hpp │ │ │ │ ├── circular_buffer.hpp │ │ │ │ ├── compare_and_swap.hpp │ │ │ │ ├── cooperative_pool.hpp │ │ │ │ ├── cooperative_pool2.hpp │ │ │ │ ├── cpp_array.hpp │ │ │ │ ├── divisor.hpp │ │ │ │ ├── dumper.hpp │ │ │ │ ├── err.hpp │ │ │ │ ├── file_header.hpp │ │ │ │ ├── generator_manager.hpp │ │ │ │ ├── generic_file_header.hpp │ │ │ │ ├── hash_counter.hpp │ │ │ │ ├── int128.hpp │ │ │ │ ├── jellyfish.hpp │ │ │ │ ├── json.h │ │ │ │ ├── large_hash_array.hpp │ │ │ │ ├── large_hash_iterator.hpp │ │ │ │ ├── locks_pthread.hpp │ │ │ │ ├── mapped_file.hpp │ │ │ │ ├── mer_dna.hpp │ │ │ │ ├── mer_dna_bloom_counter.hpp │ │ │ │ ├── mer_heap.hpp │ │ │ │ ├── mer_iterator.hpp │ │ │ │ ├── mer_overlap_sequence_parser.hpp │ │ │ │ ├── mer_qual_iterator.hpp │ │ │ │ ├── misc.hpp │ │ │ │ ├── offsets_key_value.hpp │ │ │ │ ├── rectangular_binary_matrix.hpp │ │ │ │ ├── simple_circular_buffer.hpp │ │ │ │ ├── sorted_dumper.hpp │ │ │ │ ├── stdio_filebuf.hpp │ │ │ │ ├── storage.hpp │ │ │ │ ├── stream_iterator.hpp │ │ │ │ ├── stream_manager.hpp │ │ │ │ ├── text_dumper.hpp │ │ │ │ ├── thread_exec.hpp │ │ │ │ ├── time.hpp │ │ │ │ ├── token_ring.hpp │ │ │ │ └── whole_sequence_parser.hpp │ │ ├── jellyfish-2.0.pc.in │ │ ├── jellyfish │ │ │ ├── backtrace.cc │ │ │ ├── dbg.cc │ │ │ ├── dbg.hpp │ │ │ ├── fstream_default.hpp │ │ │ ├── generate_sequence.cc │ │ │ ├── generate_sequence_cmdline.hpp │ │ │ ├── merge_files.cc │ │ │ ├── merge_files.hpp │ │ │ ├── mersenne.cpp │ │ │ └── randomc.h │ │ ├── lib │ │ │ ├── allocators_mmap.cc │ │ │ ├── generator_manager.cc │ │ │ ├── int128.cc │ │ │ ├── jsoncpp.cpp │ │ │ ├── mer_dna.cc │ │ │ ├── misc.cc │ │ │ ├── rectangular_binary_matrix.cc │ │ │ ├── storage.cc │ │ │ ├── thread_exec.cc │ │ │ └── time.cc │ │ ├── sub_commands │ │ │ ├── bc_main.cc │ │ │ ├── bc_main_cmdline.hpp │ │ │ ├── cite_main.cc │ │ │ ├── cite_main_cmdline.hpp │ │ │ ├── count_main.cc │ │ │ ├── count_main_cmdline.hpp │ │ │ ├── dump_main.cc │ │ │ ├── dump_main_cmdline.hpp │ │ │ ├── histo_main.cc │ │ │ ├── histo_main_cmdline.hpp │ │ │ ├── info_main.cc │ │ │ ├── info_main_cmdline.hpp │ │ │ ├── jellyfish.cc │ │ │ ├── mem_main.cc │ │ │ ├── mem_main_cmdline.hpp │ │ │ ├── merge_main.cc │ │ │ ├── merge_main_cmdline.hpp │ │ │ ├── query_main.cc │ │ │ ├── query_main_cmdline.hpp │ │ │ ├── stats_main.cc │ │ │ └── stats_main_cmdline.hpp │ │ ├── swig │ │ │ ├── Makefile.am │ │ │ ├── hash_counter.i │ │ │ ├── hash_set.i │ │ │ ├── jellyfish.i │ │ │ ├── mer_dna.i │ │ │ ├── mer_file.i │ │ │ ├── perl5 │ │ │ │ ├── jellyfish.pm │ │ │ │ ├── swig_wrap.cpp │ │ │ │ └── t │ │ │ │ │ ├── test_hash_counter.t │ │ │ │ │ ├── test_mer_file.t │ │ │ │ │ └── test_string_mers.t │ │ │ ├── python │ │ │ │ ├── swig_wrap.cpp │ │ │ │ ├── test_hash_counter.py │ │ │ │ ├── test_mer_file.py │ │ │ │ └── test_string_mers.py │ │ │ ├── ruby │ │ │ │ ├── swig_wrap.cpp │ │ │ │ ├── test_hash_counter.rb │ │ │ │ ├── test_mer_file.rb │ │ │ │ └── test_string_mers.rb │ │ │ └── string_mers.i │ │ ├── tests │ │ │ ├── big.sh │ │ │ ├── bloom_counter.sh │ │ │ ├── bloom_filter.sh │ │ │ ├── generate_sequence.sh │ │ │ ├── large_key.sh │ │ │ ├── merge.sh │ │ │ ├── multi_file.sh │ │ │ ├── parallel_hashing.sh │ │ │ ├── subset_hashing.sh │ │ │ ├── swig_perl.sh │ │ │ ├── swig_python.sh │ │ │ └── swig_ruby.sh │ │ └── unit_tests │ │ │ ├── gtest │ │ │ ├── gtest.h │ │ │ └── src │ │ │ │ ├── gtest-all.cc │ │ │ │ └── gtest_main.cc │ │ │ ├── test_allocators_mmap.cc │ │ │ ├── test_atomic_bits_array.cc │ │ │ ├── test_cooperative_pool2.cc │ │ │ ├── test_dumpers.cc │ │ │ ├── test_file_header.cc │ │ │ ├── test_generator_manager.cc │ │ │ ├── test_hash_counter.cc │ │ │ ├── test_int128.cc │ │ │ ├── test_large_hash_array.cc │ │ │ ├── test_main.cc │ │ │ ├── test_main.hpp │ │ │ ├── test_main_cmdline.hpp │ │ │ ├── test_mapped_file.cc │ │ │ ├── test_mer_dna.cc │ │ │ ├── test_mer_dna_bloom_counter.cc │ │ │ ├── test_mer_heap.cc │ │ │ ├── test_mer_iterator.cc │ │ │ ├── test_mer_overlap_sequence_parser.cc │ │ │ ├── test_misc.cc │ │ │ ├── test_offsets_key_value.cc │ │ │ ├── test_rectangular_binary_matrix.cc │ │ │ ├── test_simple_circular_buffer.cc │ │ │ ├── test_stdio_filebuf.cc │ │ │ ├── test_stream_iterator.cc │ │ │ ├── test_text_dumper.cc │ │ │ ├── test_token_ring.cc │ │ │ ├── test_whole_sequence_parser.cc │ │ │ └── unit_tests.sh │ ├── m4 │ │ ├── ax_openmp.m4 │ │ ├── m4-ax_perl_ext.m4 │ │ ├── m4-ax_pkg_swig.m4 │ │ └── m4-ax_swig_enable_cxx.m4 │ ├── quorum │ │ ├── AUTHORS │ │ ├── COPYING │ │ ├── ChangeLog │ │ ├── INSTALL │ │ ├── Makefile.am │ │ ├── NEWS │ │ ├── README │ │ ├── data │ │ │ └── adapter.jf │ │ ├── gtest.mk │ │ ├── include │ │ │ ├── gzip_stream.hpp │ │ │ ├── jflib │ │ │ │ ├── locks_pthread.hpp │ │ │ │ ├── multiplexed_io.hpp │ │ │ │ └── pool.hpp │ │ │ └── misc.hpp │ │ ├── src │ │ │ ├── create_database.cc │ │ │ ├── create_database_cmdline.hpp │ │ │ ├── err_log.cc │ │ │ ├── err_log.hpp │ │ │ ├── error_correct_reads.cc │ │ │ ├── error_correct_reads.hpp │ │ │ ├── error_correct_reads_cmdline.hpp │ │ │ ├── histo_mer_database.cc │ │ │ ├── kmer.hpp │ │ │ ├── mer_database.hpp │ │ │ ├── merge_mate_pairs.cc │ │ │ ├── merge_mate_pairs_cmdline.hpp │ │ │ ├── query_mer_database.cc │ │ │ ├── quorum.in │ │ │ ├── split_mate_pairs.cc │ │ │ ├── split_mate_pairs_cmdline.hpp │ │ │ └── verbose_log.hpp │ │ └── unit_tests │ │ │ ├── gtest │ │ │ ├── gtest.h │ │ │ └── src │ │ │ │ ├── gtest-all.cc │ │ │ │ └── gtest_main.cc │ │ │ ├── test_mer_database.cc │ │ │ └── test_misc.hpp │ └── ufasta │ │ ├── Makefile.am │ │ ├── common.hpp │ │ ├── dgrep.cc │ │ ├── dgrep_cmdline.hpp │ │ ├── dsort.cc │ │ ├── dsort_cmdline.hpp │ │ ├── extract.cc │ │ ├── extract_cmdline.hpp │ │ ├── format.cc │ │ ├── format_cmdline.hpp │ │ ├── head.cc │ │ ├── head_cmdline.hpp │ │ ├── hgrep.cc │ │ ├── hgrep_cmdline.hpp │ │ ├── n50.cc │ │ ├── n50_cmdline.hpp │ │ ├── one.cc │ │ ├── one_cmdline.hpp │ │ ├── rc.cc │ │ ├── rc_cmdline.hpp │ │ ├── sizes.cc │ │ ├── sizes_cmdline.hpp │ │ ├── sort.cc │ │ ├── sort_cmdline.hpp │ │ ├── split.cc │ │ ├── split_cmdline.hpp │ │ ├── tail.cc │ │ ├── tail_cmdline.hpp │ │ ├── tests │ │ ├── test1.fasta │ │ ├── test_dgrep.sh │ │ ├── test_dsort.sh │ │ ├── test_extract.sh │ │ ├── test_format.sh │ │ ├── test_head.sh │ │ ├── test_hgrep.sh │ │ ├── test_n50.sh │ │ ├── test_one.sh │ │ ├── test_rc.sh │ │ ├── test_sizes.sh │ │ ├── test_sort.sh │ │ ├── test_split.sh │ │ ├── test_tail.sh │ │ └── testsh.in │ │ └── ufasta.cc └── install.sh ├── TODO.md ├── bundle.cpp ├── bundle.h ├── gclib ├── GArgs.cpp ├── GArgs.h ├── GBase.cpp ├── GBase.h ├── GBitVec.h ├── GFaSeqGet.cpp ├── GFaSeqGet.h ├── GFastaIndex.cpp ├── GFastaIndex.h ├── GHashMap.hh ├── GList.hh ├── GSam.cpp ├── GSam.h ├── GStr.cpp ├── GStr.h ├── GThreads.cpp ├── GThreads.h ├── GVec.hh ├── codons.cpp ├── codons.h ├── gdna.cpp ├── gdna.h ├── gff.cpp ├── gff.h ├── khashl.hh ├── proc_mem.cpp ├── proc_mem.h ├── wyhash.h └── xxhash.h ├── htslib ├── Makefile ├── Makefile.libdeflate ├── README.large_positions.md ├── README.md ├── annot-tsv.1 ├── annot-tsv.c ├── bcf_sr_sort.c ├── bcf_sr_sort.h ├── bgzf.c ├── bgzip.1 ├── bgzip.c ├── build_lib.sh ├── builddir_vars.mk.in ├── config.mk.in ├── configure.ac ├── cram │ ├── cram.h │ ├── cram_codecs.c │ ├── cram_codecs.h │ ├── cram_decode.c │ ├── cram_decode.h │ ├── cram_encode.c │ ├── cram_encode.h │ ├── cram_external.c │ ├── cram_index.c │ ├── cram_index.h │ ├── cram_io.c │ ├── cram_io.h │ ├── cram_samtools.h │ ├── cram_stats.c │ ├── cram_stats.h │ ├── cram_structs.h │ ├── mFILE.c │ ├── mFILE.h │ ├── misc.h │ ├── open_trace_file.c │ ├── open_trace_file.h │ ├── os.h │ ├── pooled_alloc.c │ ├── pooled_alloc.h │ ├── string_alloc.c │ └── string_alloc.h ├── errmod.c ├── faidx.5 ├── faidx.c ├── fuzz_settings.h ├── header.c ├── header.h ├── hfile.c ├── hfile_gcs.c ├── hfile_internal.h ├── hfile_libcurl.c ├── hfile_s3.c ├── hfile_s3_write.c ├── hts.c ├── hts_expr.c ├── hts_internal.h ├── hts_os.c ├── hts_probe_cc.sh ├── hts_time_funcs.h ├── htscodecs │ ├── LICENSE.md │ ├── README.md │ ├── configure.ac │ └── htscodecs │ │ ├── Makefile.am │ │ ├── arith_dynamic.c │ │ ├── arith_dynamic.h │ │ ├── c_range_coder.h │ │ ├── c_simple_model.h │ │ ├── fqzcomp_qual.c │ │ ├── fqzcomp_qual.h │ │ ├── htscodecs.c │ │ ├── htscodecs.h │ │ ├── htscodecs_endian.h │ │ ├── pack.c │ │ ├── pack.h │ │ ├── permute.h │ │ ├── pooled_alloc.h │ │ ├── rANS_byte.h │ │ ├── rANS_static.c │ │ ├── rANS_static.h │ │ ├── rANS_static16_int.h │ │ ├── rANS_static32x16pr.c │ │ ├── rANS_static32x16pr.h │ │ ├── rANS_static32x16pr_avx2.c │ │ ├── rANS_static32x16pr_avx512.c │ │ ├── rANS_static32x16pr_neon.c │ │ ├── rANS_static32x16pr_sse4.c │ │ ├── rANS_static4x16.h │ │ ├── rANS_static4x16pr.c │ │ ├── rANS_word.h │ │ ├── rle.c │ │ ├── rle.h │ │ ├── tokenise_name3.c │ │ ├── tokenise_name3.h │ │ ├── utils.c │ │ ├── utils.h │ │ ├── varint.h │ │ └── varint2.h ├── htscodecs_bundled.mk ├── htscodecs_external.mk ├── htsfile.1 ├── htsfile.c ├── htslib-s3-plugin.7 ├── htslib.map ├── htslib.mk ├── htslib.pc.in ├── htslib │ ├── bgzf.h │ ├── cram.h │ ├── faidx.h │ ├── hfile.h │ ├── hts.h │ ├── hts_defs.h │ ├── hts_endian.h │ ├── hts_expr.h │ ├── hts_log.h │ ├── hts_os.h │ ├── kbitset.h │ ├── kfunc.h │ ├── khash.h │ ├── khash_str2int.h │ ├── klist.h │ ├── knetfile.h │ ├── kroundup.h │ ├── kseq.h │ ├── ksort.h │ ├── kstring.h │ ├── regidx.h │ ├── sam.h │ ├── synced_bcf_reader.h │ ├── tbx.h │ ├── thread_pool.h │ ├── vcf.h │ ├── vcf_sweep.h │ └── vcfutils.h ├── htslib_vars.mk ├── kfunc.c ├── kstring.c ├── md5.c ├── multipart.c ├── os │ ├── lzma_stub.h │ └── rand.c ├── plugin.c ├── probaln.c ├── realn.c ├── regidx.c ├── region.c ├── sam.5 ├── sam.c ├── sam_internal.h ├── sam_mods.c ├── simd.c ├── synced_bcf_reader.c ├── tabix.1 ├── tabix.c ├── tbx.c ├── textutils.c ├── textutils_internal.h ├── thread_pool.c ├── thread_pool_internal.h ├── vcf.5 ├── vcf.c ├── vcf_sweep.c ├── vcfutils.c └── version.sh ├── prepDE.py ├── prepDE.py3 ├── prep_linux.sh ├── prep_mac.sh ├── prep_offline_source.sh ├── prep_source.sh ├── rlink.cpp ├── rlink.h ├── run_tests.sh ├── run_tests_valgrind.sh ├── stringtie.cpp ├── tablemaker.cpp ├── tablemaker.h ├── tag_git.sh ├── tests └── README.md ├── tmerge.cpp └── tmerge.h /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gpertea/stringtie/HEAD/LICENSE -------------------------------------------------------------------------------- /Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gpertea/stringtie/HEAD/Makefile 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