[med-svn] [Git][med-team/vg][upstream] New upstream version 1.78.0+ds

[Andreas Tille (@tille)]

Andreas Tille pushed to branch upstream at Debian Med / vg


Commits:
e106f36e by Andreas Tille at 2026-10-21T13:50:20+02:00
New upstream version 1.78.0+ds
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8501 changed files:

- .github/workflows/testmac.yml
- .gitignore
- .gitlab-ci.yml
- .gitmodules
- + BOTS.md
- Brewfile
- + CLAUDE.md
- + CONTRIBUTING.md
- Dockerfile
- Dockerfile.static
- Makefile
- README.md
- autocomp.bash
- autocomplete.sh
- − configure.py
- − deps/BBHash/.travis.yml
- − deps/BBHash/BooPHF.h
- − deps/BBHash/LICENSE
- − deps/BBHash/README.md
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- + scripts/build-chain-viz.py
- scripts/chunked_call
- scripts/giraffe-facts.py
- scripts/giraffe-wrangler.sh
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- scripts/make_pbsim_reads.sh
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- scripts/plot-roc-log.R
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- + scripts/plot_chains.sh
- + scripts/reinsert_qualities.py
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- scripts/setup-server
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- source_me.sh
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- src/algorithms/alignment_path_offsets.cpp
- src/algorithms/alignment_path_offsets.hpp
- src/algorithms/chain_items.cpp
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- src/algorithms/coverage_depth.cpp
- src/algorithms/extract_connecting_graph.cpp
- src/algorithms/extract_connecting_graph.hpp
- src/algorithms/extract_extending_graph.cpp
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- src/algorithms/gfa_to_handle.cpp
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- src/aligner.cpp
- src/aligner.hpp
- src/alignment.cpp
- src/alignment.hpp
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- src/annotation.hpp
- src/augment.cpp
- src/back_translating_alignment_emitter.cpp
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- src/banded_global_aligner.cpp
- src/banded_global_aligner.hpp
- src/cactus.cpp
- src/cactus.hpp
- src/chunker.cpp
- src/chunker.hpp
- src/clip.cpp
- src/clip.hpp
- src/cluster.cpp
- src/cluster.hpp
- src/config/allocator_config.hpp
- src/config/allocator_config_jemalloc.cpp
- + src/config/allocator_config_jemalloc_debug.cpp
- + src/config/allocator_config_mimalloc.cpp
- src/config/allocator_config_system.cpp
- src/constructor.cpp
- src/crash.cpp
- src/crash.hpp
- src/dagified_graph.cpp
- src/deconstructor.cpp
- src/deconstructor.hpp
- src/deletion_aligner.cpp
- src/dozeu_interface.cpp
- src/dozeu_interface.hpp
- − src/endianness.hpp
- − src/entropy.cpp
- − src/entropy.hpp
- src/explainer.cpp
- src/explainer.hpp
- − src/extra_node_graph.cpp
- − src/extra_node_graph.hpp
- − src/filter.cpp
- − src/filter.hpp
- + src/flow_caller.cpp
- + src/flow_caller.hpp
- src/funnel.cpp
- src/funnel.hpp
- + src/gaf_output_caller.cpp
- + src/gaf_output_caller.hpp
- + src/gaf_sorter.cpp
- + src/gaf_sorter.hpp
- src/gbwt_extender.cpp
- src/gbwt_extender.hpp
- src/gbwt_helper.cpp
- src/gbwt_helper.hpp
- src/gbwtgraph_helper.cpp
- src/gbwtgraph_helper.hpp
- src/gbzgraph.hpp
- − src/genome_state.cpp
- − src/genome_state.hpp
- src/genotyper.cpp
- src/genotyper.hpp
- src/gfa.cpp
- src/gff_reader.cpp
- src/graph.cpp
- src/graph.hpp
- src/graph_caller.cpp
- src/graph_caller.hpp
- src/graph_synchronizer.cpp
- + src/gref.cpp
- + src/gref.hpp
- src/haplotype_extracter.cpp
- src/haplotype_indexer.cpp
- src/haplotype_indexer.hpp
- src/haplotypes.cpp
- src/hts_alignment_emitter.cpp
- src/hts_alignment_emitter.hpp
- src/incremental_subgraph.cpp
- src/incremental_subgraph.hpp
- src/index_registry.cpp
- src/index_registry.hpp
- − src/indexed_vg.cpp
- − src/indexed_vg.hpp
- src/integrated_snarl_finder.cpp
- src/integrated_snarl_finder.hpp
- + src/interval_union.cpp
- + src/interval_union.hpp
- + src/io/json2graph.hpp
- src/io/json_stream_helper.hpp
- src/io/register_libvg_io.cpp
- + src/io/register_loader_gfaz.cpp
- + src/io/register_loader_gfaz.hpp
- src/io/register_loader_saver_distance_index.cpp
- src/io/register_loader_saver_gbwt.cpp
- src/io/register_loader_saver_gbwtgraph.cpp
- src/io/register_loader_saver_gbz.cpp
- src/io/register_loader_saver_gbzgraph.cpp
- src/io/register_loader_saver_gcsa.cpp
- src/io/register_loader_saver_hash_graph.cpp
- src/io/register_loader_saver_lcp.cpp
- src/io/register_loader_saver_minimizer.cpp
- src/io/register_loader_saver_r_index.cpp
- + src/io/register_loader_saver_zip_codes.cpp
- + src/io/register_loader_saver_zip_codes.hpp
- src/kff.hpp
- src/kmer.cpp
- + src/legacy_caller.cpp
- + src/legacy_caller.hpp
- + src/log.cpp
- + src/log.hpp
- + src/logged_gap_alignment_scorer.cpp
- + src/logged_gap_alignment_scorer.hpp
- + src/longest_overlap.hpp
- src/main.cpp
- src/mapper.cpp
- + src/mapping_quality_calculator.cpp
- + src/mapping_quality_calculator.hpp
- + src/masker.cpp
- + src/masker.hpp
- src/mcmc_caller.hpp
- src/mcmc_genotyper.cpp
- src/minimizer_mapper.cpp
- src/minimizer_mapper.hpp
- src/minimizer_mapper_from_chains.cpp
- src/msa_converter.cpp
- src/multipath_alignment.cpp
- src/multipath_alignment.hpp
- src/multipath_alignment_emitter.cpp
- src/multipath_alignment_emitter.hpp
- src/multipath_alignment_graph.cpp
- src/multipath_alignment_graph.hpp
- src/multipath_mapper.cpp
- + src/nested_flow_caller.cpp
- + src/nested_flow_caller.hpp
- − src/nested_traversal_finder.cpp
- − src/nested_traversal_finder.hpp
- src/packer.cpp
- src/path.cpp
- src/path.hpp
- src/path_index.cpp
- src/preflight.cpp
- src/preflight.hpp
- + src/primer_filter.cpp
- + src/primer_filter.hpp
- src/progressive.cpp
- src/progressive.hpp
- src/qual_adj_xdrop_aligner.cpp
- src/rare_variant_simplifier.cpp
- src/readfilter.cpp
- src/readfilter.hpp
- src/recombinator.cpp
- src/recombinator.hpp
- src/region.cpp
- src/region.hpp
- src/region_expander.cpp
- src/sampler.cpp
- src/sampler.hpp
- src/scanner.hpp
- src/small_snarl_simplifier.cpp
- src/snarl_caller.cpp
- src/snarl_caller.hpp
- src/snarl_distance_index.cpp
- src/snarl_distance_index.hpp
- + src/snarl_graph.cpp
- + src/snarl_graph.hpp
- src/snarl_seed_clusterer.cpp
- src/snarl_seed_clusterer.hpp
- src/snarls.cpp
- src/snarls.hpp
- src/splicing.cpp
- src/splicing.hpp
- src/statistics.hpp
- src/stream_index.cpp
- src/stream_index.hpp
- src/stream_sorter.hpp
- src/subcommand/add_main.cpp
- src/subcommand/align_main.cpp
- src/subcommand/annotate_main.cpp
- src/subcommand/augment_main.cpp
- src/subcommand/autoindex_main.cpp
- + src/subcommand/bench_dist_query_main.cpp
- src/subcommand/benchmark_main.cpp
- src/subcommand/call_main.cpp
- − src/subcommand/chain_main.cpp
- + src/subcommand/chains_main.cpp
- src/subcommand/chunk_main.cpp
- src/subcommand/circularize_main.cpp
- src/subcommand/clip_main.cpp
- src/subcommand/cluster_main.cpp
- src/subcommand/combine_main.cpp
- src/subcommand/concat_main.cpp
- src/subcommand/construct_main.cpp
- src/subcommand/convert_main.cpp
- src/subcommand/deconstruct_main.cpp
- src/subcommand/depth_main.cpp
- + src/subcommand/describe_main.cpp
- src/subcommand/dotplot_main.cpp
- − src/subcommand/explode_main.cpp
- src/subcommand/filter_main.cpp
- src/subcommand/find_main.cpp
- src/subcommand/gamcompare_main.cpp
- src/subcommand/gampcompare_main.cpp
- src/subcommand/gamsort_main.cpp
- src/subcommand/gbwt_main.cpp
- src/subcommand/genotype_main.cpp
- src/subcommand/giraffe_main.cpp
- src/subcommand/haplotypes_main.cpp
- src/subcommand/help_main.cpp
- src/subcommand/ids_main.cpp
- src/subcommand/index_main.cpp
- src/subcommand/inject_main.cpp
- − src/subcommand/join_main.cpp
- src/subcommand/kmers_main.cpp
- src/subcommand/map_main.cpp
- + src/subcommand/mask_main.cpp
- src/subcommand/mcmc_main.cpp
- src/subcommand/minimizer_main.cpp
- src/subcommand/mod_main.cpp
- src/subcommand/mpmap_main.cpp
- − src/subcommand/msga_main.cpp
- src/subcommand/options.cpp
- src/subcommand/options.hpp
- src/subcommand/pack_main.cpp
- src/subcommand/paths_main.cpp
- + src/subcommand/primers_main.cpp
- src/subcommand/prune_main.cpp
- src/subcommand/rna_main.cpp
- − src/subcommand/sift_main.cpp
- src/subcommand/sim_main.cpp
- src/subcommand/simplify_main.cpp
- src/subcommand/snarls_main.cpp
- src/subcommand/sort_main.cpp
- src/subcommand/stats_main.cpp
- src/subcommand/subcommand.hpp
- src/subcommand/surject_main.cpp
- src/subcommand/trace_main.cpp
- src/subcommand/translate_main.cpp
- src/subcommand/validate_main.cpp
- src/subcommand/vectorize_main.cpp
- src/subcommand/version_main.cpp
- src/subcommand/view_main.cpp
- src/subcommand/viz_main.cpp
- + src/subcommand/zipcode_main.cpp
- src/surjecting_alignment_emitter.cpp
- src/surjecting_alignment_emitter.hpp
- src/surjector.cpp
- src/surjector.hpp
- src/transcriptome.cpp
- src/transcriptome.hpp
- src/traversal_clusters.cpp
- src/traversal_clusters.hpp
- src/traversal_finder.cpp
- src/traversal_finder.hpp
- src/types.hpp
- src/unittest/aligner.cpp
- src/unittest/alignment.cpp
- src/unittest/banded_global_aligner.cpp
- src/unittest/cactus.cpp
- src/unittest/chain_items.cpp
- src/unittest/chunker.cpp
- src/unittest/cluster.cpp
- src/unittest/copy_graph.cpp
- src/unittest/dagified_graph.cpp
- src/unittest/dagify.cpp
- src/unittest/deletion_aligner.cpp
- src/unittest/dijkstra.cpp
- + src/unittest/funnel.cpp
- + src/unittest/gaf_sorter.cpp
- src/unittest/gbwt_extender.cpp
- − src/unittest/genome_state.cpp
- src/unittest/genotypekit.cpp
- src/unittest/genotyper.cpp
- + src/unittest/graph_algorithms.cpp
- src/unittest/haplotypes.cpp
- src/unittest/hash_graph.cpp
- + src/unittest/hts_alignment_emitter.cpp
- src/unittest/index_helpers.cpp
- src/unittest/index_registry.cpp
- − src/unittest/indexed_vg.cpp
- + src/unittest/interval_union.cpp
- src/unittest/kff.cpp
- + src/unittest/longest_overlap.cpp
- src/unittest/mapper.cpp
- + src/unittest/masker.cpp
- src/unittest/mem_accelerator.cpp
- src/unittest/minimizer_mapper.cpp
- src/unittest/multipath_alignment_graph.cpp
- src/unittest/multipath_mapper.cpp
- src/unittest/overlays.cpp
- src/unittest/packed_graph.cpp
- src/unittest/packed_structs.cpp
- + src/unittest/path.cpp
- src/unittest/path_component_index.cpp
- src/unittest/path_index.cpp
- src/unittest/phase_unfolder.cpp
- src/unittest/pinned_alignment.cpp
- + src/unittest/randomly_flipped_nodes.cpp
- src/unittest/readfilter.cpp
- + src/unittest/recombinator.cpp
- + src/unittest/sample_minimal.cpp
- src/unittest/sampler.cpp
- + src/unittest/snarl_decomposition_fuzzer.cpp
- src/unittest/snarl_distance_index.cpp
- src/unittest/snarl_seed_clusterer.cpp
- src/unittest/snarls.cpp
- src/unittest/source_sink_overlay.cpp
- src/unittest/splicing.cpp
- src/unittest/statistics.cpp
- src/unittest/support/driver.cpp
- src/unittest/random_graph.cpp → src/unittest/support/random_graph.cpp
- src/unittest/random_graph.hpp → src/unittest/support/random_graph.hpp
- + src/unittest/support/randomly_flipped_nodes.hpp
- src/unittest/randomness.hpp → src/unittest/support/randomness.hpp
- + src/unittest/support/snarl_decomposition_fuzzer.cpp
- + src/unittest/support/snarl_decomposition_fuzzer.hpp
- src/unittest/test_aligner.hpp → src/unittest/support/test_aligner.hpp
- src/unittest/surject.cpp
- − src/unittest/three_edge_connected_components.cpp
- src/unittest/transcriptome.cpp
- + src/unittest/traversal_clusters.cpp
- src/unittest/traversal_support.cpp
- src/unittest/variant_adder.cpp
- + src/unittest/varint.cpp
- src/unittest/vg.cpp
- src/unittest/vg_algorithms.cpp
- src/unittest/vpkg.cpp
- src/unittest/xdrop_aligner.cpp
- src/unittest/xg.cpp
- + src/unittest/zip_code.cpp
- + src/unittest/zip_code_tree.cpp
- + src/unittest/zstdutil.cpp
- src/utility.cpp
- src/utility.hpp
- src/variant_adder.cpp
- src/variant_recall.cpp
- src/variant_recall.hpp
- + src/varint.cpp
- + src/varint.hpp
- + src/vcf_genotyper.cpp
- + src/vcf_genotyper.hpp
- + src/vcf_output_caller.cpp
- + src/vcf_output_caller.hpp
- src/version.cpp
- src/version.hpp
- src/vg.cpp
- src/vg.hpp
- src/viz.cpp
- src/xdrop_aligner.cpp
- + src/zip_code.cpp
- + src/zip_code.hpp
- + src/zip_code_tree.cpp
- + src/zip_code_tree.hpp
- src/zstdutil.cpp
- src/zstdutil.hpp
- test/Makefile
- test/correct/10_vg_stats/15.txt
- test/msgas/inv-mess-normalized.gfa → test/correct/14_vg_mod/inv-mess-normalized.gfa
- test/msgas/inv-mess-unchopped.gfa → test/correct/14_vg_mod/inv-mess-unchopped.gfa
- test/msgas/cycle.fa → test/cyclic/cycle.fa
- + test/graphs/chain-clip.gfa
- test/graphs/chopping_walks.gfa
- test/graphs/components_walks.gfa
- + test/graphs/components_walks_compressed.gfa
- + test/graphs/disconnected.gfa
- + test/graphs/haplotypes.gfa
- test/msgas/inv-mess.json → test/graphs/inv-mess.json
- + test/graphs/long_deletion.gfa
- + test/graphs/long_insertion.gfa
- + test/graphs/long_inversion.gfa
- + test/graphs/path_norm_test.gfa
- test/msgas/q_redundant.vg → test/graphs/q_redundant.vg
- + test/graphs/snarl-clip.gfa
- + test/graphs/snarl_ref_coords.gfa
- + test/graphs/snarl_ref_coords_chopped.gfa
- + test/graphs/snarl_ref_coords_offref.gfa
- + test/graphs/snarl_ref_coords_offref_rev.gfa
- + test/graphs/snarl_ref_coords_rev.gfa
- + test/graphs/snarl_ref_coords_sub.gfa
- + test/graphs/snarl_ref_coords_sub_rev.gfa
- + test/graphs/wrap_fragmented.gfa
- + test/graphs/wrap_nonzero_offset.gfa
- test/haplotype-sampling/README.md
- + test/longread/annotations.gff3
- + test/longread/graph.gfa
- + test/longread/hifi.fq
- + test/longread/kinnex.fq
- + test/msgas/README.md
- + test/msgas/c1.vg
- + test/msgas/c2.vg
- − test/msgas/cycle.fa.fai
- − test/msgas/f.fa
- − test/msgas/f.fa.fai
- + test/msgas/flat.vg
- + test/msgas/hla_b.vg
- + test/msgas/hla_k.vg
- + test/msgas/hla_v.vg
- − test/msgas/inv.fa
- − test/msgas/l.fa
- − test/msgas/l.fa.fai
- + test/msgas/l.vg
- − test/msgas/q.fa
- − test/msgas/q.fa.fai
- + test/msgas/q.vg
- − test/msgas/q_redundant.gfa
- − test/msgas/s-rev.fa
- − test/msgas/s.fa
- − test/msgas/s.fa.fai
- + test/msgas/s.vg
- + test/msgas/s2.vg
- − test/msgas/w.fa
- − test/msgas/w.fa.fai
- + test/nesting/base_and_gref.gfa
- + test/nesting/bridged_ref_contigs.gfa
- + test/nesting/consecutive_nested.gfa
- + test/nesting/core_del61.gfa
- + test/nesting/core_ins49.gfa
- + test/nesting/core_ins50.gfa
- + test/nesting/core_snp_in_flanks.gfa
- + test/nesting/core_sv60.gfa
- + test/nesting/cross_path_merge.gfa
- + test/nesting/cross_path_merge_reject.gfa
- + test/nesting/cross_path_merge_right.gfa
- + test/nesting/cyclic_ref_multiple_variants.gfa
- + test/nesting/cyclic_ref_nested.gfa
- + test/nesting/dangling_node.gfa
- + test/nesting/del1_vs_snp1.gfa
- + test/nesting/del59_vs_del60.gfa
- + test/nesting/del60_vs_del59ins1.gfa
- + test/nesting/del60_vs_snp.gfa
- + test/nesting/gref_island_no_parent_record.gfa
- + test/nesting/gref_name_collision.gfa
- + test/nesting/hap_extends_ref_end.gfa
- + test/nesting/hap_extends_ref_start.gfa
- + test/nesting/haplotype_sense_ref.gfa
- + test/nesting/insertion_with_three_snps.gfa
- + test/nesting/inv60_in_2kb.gfa
- + test/nesting/inv60_vs_del60.gfa
- + test/nesting/inverted_allele.gfa
- + test/nesting/merge_support.gfa
- + test/nesting/mnp.gfa
- + test/nesting/nested_del_star_indel.gfa
- + test/nesting/nested_del_star_indel_rev.gfa
- + test/nesting/nested_ins_star_only.gfa
- + test/nesting/nested_mnp_star.gfa
- + test/nesting/nested_snp_in_del_rev.gfa
- + test/nesting/orientation_flip.gfa
- + test/nesting/simplify_del_absorbs.gfa
- + test/nesting/star_allele_cluster.gfa
- + test/nesting/star_cluster.gfa
- + test/nesting/subranged_ref.gfa
- + test/nesting/thread_determinism.gfa
- + test/nesting/triple_nested.gfa
- + test/nesting/triple_nested_multisnp.gfa
- + test/nesting/two_contig_gref.gfa
- + test/nesting/two_contig_gref_nors.gfa
- + test/nesting/unanchored_component.gfa
- + test/nesting/unpathed_node.gfa
- + test/nesting/unrelated10_in_2kb.gfa
- test/pileup/edit.json
- test/pileup/edits.json
- + test/primers/index.dist
- + test/primers/y.dist
- + test/primers/y.gbwt
- + test/primers/y.gg
- + test/primers/y.giraffe.gbz
- + test/primers/y.min
- + test/primers/y.primer3.split.config
- + test/primers/y.primer3_with_ref_pos.out
- + test/primers/y.primer3_with_ref_pos_11.nopath.out
- + test/primers/y.primer3_with_ref_pos_11.out
- + test/primers/y.primer3config.split
- + test/primers/y.ref_pos_0.out
- + test/primers/y.ref_pos_11.out
- + test/primers/y.ri
- + test/primers/y.split.out
- + test/primers/y.xg
- + test/primers/y.zipcodes
- + test/reads/cactus-BRCA2.fastq
- + test/reads/disconnected.fq
- + test/reads/disconnected_pair.fq
- + test/reads/haplotypes_read.json
- + test/reads/small.middle.ref.indel.multi.fq
- + test/reads/small.middle.ref.mismatched.fq
- + test/reads/small.recombined.fq
- + test/reads/ts.fq
- + test/small/atend.sam
- + test/small/atstart.sam
- + test/small/bad_contig.sam
- + test/small/pastend.sam
- + test/small/paststart.sam
- + test/small/unmapped.sam
- + test/surject/opposite_strands.gaf
- + test/surject/opposite_strands.gfa
- test/t/01_build_graph.t
- test/t/02_vg_construct.t
- test/t/03_vg_view.t
- test/t/04_vg_align.t
- test/t/05_vg_find.t
- test/t/06_vg_index.t
- test/t/07_vg_map.t
- test/t/10_vg_stats.t
- test/t/11_vg_paths.t
- test/t/13_vg_sim.t
- test/t/14_vg_mod.t
- test/t/15_vg_surject.t
- − test/t/16_vg_msga.t
- test/t/17_vg_augment.t
- test/t/18_vg_call.t
- − test/t/19_vg_compare.t
- test/t/21_vg_filter.t
- − test/t/22_ggsv.t
- test/t/25_circularize.t
- test/t/26_deconstruct.t
- test/t/27_vg_genotype.t
- test/t/30_vg_chunk.t
- test/t/32_vg_snarls.t
- test/t/33_vg_mpmap.t
- test/t/37_vg_gbwt.t
- test/t/38_vg_prune.t
- test/t/39_vg_inject.t
- test/t/42_vg_gamsort.t
- test/t/43_vg_simplify.t
- test/t/45_vg_sort.t
- test/t/46_vg_minimizer.t
- test/t/47_vg_dotplot.t
- test/t/48_vg_convert.t
- test/t/49_vg_depth.t
- test/t/50_vg_giraffe.t
- test/t/52_vg_autoindex.t
- test/t/53_clip.t
- test/t/54_vg_haplotypes.t
- + test/t/55_vg_mask.t
- + test/t/56_vg_primers.t
- + test/t/57_vg_chains.t
- + test/t/99_scripts.t
- + test/tiny/tiny.gfaz
- vgci/mine-logs.py
- vgci/post-report
- vgci/test-list.txt
- vgci/vgci.py
- vgci/vgci.sh


The diff was not included because it is too large.


View it on GitLab: https://salsa.debian.org/med-team/vg/-/commit/e106f36e2d76ae7e9c232e7232c70cf3ca253d7d

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