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mccortex/src/basic/binary_seq.c
mccortex/src/basic/binary_seq.h
mccortex/src/basic/call_file_reader.c
mccortex/src/basic/call_file_reader.h
mccortex/src/basic/chrom_pos_list.c
mccortex/src/basic/chrom_pos_list.h
mccortex/src/basic/cmd.c
mccortex/src/basic/cmd.h
mccortex/src/basic/common_buffers.h
mccortex/src/basic/decomp_breakpoint.c
mccortex/src/basic/decomp_breakpoint.h
mccortex/src/basic/decomp_bubble.c
mccortex/src/basic/decomp_bubble.h
mccortex/src/basic/dna.c
mccortex/src/basic/dna.h
mccortex/src/basic/file_filter.c
mccortex/src/basic/file_filter.h
mccortex/src/basic/file_util.c
mccortex/src/basic/file_util.h
mccortex/src/basic/graph_info.c
mccortex/src/basic/graph_info.h
mccortex/src/basic/hash.h
mccortex/src/basic/hash_mem.c
mccortex/src/basic/hash_mem.h
mccortex/src/basic/range.c
mccortex/src/basic/range.h
mccortex/src/basic/seq_loading_stats.c
mccortex/src/basic/seq_loading_stats.h
mccortex/src/basic/seq_reader.c
mccortex/src/basic/seq_reader.h
mccortex/src/basic/seqout.c
mccortex/src/basic/seqout.h
mccortex/src/basic/str_parsing.c
mccortex/src/basic/str_parsing.h
mccortex/src/commands/commands.h
mccortex/src/commands/ctx_breakpoints.c
mccortex/src/commands/ctx_bubbles.c
mccortex/src/commands/ctx_build.c
mccortex/src/commands/ctx_calls2vcf.c
mccortex/src/commands/ctx_clean.c
mccortex/src/commands/ctx_contigs.c
mccortex/src/commands/ctx_correct.c
mccortex/src/commands/ctx_coverage.c
mccortex/src/commands/ctx_dist_matrix.c
mccortex/src/commands/ctx_exp_abc.c
mccortex/src/commands/ctx_exp_hashtest.c
mccortex/src/commands/ctx_geno.c
mccortex/src/commands/ctx_health_check.c
mccortex/src/commands/ctx_index.c
mccortex/src/commands/ctx_infer_edges.c
mccortex/src/commands/ctx_join.c
mccortex/src/commands/ctx_links.c
mccortex/src/commands/ctx_pjoin.c
mccortex/src/commands/ctx_pop_bubbles.c
mccortex/src/commands/ctx_pview.c
mccortex/src/commands/ctx_reads.c
mccortex/src/commands/ctx_rmsubstr.c
mccortex/src/commands/ctx_server.c
mccortex/src/commands/ctx_sort.c
mccortex/src/commands/ctx_subgraph.c
mccortex/src/commands/ctx_thread.c
mccortex/src/commands/ctx_uniqkmers.c
mccortex/src/commands/ctx_unitigs.c
mccortex/src/commands/ctx_vcfcov.c
mccortex/src/commands/ctx_vcfgeno.c
mccortex/src/commands/ctx_view.c
mccortex/src/commands/read_thread_cmd.c
mccortex/src/commands/read_thread_cmd.h
mccortex/src/global/cortex_types.h
mccortex/src/global/ctx_alloc.c
mccortex/src/global/ctx_alloc.h
mccortex/src/global/ctx_assert.c
mccortex/src/global/ctx_assert.h
mccortex/src/global/ctx_output.c
mccortex/src/global/ctx_output.h
mccortex/src/global/global.c
mccortex/src/global/global.h
mccortex/src/global/util.c
mccortex/src/global/util.h
mccortex/src/global/version.h
mccortex/src/graph/binary_kmer.c
mccortex/src/graph/binary_kmer.h
mccortex/src/graph/cmd_mem.c
mccortex/src/graph/cmd_mem.h
mccortex/src/graph/contig_confidence.c
mccortex/src/graph/contig_confidence.h
mccortex/src/graph/db_graph.c
mccortex/src/graph/db_graph.h
mccortex/src/graph/db_node.c
mccortex/src/graph/db_node.h
mccortex/src/graph/graph_cache.c
mccortex/src/graph/graph_cache.h
mccortex/src/graph/graph_crawler.c
mccortex/src/graph/graph_crawler.h
mccortex/src/graph/graph_file_reader.c
mccortex/src/graph/graph_file_reader.h
mccortex/src/graph/graph_format.c
mccortex/src/graph/graph_format.h
mccortex/src/graph/graph_step.c
mccortex/src/graph/graph_step.h
mccortex/src/graph/graph_walker.c
mccortex/src/graph/graph_walker.h
mccortex/src/graph/graph_writer.c
mccortex/src/graph/graph_writer.h
mccortex/src/graph/graphs_load.c
mccortex/src/graph/graphs_load.h
mccortex/src/graph/hash_table.c
mccortex/src/graph/hash_table.h
mccortex/src/graph/json_hdr.c
mccortex/src/graph/json_hdr.h
mccortex/src/graph/kmer_occur.c
mccortex/src/graph/kmer_occur.h
mccortex/src/graph/prune_nodes.c
mccortex/src/graph/prune_nodes.h
mccortex/src/graph/repeat_walker.h
mccortex/src/graph/supernode.c
mccortex/src/graph/supernode.h
mccortex/src/graph/unitig_graph.c
mccortex/src/graph/unitig_graph.h
mccortex/src/graph/vcf_misc.c
mccortex/src/graph/vcf_misc.h
mccortex/src/graph_paths/gpath_checks.c
mccortex/src/graph_paths/gpath_checks.h
mccortex/src/graph_paths/gpath_reader.c
mccortex/src/graph_paths/gpath_reader.h
mccortex/src/graph_paths/gpath_save.c
mccortex/src/graph_paths/gpath_save.h
mccortex/src/kmer/kmer_hash.h
mccortex/src/kmer/kmer_size.c
mccortex/src/kmer/kmer_size.h
mccortex/src/main/debug.c
mccortex/src/main/mccortex.c
mccortex/src/main/tables.c
mccortex/src/main/tests.c
mccortex/src/paths/gpath.c
mccortex/src/paths/gpath.h
mccortex/src/paths/gpath_follow.c
mccortex/src/paths/gpath_follow.h
mccortex/src/paths/gpath_hash.c
mccortex/src/paths/gpath_hash.h
mccortex/src/paths/gpath_set.c
mccortex/src/paths/gpath_set.h
mccortex/src/paths/gpath_store.c
mccortex/src/paths/gpath_store.h
mccortex/src/paths/gpath_subset.c
mccortex/src/paths/gpath_subset.h
mccortex/src/paths/link_tree.c
mccortex/src/paths/link_tree.h
mccortex/src/tests/all_tests.c
mccortex/src/tests/all_tests.h
mccortex/src/tests/binary_seq_tests.c
mccortex/src/tests/bkmer_tests.c
mccortex/src/tests/bubble_caller_tests.c
mccortex/src/tests/build_graph_tests.c
mccortex/src/tests/cleaning_tests.c
mccortex/src/tests/corrected_aln_tests.c
mccortex/src/tests/dna_tests.c
mccortex/src/tests/graph_crawler_tests.c
mccortex/src/tests/graph_walker_tests.c
mccortex/src/tests/hash_table_tests.c
mccortex/src/tests/infer_edges_tests.c
mccortex/src/tests/kmer_occur_tests.c
mccortex/src/tests/node_tests.c
mccortex/src/tests/path_tests.c
mccortex/src/tests/repeat_walker_tests.c
mccortex/src/tests/subgraph_tests.c
mccortex/src/tests/supernode_tests.c
mccortex/src/tests/util_tests.c
mccortex/src/tools/assemble_contigs.c
mccortex/src/tools/assemble_contigs.h
mccortex/src/tools/assemble_stats.c
mccortex/src/tools/assemble_stats.h
mccortex/src/tools/breakpoint_caller.c
mccortex/src/tools/breakpoint_caller.h
mccortex/src/tools/bubble_caller.c
mccortex/src/tools/bubble_caller.h
mccortex/src/tools/build_graph.c
mccortex/src/tools/build_graph.h
mccortex/src/tools/clean_graph.c
mccortex/src/tools/clean_graph.h
mccortex/src/tools/correct_reads.c
mccortex/src/tools/correct_reads.h
mccortex/src/tools/generate_paths.c
mccortex/src/tools/generate_paths.h
mccortex/src/tools/genotyping.c
mccortex/src/tools/genotyping.h
mccortex/src/tools/infer_edges.c
mccortex/src/tools/infer_edges.h
mccortex/src/tools/pop_bubbles.c
mccortex/src/tools/pop_bubbles.h
mccortex/src/tools/subgraph.c
mccortex/src/tools/subgraph.h
mccortex/src/tools/vcf_coverage.c
mccortex/src/tools/vcf_coverage.h
mccortex/tests/run.sh
mccortex/tests/breakpoint/Makefile
mccortex/tests/breakpoint_empty/Makefile
mccortex/tests/bubble_one/Makefile
mccortex/tests/bubble_test/Makefile
mccortex/tests/bubble_test/truth.vcf
mccortex/tests/bubbles/Makefile
mccortex/tests/bubbles/bubbles1/Makefile
mccortex/tests/bubbles/bubbles2/Makefile
mccortex/tests/bubbles/bubbles2/itchy.fa
mccortex/tests/bubbles/bubbles2/make-exhaustive-alleles.py
mccortex/tests/bubbles/bubbles2/ref.fa
mccortex/tests/bubbles/bubbles2/scratchy.fa
mccortex/tests/bubbles/bubbles3/Makefile
mccortex/tests/build/Makefile
mccortex/tests/build/build0/Makefile
mccortex/tests/build/build1/Makefile
mccortex/tests/clean/Makefile
mccortex/tests/clean2/Makefile
mccortex/tests/clean3/Makefile
mccortex/tests/contigs/Makefile
mccortex/tests/correct/Makefile
mccortex/tests/coverage/Makefile
mccortex/tests/dist_matrix/Makefile
mccortex/tests/graphviz/Makefile
mccortex/tests/inferedges/Makefile
mccortex/tests/join/Makefile
mccortex/tests/largeK/Makefile
mccortex/tests/loop/Makefile
mccortex/tests/lossless/Makefile
mccortex/tests/lossless_reads/Makefile
mccortex/tests/old/calling_repeats/Makefile
mccortex/tests/path_check/Makefile
mccortex/tests/pipeline/Makefile
mccortex/tests/pjoin/Makefile
mccortex/tests/pop_bubbles1/Makefile
mccortex/tests/pop_bubbles2/Makefile
mccortex/tests/reads/Makefile
mccortex/tests/rmsubstr/Makefile
mccortex/tests/sort/Makefile
mccortex/tests/subgraph/Makefile
mccortex/tests/subgraph_supernodes/Makefile
mccortex/tests/supernodes/Makefile
mccortex/tests/thread2/Makefile
mccortex/tests/thread_pe/Makefile
mccortex/tests/thread_pe_short/Makefile
mccortex/tests/threading/Makefile
mccortex/tests/vcfcov/Makefile
mccortex/tests/vcfcov/calls0/Makefile
mccortex/tests/vcfcov/calls0/calls.vcf
mccortex/tests/vcfcov/calls0/truth.cov.vcf
mccortex/tests/vcfcov/calls1/Makefile
mccortex/tests/vcfcov/calls1/calls.vcf
mccortex/tests/vcfcov/calls1/jane.fa
mccortex/tests/vcfcov/calls1/john.fa
mccortex/tests/vcfcov/calls1/truth.cov.vcf
mccortex/tests/vcfcov/calls2/Makefile
mccortex/tests/vcfcov/calls2/calls.vcf
mccortex/tests/vcfcov/calls2/fake-vcf.py
mccortex/tests/vcfcov/calls2/sample.fa
mccortex/tests/vcfcov/calls2/truth.cov.vcf
mccortex/tests/vcfcov/calls3/Makefile
mccortex/tests/vcfcov/calls3/calls.vcf
mccortex/tests/vcfcov/calls3/hardy.fa
mccortex/tests/vcfcov/calls3/laurel.fa
mccortex/tests/vcfcov/calls3/truth.cov.vcf
mccortex/tests/vcfcov/calls4/Makefile
mccortex/tests/vcfcov/calls4/calls.vcf
mccortex/tests/vcfcov/calls4/fake-spaced-vcf.py
mccortex/tests/vcfcov/calls4/pluto.fa
mccortex/tests/vcfcov/calls4/truth.cov.vcf
mccortex/tests/vcfcov/calls5/Makefile
mccortex/tests/vcfcov/calls5/calls.vcf
mccortex/tests/vcfcov/calls5/truth.cov.vcf
mccortex/tests/vcfcov/ref/ref.fa
mccortex/travis/install.sh
mccortex/travis/script.sh
mykatlas/__init__.py
mykatlas/atlas_main.py
mykatlas/base.py
mykatlas/utils.py
mykatlas/version.py
mykatlas.egg-info/PKG-INFO
mykatlas.egg-info/SOURCES.txt
mykatlas.egg-info/dependency_links.txt
mykatlas.egg-info/entry_points.txt
mykatlas.egg-info/requires.txt
mykatlas.egg-info/top_level.txt
mykatlas/analysis/__init__.py
mykatlas/analysis/models.py
mykatlas/cmds/__init__.py
mykatlas/cmds/add-gt.py
mykatlas/cmds/add.py
mykatlas/cmds/atlasadd.py
mykatlas/cmds/diff.py
mykatlas/cmds/dump.py
mykatlas/cmds/genotype.py
mykatlas/cmds/makeprobes.py
mykatlas/cmds/place.py
mykatlas/cmds/walk.py
mykatlas/cortex/__init__.py
mykatlas/cortex/mccortex.py
mykatlas/cortex/server.py
mykatlas/stats/__init__.py
mykatlas/stats/stats.py
mykatlas/typing/__init__.py
mykatlas/typing/models/__init__.py
mykatlas/typing/models/base.py
mykatlas/typing/models/panel.py
mykatlas/typing/models/presence.py
mykatlas/typing/models/variant.py
mykatlas/typing/typer/__init__.py
mykatlas/typing/typer/base.py
mykatlas/typing/typer/genotyper.py
mykatlas/typing/typer/presence.py
mykatlas/typing/typer/variant.py