├── .gitignore ├── .gitmodules ├── .travis.yml ├── AUTHORS ├── LICENSE ├── Makefile ├── README.md ├── Vagrantfile ├── dev └── bkmer_revcmp │ ├── Makefile │ └── revcmp.c ├── docs └── file_formats │ ├── graph_file_format.txt │ ├── graph_format_v7.txt │ └── paths_file_format.txt ├── libs ├── Makefile ├── cJSON │ ├── LICENSE │ ├── README │ ├── cJSON.c │ ├── cJSON.h │ ├── test.c │ └── tests │ │ ├── test1 │ │ ├── test2 │ │ ├── test3 │ │ ├── test4 │ │ └── test5 ├── maximal_substrs │ ├── Makefile │ ├── maxsubstrs.c │ ├── maxsubstrs.pl │ └── stream_buffer.h ├── misc │ ├── Makefile │ ├── README.md │ ├── city.c │ ├── city.h │ ├── citycrc.h │ ├── jenkins.h │ ├── lookup3.h │ ├── mem_size.c │ ├── mem_size.h │ └── twang.h └── update-modules.sh ├── results ├── NA12878 │ └── callcov │ │ └── run.sh ├── README.txt ├── assembly │ ├── Makefile │ └── results │ │ ├── 20150506.wed.txt │ │ ├── 20150511.mon.txt │ │ └── 20180715.sun.txt ├── benchmark │ ├── 10diploid10X │ │ ├── run-sim.sh │ │ └── smaller.fa │ ├── calling-comparison.mk │ ├── diploid60X │ │ └── run-sim.sh │ ├── minidiploid │ │ └── run-sim.sh │ └── paperSimulations │ │ ├── Makefile │ │ └── README ├── breakpoint_calling │ ├── Makefile │ └── results │ │ ├── 20150505.tues.txt │ │ ├── 20150506.wed.txt │ │ └── 20150511.mon.hapdip.txt ├── contig_confidence │ ├── Makefile │ ├── confidence.tex │ └── plot-confidence.R ├── correct │ ├── ecoli │ │ └── Makefile │ └── hg_chr22 │ │ ├── Makefile │ │ ├── README.txt │ │ └── results │ │ ├── historic.results.txt │ │ ├── results.20140926.txt │ │ └── results.chr22_28M_29M.20170206.txt ├── data │ ├── PhiX │ │ └── about.txt │ ├── chr22 │ │ ├── Makefile │ │ ├── about.txt │ │ └── uniq_flanks │ │ │ ├── Makefile │ │ │ └── README.txt │ ├── download.sh │ └── ecoli │ │ ├── Makefile │ │ └── README.txt ├── file_buffering │ ├── README.txt │ ├── file-buffering.sh │ ├── results20150413mon.mac.csv │ └── results20150413mon.mac.txt ├── hash_table_benchmark │ ├── README.txt │ ├── benchmark-tables.sh │ ├── results20150409thurs.linux.log │ ├── results20150409thurs.linux.txt │ ├── results20150409thurs.mac.log │ ├── results20150409thurs.mac.txt │ └── stats.R ├── klebsiella │ └── kleb_pneumoniae │ │ ├── assembly │ │ ├── get-max-covg.sh │ │ └── make-dot-plots.sh │ │ ├── cortex │ │ ├── analysis.sh │ │ └── call-cortex.sh │ │ ├── freebayes │ │ ├── analysis.sh │ │ └── freebayes.sh │ │ ├── indels │ │ ├── about.txt │ │ ├── kleb-plot-hist.R │ │ ├── kleb-plot-split.R │ │ └── run.sh │ │ ├── large_events │ │ ├── combined-plot.R │ │ ├── large-event-mappings.py │ │ └── large-events-plot.R │ │ ├── mcrun │ │ └── analysis.sh │ │ └── platypus │ │ ├── analysis.sh │ │ └── call-platypus.sh ├── kmer_size_experiment │ ├── Makefile │ ├── notes.txt │ ├── results │ │ ├── 20160912mon │ │ │ ├── notes.txt │ │ │ ├── perfect.cov.pdf │ │ │ ├── perfect.links.csv │ │ │ ├── perfect.plain.csv │ │ │ ├── seqn.errors.csv │ │ │ ├── stoch.cov.pdf │ │ │ ├── stoch.links.csv │ │ │ ├── stoch.plain.csv │ │ │ ├── stocherr.cov.pdf │ │ │ ├── stocherr.links.csv │ │ │ └── stocherr.plain.csv │ │ ├── 20160929thurs │ │ │ ├── bad.edges.csv │ │ │ ├── cleaning.table.csv │ │ │ ├── perfect.cov.pdf │ │ │ ├── perfect.links.csv │ │ │ ├── perfect.pe.csv │ │ │ ├── perfect.plain.csv │ │ │ ├── perfect_no_pe.pdf │ │ │ ├── stoch.cov.pdf │ │ │ ├── stoch.links.csv │ │ │ ├── stoch.pe.csv │ │ │ ├── stoch.plain.csv │ │ │ ├── stocherr.cov.pdf │ │ │ ├── stocherr.links.csv │ │ │ ├── stocherr.pe.csv │ │ │ └── stocherr.plain.csv │ │ ├── 20161012wed │ │ │ ├── bad.edges.csv │ │ │ ├── cleaning.corr.table.csv │ │ │ ├── cleaning.table.csv │ │ │ ├── perfect.links.csv │ │ │ ├── perfect.pdf │ │ │ ├── perfect.pe.csv │ │ │ ├── perfect.plain.csv │ │ │ ├── perfect_nope.pdf │ │ │ ├── stoch.links.csv │ │ │ ├── stoch.pdf │ │ │ ├── stoch.pe.csv │ │ │ ├── stoch.plain.csv │ │ │ ├── stocherr.links.csv │ │ │ ├── stocherr.pdf │ │ │ ├── stocherr.pe.csv │ │ │ ├── stocherr.plain.csv │ │ │ ├── stocherrcorr.links.csv │ │ │ ├── stocherrcorr.pdf │ │ │ ├── stocherrcorr.pe.csv │ │ │ └── stocherrcorr.plain.csv │ │ ├── 20170206mon_chr22_28M │ │ │ ├── bad.edges.csv │ │ │ ├── cleaning.corr.table.csv │ │ │ ├── cleaning.table.csv │ │ │ ├── corr-links-vs-raw-sga-errs.pdf │ │ │ ├── corr-links-vs-raw-sga-ng50.pdf │ │ │ ├── corr-links-vs-sga-errs.pdf │ │ │ ├── corr-links-vs-sga-ng50.pdf │ │ │ ├── corr-pe-vs-raw-sga-errs.pdf │ │ │ ├── corr-pe-vs-raw-sga-ng50.pdf │ │ │ ├── corr-pe-vs-sga-errs.pdf │ │ │ ├── corr-pe-vs-sga-ng50.pdf │ │ │ ├── err-corr-plots │ │ │ │ ├── Makefile │ │ │ │ └── errcorr.tex │ │ │ ├── linkcounts.pe.pdf │ │ │ ├── linkcounts.se.pdf │ │ │ ├── links-vs-sga-errs.pdf │ │ │ ├── links-vs-sga-ng50.pdf │ │ │ ├── pe-vs-sga-errs.pdf │ │ │ ├── pe-vs-sga-ng50.pdf │ │ │ ├── perfect.linkcounts.pe.csv │ │ │ ├── perfect.linkcounts.pe.pdf │ │ │ ├── perfect.linkcounts.se.csv │ │ │ ├── perfect.linkcounts.se.pdf │ │ │ ├── perfect.links.csv │ │ │ ├── perfect.pdf │ │ │ ├── perfect.pe.csv │ │ │ ├── perfect.plain.csv │ │ │ ├── perfect_no_pe.pdf │ │ │ ├── plain-vs-links-corr.pdf │ │ │ ├── plain-vs-links.pdf │ │ │ ├── plain-vs-pe-corr.pdf │ │ │ ├── plain-vs-pe.pdf │ │ │ ├── stoch.linkcounts.pe.csv │ │ │ ├── stoch.linkcounts.pe.pdf │ │ │ ├── stoch.linkcounts.se.csv │ │ │ ├── stoch.linkcounts.se.pdf │ │ │ ├── stoch.links.csv │ │ │ ├── stoch.pdf │ │ │ ├── stoch.pe.csv │ │ │ ├── stoch.plain.csv │ │ │ ├── stocherr.linkcounts.pe.csv │ │ │ ├── stocherr.linkcounts.pe.pdf │ │ │ ├── stocherr.linkcounts.se.csv │ │ │ ├── stocherr.linkcounts.se.pdf │ │ │ ├── stocherr.links.csv │ │ │ ├── stocherr.pdf │ │ │ ├── stocherr.pe.csv │ │ │ ├── stocherr.plain.csv │ │ │ ├── stocherr.sga.csv │ │ │ ├── stocherrcorr.linkcounts.pe.csv │ │ │ ├── stocherrcorr.linkcounts.pe.pdf │ │ │ ├── stocherrcorr.linkcounts.se.csv │ │ │ ├── stocherrcorr.linkcounts.se.pdf │ │ │ ├── stocherrcorr.links.csv │ │ │ ├── stocherrcorr.pdf │ │ │ ├── stocherrcorr.pe.csv │ │ │ ├── stocherrcorr.plain.csv │ │ │ └── stocherrcorr.sga.csv │ │ ├── 20170211sat_chr22_28M_confidstep │ │ │ ├── README.md │ │ │ ├── bad.edges.csv │ │ │ ├── cleaning.corr.table.csv │ │ │ ├── cleaning.table.csv │ │ │ ├── corr-links-vs-sga-errs.pdf │ │ │ ├── corr-links-vs-sga-ng50.pdf │ │ │ ├── corr-pe-vs-sga-errs.pdf │ │ │ ├── corr-pe-vs-sga-ng50.pdf │ │ │ ├── links-vs-sga-errs.pdf │ │ │ ├── links-vs-sga-ng50.pdf │ │ │ ├── pe-vs-sga-errs.pdf │ │ │ ├── pe-vs-sga-ng50.pdf │ │ │ ├── perfect.links.csv │ │ │ ├── perfect.pdf │ │ │ ├── perfect.pe.csv │ │ │ ├── perfect.plain.csv │ │ │ ├── perfect_no_pe.pdf │ │ │ ├── plain-vs-links-corr.pdf │ │ │ ├── plain-vs-links.pdf │ │ │ ├── plain-vs-pe-corr.pdf │ │ │ ├── plain-vs-pe.pdf │ │ │ ├── stoch.links.csv │ │ │ ├── stoch.pdf │ │ │ ├── stoch.pe.csv │ │ │ ├── stoch.plain.csv │ │ │ ├── stocherr.links.csv │ │ │ ├── stocherr.pdf │ │ │ ├── stocherr.pe.csv │ │ │ ├── stocherr.plain.csv │ │ │ ├── stocherr.sga.csv │ │ │ ├── stocherrcorr.links.csv │ │ │ ├── stocherrcorr.pdf │ │ │ ├── stocherrcorr.pe.csv │ │ │ ├── stocherrcorr.plain.csv │ │ │ └── stocherrcorr.sga.csv │ │ ├── 20170211sat_chr22_28M_nomissing │ │ │ ├── README.md │ │ │ ├── bad.edges.csv │ │ │ ├── cleaning.corr.table.csv │ │ │ ├── cleaning.table.csv │ │ │ ├── corr-links-vs-sga-errs.pdf │ │ │ ├── corr-links-vs-sga-ng50.pdf │ │ │ ├── corr-pe-vs-sga-errs.pdf │ │ │ ├── corr-pe-vs-sga-ng50.pdf │ │ │ ├── links-vs-sga-errs.pdf │ │ │ ├── links-vs-sga-ng50.pdf │ │ │ ├── pe-vs-sga-errs.pdf │ │ │ ├── pe-vs-sga-ng50.pdf │ │ │ ├── perfect.links.csv │ │ │ ├── perfect.pdf │ │ │ ├── perfect.pe.csv │ │ │ ├── perfect.plain.csv │ │ │ ├── perfect_no_pe.pdf │ │ │ ├── plain-vs-links-corr.pdf │ │ │ ├── plain-vs-links.pdf │ │ │ ├── plain-vs-pe-corr.pdf │ │ │ ├── plain-vs-pe.pdf │ │ │ ├── stoch.links.csv │ │ │ ├── stoch.pdf │ │ │ ├── stoch.pe.csv │ │ │ ├── stoch.plain.csv │ │ │ ├── stocherr.links.csv │ │ │ ├── stocherr.pdf │ │ │ ├── stocherr.pe.csv │ │ │ ├── stocherr.plain.csv │ │ │ ├── stocherr.sga.csv │ │ │ ├── stocherrcorr.links.csv │ │ │ ├── stocherrcorr.pdf │ │ │ ├── stocherrcorr.pe.csv │ │ │ ├── stocherrcorr.plain.csv │ │ │ └── stocherrcorr.sga.csv │ │ ├── count-links.pl │ │ ├── generate-results.sh │ │ ├── make-cleaning-table.py │ │ ├── make-csv.sh │ │ ├── plot-link-counts-threeway.R │ │ ├── plot-link-counts-together.R │ │ ├── plot-link-counts.R │ │ ├── plot-mccortex-vs-sga.R │ │ ├── plot-ng50-and-errs.R │ │ ├── plot-ng50-four-sets.R │ │ └── plot-ng50-three-sets.R │ ├── runk.mk │ ├── sga-all-kmers.sh │ └── sga.sh ├── traversal_conjecture │ ├── Makefile │ └── README.txt ├── var_calling_10ecoli │ ├── Makefile │ ├── about.txt │ ├── cortex │ │ └── Makefile │ └── results │ │ ├── 20150510_sun_initrun │ │ ├── 20150510.sun.txt │ │ ├── 20150510.sun.txt.2 │ │ ├── 20150510.sun.txt.3 │ │ └── 20150510.sun.txt.4 │ │ ├── 20150615_joint_1by1_links_plain │ │ ├── 20150617.wed.1by1.links.log │ │ ├── 20150617.wed.1by1.plain.log │ │ ├── 20150617.wed.joint.links.log │ │ ├── 20150617.wed.joint.plain.log │ │ └── 20150617.wed.stats.txt │ │ └── 20150713_cortex │ │ ├── 20150713_cortex.log │ │ ├── 20150713_cortex.log.2 │ │ └── all.log └── var_calling_diploid_chr22_1Mbp │ ├── Makefile │ ├── about.txt │ ├── cortex │ └── Makefile │ └── results │ ├── 20150720 │ └── 20150720_mon.log │ ├── 20150428.tues.k21.linux.txt │ ├── 20150428.tues.k31.linux.txt │ ├── 20150429.wed.k21.linux.txt │ ├── 20150429.wed.k31.linux.txt │ ├── 20150501.fri.run1.log │ ├── 20150501.fri.run2.log │ └── 20150506.wed.txt ├── scripts ├── R │ ├── get_auto_cleaning_cutoff.R │ ├── gil_fit_cleaning_model.R │ ├── install-deps.R │ ├── link-cov-heatmap.R │ ├── make_link_cutoffs.R │ ├── plot-covg-hist.R │ ├── plot-length-hist.R │ ├── plot-link-counts.R │ └── plot-link-dist-cov.R ├── analysis │ ├── calls-covg.pl │ ├── gt-compare.pl │ ├── haploid-sam-compare.py │ ├── haploid-vcf-haplotypes.py │ ├── mapping-vars-test.sh │ ├── mummer-vcf-isec.sh │ ├── mummer2vcf.sh │ └── sam-count-vars.pl ├── bash │ ├── links-bytes.sh │ ├── links-count.sh │ ├── links-median-threshold.sh │ ├── mccortex-to-ray.sh │ └── vcf-longest-haplotype.sh ├── build │ ├── mccortex │ ├── multik-build.sh │ └── update.sh ├── calculations │ ├── bloom-filter-fpr.pl │ └── c-within-rand-a-b-bounds.pl ├── cortex │ └── cortex-clean-bubbles.pl ├── cortex_print_flanks.sh ├── make-circos.pl ├── make-isec.sh ├── make-pipeline.pl ├── make-report.pl ├── mccortex-kcovg.pl ├── perl │ ├── LineReader.pm │ ├── McCortexBreakpoints.pm │ ├── McCortexBubbles.pm │ ├── McCortexGraph.pm │ ├── McCortexLinks.pm │ ├── McCortexScripts.pm │ ├── breakpoints-check-ref.pl │ ├── breakpoints-check.pl │ ├── breakpoints-example.pl │ ├── bubbles-example.pl │ ├── bubbles-to-contigs.pl │ ├── links-filter.pl │ ├── links-view.pl │ ├── mccortex-contig-stats.pl │ ├── mccortex-graph-kmer-size.pl │ ├── mccortex-graph-stats.pl │ ├── mccortex-graph-to-graphviz.pl │ ├── mccortex-header.pl │ ├── mccortex-links.pl │ └── mccortex-thread-stats.pl ├── python │ ├── break-contigs-vs-truth.py │ ├── count-bad-edges.py │ ├── generate-reads.py │ ├── mccortex-server.py │ ├── mccortex.py │ ├── pyRBT.py │ └── snp-pileup.py ├── report │ ├── make-kmer-plot.sh │ └── make-link-plot.sh └── seq2pdf.sh ├── src ├── alignment │ ├── correct_alignment.c │ ├── correct_alignment.h │ ├── correct_aln_input.c │ ├── correct_aln_input.h │ ├── correct_aln_stats.c │ ├── correct_aln_stats.h │ ├── db_alignment.c │ └── db_alignment.h ├── basic │ ├── aligned_call.c │ ├── aligned_call.h │ ├── async_read_io.c │ ├── async_read_io.h │ ├── binary_seq.c │ ├── binary_seq.h │ ├── call_file_reader.c │ ├── call_file_reader.h │ ├── chrom_pos_list.c │ ├── chrom_pos_list.h │ ├── cmd.c │ ├── cmd.h │ ├── common_buffers.h │ ├── decomp_breakpoint.c │ ├── decomp_breakpoint.h │ ├── decomp_bubble.c │ ├── decomp_bubble.h │ ├── dna.c │ ├── dna.h │ ├── file_filter.c │ ├── file_filter.h │ ├── file_util.c │ ├── file_util.h │ ├── graph_info.c │ ├── graph_info.h │ ├── hash.h │ ├── hash_mem.c │ ├── hash_mem.h │ ├── range.c │ ├── range.h │ ├── seq_loading_stats.c │ ├── seq_loading_stats.h │ ├── seq_reader.c │ ├── seq_reader.h │ ├── seqout.c │ ├── seqout.h │ ├── str_parsing.c │ └── str_parsing.h ├── commands │ ├── commands.h │ ├── ctx_breakpoints.c │ ├── ctx_bubbles.c │ ├── ctx_build.c │ ├── ctx_calls2vcf.c │ ├── ctx_clean.c │ ├── ctx_contigs.c │ ├── ctx_correct.c │ ├── ctx_coverage.c │ ├── ctx_dist_matrix.c │ ├── ctx_exp_abc.c │ ├── ctx_exp_hashtest.c │ ├── ctx_health_check.c │ ├── ctx_index.c │ ├── ctx_infer_edges.c │ ├── ctx_join.c │ ├── ctx_links.c │ ├── ctx_pjoin.c │ ├── ctx_pop_bubbles.c │ ├── ctx_pview.c │ ├── ctx_reads.c │ ├── ctx_rmsubstr.c │ ├── ctx_server.c │ ├── ctx_sort.c │ ├── ctx_subgraph.c │ ├── ctx_thread.c │ ├── ctx_uniqkmers.c │ ├── ctx_unitigs.c │ ├── ctx_vcfcov.c │ ├── ctx_vcfgeno.c │ ├── ctx_view.c │ ├── read_thread_cmd.c │ └── read_thread_cmd.h ├── global │ ├── cortex_types.h │ ├── ctx_alloc.c │ ├── ctx_alloc.h │ ├── ctx_assert.c │ ├── ctx_assert.h │ ├── ctx_output.c │ ├── ctx_output.h │ ├── global.c │ ├── global.h │ ├── util.c │ └── util.h ├── graph │ ├── binary_kmer.c │ ├── binary_kmer.h │ ├── cmd_mem.c │ ├── cmd_mem.h │ ├── contig_confidence.c │ ├── contig_confidence.h │ ├── db_graph.c │ ├── db_graph.h │ ├── db_node.c │ ├── db_node.h │ ├── db_unitig.c │ ├── db_unitig.h │ ├── graph_cache.c │ ├── graph_cache.h │ ├── graph_crawler.c │ ├── graph_crawler.h │ ├── graph_file_reader.c │ ├── graph_file_reader.h │ ├── graph_format.c │ ├── graph_format.h │ ├── graph_search.c │ ├── graph_search.h │ ├── graph_step.c │ ├── graph_step.h │ ├── graph_walker.c │ ├── graph_walker.h │ ├── graph_writer.c │ ├── graph_writer.h │ ├── graphs_load.c │ ├── graphs_load.h │ ├── hash_table.c │ ├── hash_table.h │ ├── json_hdr.c │ ├── json_hdr.h │ ├── kmer_occur.c │ ├── kmer_occur.h │ ├── prune_nodes.c │ ├── prune_nodes.h │ ├── repeat_walker.h │ ├── unitig_graph.c │ ├── unitig_graph.h │ ├── vcf_misc.c │ └── vcf_misc.h ├── graph_paths │ ├── gpath_checks.c │ ├── gpath_checks.h │ ├── gpath_reader.c │ ├── gpath_reader.h │ ├── gpath_save.c │ └── gpath_save.h ├── kmer │ ├── kmer_hash.h │ ├── kmer_size.c │ └── kmer_size.h ├── main │ ├── debug.c │ ├── mccortex.c │ ├── tables.c │ └── tests.c ├── paths │ ├── gpath.c │ ├── gpath.h │ ├── gpath_follow.c │ ├── gpath_follow.h │ ├── gpath_hash.c │ ├── gpath_hash.h │ ├── gpath_set.c │ ├── gpath_set.h │ ├── gpath_store.c │ ├── gpath_store.h │ ├── gpath_subset.c │ ├── gpath_subset.h │ ├── link_tree.c │ └── link_tree.h ├── tests │ ├── all_tests.c │ ├── all_tests.h │ ├── binary_seq_tests.c │ ├── bkmer_tests.c │ ├── bubble_caller_tests.c │ ├── build_graph_tests.c │ ├── cleaning_tests.c │ ├── corrected_aln_tests.c │ ├── db_unitig_tests.c │ ├── dna_tests.c │ ├── graph_crawler_tests.c │ ├── graph_walker_tests.c │ ├── hash_table_tests.c │ ├── infer_edges_tests.c │ ├── kmer_occur_tests.c │ ├── node_tests.c │ ├── path_tests.c │ ├── repeat_walker_tests.c │ ├── subgraph_tests.c │ └── util_tests.c └── tools │ ├── assemble_contigs.c │ ├── assemble_contigs.h │ ├── assemble_stats.c │ ├── assemble_stats.h │ ├── breakpoint_caller.c │ ├── breakpoint_caller.h │ ├── bubble_caller.c │ ├── bubble_caller.h │ ├── build_graph.c │ ├── build_graph.h │ ├── clean_graph.c │ ├── clean_graph.h │ ├── correct_reads.c │ ├── correct_reads.h │ ├── generate_paths.c │ ├── generate_paths.h │ ├── genotyping.c │ ├── genotyping.h │ ├── infer_edges.c │ ├── infer_edges.h │ ├── pop_bubbles.c │ ├── pop_bubbles.h │ ├── subgraph.c │ ├── subgraph.h │ ├── vcf_coverage.c │ └── vcf_coverage.h ├── tests ├── breakpoint │ ├── Makefile │ ├── breakpoint0 │ │ └── Makefile │ ├── breakpoint1 │ │ └── Makefile │ └── breakpoint2 │ │ └── Makefile ├── bubbles │ ├── Makefile │ ├── bubbles1 │ │ └── Makefile │ ├── bubbles2 │ │ ├── Makefile │ │ ├── itchy.fa │ │ ├── make-exhaustive-alleles.py │ │ ├── ref.fa │ │ └── scratchy.fa │ ├── bubbles3 │ │ └── Makefile │ ├── bubbles4 │ │ └── Makefile │ └── bubbles5 │ │ ├── Makefile │ │ └── truth.vcf ├── build │ ├── Makefile │ ├── build0 │ │ └── Makefile │ └── build1 │ │ └── Makefile ├── clean_graph │ ├── Makefile │ ├── clean1 │ │ └── Makefile │ ├── clean2 │ │ └── Makefile │ ├── clean3 │ │ └── Makefile │ └── clean4 │ │ └── Makefile ├── clean_links │ └── Makefile ├── contigs │ └── Makefile ├── correct │ └── Makefile ├── coverage │ └── Makefile ├── dist_matrix │ └── Makefile ├── graphviz │ └── Makefile ├── inferedges │ └── Makefile ├── join │ └── Makefile ├── largeK │ └── Makefile ├── loop │ └── Makefile ├── lossless │ ├── Makefile │ ├── lossless0 │ │ └── Makefile │ └── lossless1 │ │ └── Makefile ├── path_check │ └── Makefile ├── pipeline │ └── Makefile ├── pjoin │ ├── Makefile │ ├── pjoin0 │ │ └── Makefile │ └── pjoin1 │ │ └── Makefile ├── pop_bubbles │ ├── Makefile │ ├── pop_bubbles1 │ │ └── Makefile │ └── pop_bubbles2 │ │ └── Makefile ├── reads │ └── Makefile ├── rmsubstr │ └── Makefile ├── run.sh ├── sort │ └── Makefile ├── subgraph │ └── Makefile ├── subgraph_unitigs │ └── Makefile ├── threading │ ├── Makefile │ ├── threading1 │ │ └── Makefile │ ├── threading2 │ │ └── Makefile │ ├── threading3 │ │ └── Makefile │ └── threading4 │ │ └── Makefile ├── unitigs │ └── Makefile └── vcfcov │ ├── Makefile │ ├── calls0 │ ├── Makefile │ ├── calls.vcf │ └── truth.cov.vcf │ ├── calls1 │ ├── Makefile │ ├── calls.vcf │ ├── jane.fa │ ├── john.fa │ └── truth.cov.vcf │ ├── calls2 │ ├── Makefile │ ├── calls.vcf │ ├── fake-vcf.py │ ├── sample.fa │ └── truth.cov.vcf │ ├── calls3 │ ├── Makefile │ ├── calls.vcf │ ├── hardy.fa │ ├── laurel.fa │ └── truth.cov.vcf │ ├── calls4 │ ├── Makefile │ ├── calls.vcf │ ├── fake-spaced-vcf.py │ ├── pluto.fa │ └── truth.cov.vcf │ ├── calls5 │ ├── Makefile │ ├── calls.vcf │ └── truth.cov.vcf │ └── ref │ └── ref.fa └── travis ├── install.sh ├── provision-vm.sh └── script.sh /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mcveanlab/mccortex/HEAD/.gitignore -------------------------------------------------------------------------------- /.gitmodules: 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