├── .gitignore ├── .gitlab-ci.yml ├── .gitmodules ├── .travis_old.yml ├── BIN-INSTALL.md ├── DEVELOPMENT.md ├── Dockerfile ├── Dockerfile.ci-base ├── Dockerfile.kegalign ├── LICENSE.txt ├── Makefile ├── README.md ├── ReleaseNotes.md ├── api ├── Makefile ├── __init__.py ├── impl │ ├── cactusBlock.c │ ├── cactusBlockPrivate.h │ ├── cactusCap.c │ ├── cactusCapPrivate.h │ ├── cactusChain.c │ ├── cactusChainPrivate.h │ ├── cactusDisk.c │ ├── cactusDiskPrivate.h │ ├── cactusEnd.c │ ├── cactusEndPrivate.h │ ├── cactusEvent.c │ ├── cactusEventPrivate.h │ ├── cactusEventTree.c │ ├── cactusEventTreePrivate.h │ ├── cactusFlower.c │ ├── cactusFlowerPrivate.h │ ├── cactusGlobalsPrivate.h │ ├── cactusGroup.c │ ├── cactusGroupPrivate.h │ ├── cactusLink.c │ ├── cactusLinkPrivate.h │ ├── cactusMisc.c │ ├── cactusSegment.c │ ├── cactusSegmentPrivate.h │ ├── cactusSequence.c │ ├── cactusSequencePrivate.h │ ├── cactusTestCommon.c │ └── cactus_params_parser.c ├── inc │ ├── cactus.h │ ├── cactusBlock.h │ ├── cactusCap.h │ ├── cactusChain.h │ ├── cactusDisk.h │ ├── cactusEnd.h │ ├── cactusEvent.h │ ├── cactusEventTree.h │ ├── cactusFlower.h │ ├── cactusGlobals.h │ ├── cactusGroup.h │ ├── cactusLink.h │ ├── cactusMisc.h │ ├── cactusSegment.h │ ├── cactusSequence.h │ ├── cactusTestCommon.h │ └── cactus_params_parser.h └── tests │ ├── allTests.c │ ├── cactusBlockTest.c │ ├── cactusBlocksTestShared.h │ ├── cactusCapTest.c │ ├── cactusChainTest.c │ ├── cactusChainsTestShared.h │ ├── cactusDiskTest.c │ ├── cactusEndTest.c │ ├── cactusEndsTestShared.h │ ├── cactusEventTest.c │ ├── cactusEventTreeTest.c │ ├── cactusFlowerTest.c │ ├── cactusGroupTest.c │ ├── cactusLinkTest.c │ ├── cactusMiscTest.c │ ├── cactusParamsTest.c │ ├── cactusSegmentTest.c │ └── cactusSequenceTest.c ├── bar ├── Makefile ├── __init__.py ├── impl │ ├── adjacencySequences.c │ ├── bar.c │ ├── endAligner.c │ ├── flowerAligner.c │ ├── poaBarAligner.c │ └── rescue.c ├── inc │ ├── adjacencySequences.h │ ├── endAligner.h │ ├── flowerAligner.h │ ├── poaBarAligner.h │ └── rescue.h └── tests │ ├── adjacencySequencesTest.c │ ├── allTests.c │ ├── endAlignerTest.c │ ├── flowerAlignerTest.c │ ├── flowersShared.h │ ├── poaBarTest.c │ └── rescueTest.c ├── caf ├── Makefile ├── __init__.py ├── impl │ ├── addAdjacencies.c │ ├── annealing.c │ ├── cactus_setup.c │ ├── caf.c │ ├── filtering.c │ ├── finishing.c │ ├── giantComponent.c │ ├── melting.c │ ├── phylogeny.c │ ├── pinchIterator.c │ └── pinchToCactus.c ├── inc │ ├── stCaf.h │ ├── stCafPhylogeny.h │ ├── stGiantComponent.h │ └── stPinchIterator.h └── tests │ ├── allTests.c │ ├── annealingTest.c │ ├── filteringTest.c │ ├── giantComponentTest.c │ ├── phylogenyTests.c │ ├── pinchIteratorTest.c │ └── recoverableChainsTest.c ├── conftest.py ├── doc ├── INSTALL.txt ├── README.pages ├── README.pdf ├── add-genome-fig-github.png ├── cactus-update-prepare.md ├── grch38-alt-pg-lrc_kir.png ├── grch38-alt-pg-mhc.png ├── mc-pangenomes │ ├── 10-chicken-pg-2022-09-23-commands.md │ ├── 10-chicken-pg-2022-09-23-seqfile.txt │ ├── 10-chicken-pg-2023-06-27-commands.md │ ├── 10-chicken-pg-2023-06-27-seqfile.txt │ ├── 10-t2t-apes-mc-2023v2.README.md │ ├── 10-t2t-apes-mc-2023v2.seqfile.txt │ ├── 16-fly-pg-2022-05-26-commands.md │ ├── 16-fly-pg-2022-05-26-seqfile.txt │ ├── 16-fly-pg-2023-08-25-commands.md │ ├── 16-fly-pg-2023-08-25-seqfile.txt │ ├── 17-soybean-pg-2022-09-26-commands.md │ ├── 17-soybean-pg-2022-09-26-seqfile.txt │ ├── 30-mouse-pg-2022-09-23-commands.md │ ├── 30-mouse-pg-2022-09-23-seqfile.txt │ ├── 4-t2t-orangs-mc-2023v2.README.md │ ├── 4-t2t-orangs-mc-2023v2.seqfile.txt │ ├── 5-cow-pg-2022-09-22-commands.md │ ├── 5-cow-pg-2022-09-22-seqfile.txt │ ├── 5-cow-pg-2023-03-31-commands.md │ ├── 5-cow-pg-2023-03-31-seqfile.txt │ ├── 9-dog-pg-2022-09-23-commands.md │ ├── 9-dog-pg-2022-09-23-seqfile.txt │ ├── 9-dog-pg-2023-06-27-commands.md │ ├── 9-dog-pg-2023-06-27-seqfile.txt │ ├── README.md │ ├── grch38-alts-pg-2023-04-13-commands.md │ ├── grch38-alts-pg-2023-04-13-seqfile.txt │ ├── hprc-v1.1-mc-input-contigs.bed │ ├── hprc-v1.1-mc.md │ └── hprc-v1.1-mc.seqfile ├── mc-paper │ ├── README.md │ ├── fly-sra.tsv │ ├── fly │ │ ├── Dockerfile │ │ ├── README.md │ │ ├── Snakefile │ │ ├── Snakefile_aws │ │ ├── annotate-repeats.R │ │ ├── cluster-svs.R │ │ ├── compare-freebayes-calls-hetrate.R │ │ ├── compare-freebayes-calls.R │ │ ├── mapstats-analysis.R │ │ ├── scripts │ │ │ ├── compute_mapping_stats.py │ │ │ ├── decompose_graph_variants.py │ │ │ ├── decompose_graph_variants_simple.py │ │ │ ├── drop_inconsistent_sites.py │ │ │ ├── freebayes_stats.R │ │ │ ├── read_svs.R │ │ │ ├── remove_duplicates.py │ │ │ └── rename_chr_vcf.py │ │ ├── snakemake_log.compare_freebayes_calls.log │ │ ├── snakemake_log.decompose_pangenome.log │ │ ├── snakemake_log.decompose_vg_calls.log │ │ ├── snakemake_log.mapping_stats_dm6_bwa.log │ │ ├── snakemake_log.mapping_stats_mc_giraffe.log │ │ ├── snakemake_log.merge_freebayes_dm6_bwa_calls.log │ │ ├── snakemake_log.merge_freebayes_mc_giraffe_calls.log │ │ └── svs-analysis.R │ └── hprc │ │ ├── GRCh38-f1g-90-mc-jun1.minigraph.split.log.gz │ │ ├── README.md │ │ ├── Snakefile_eval_chm13 │ │ ├── Snakefile_eval_grch38 │ │ ├── Snakefile_mapstats │ │ ├── calls-evaluation-exploration.R │ │ ├── chm13-f1g-90-mc-jun1.minigraph.split.log.gz │ │ ├── contig.inclusion.stats.R │ │ ├── eval-stratification-grch38-chm13.R │ │ ├── graphs-pangenie.R │ │ ├── mapstats-analysis.R │ │ ├── resources │ │ ├── compute_mapping_stats.py │ │ ├── compute_mapping_stats_gaf.py │ │ ├── compute_mapping_stats_jq.py │ │ ├── eval-roc-summary.R │ │ ├── eval-summary.R │ │ ├── get_stratification_on_sample.R │ │ ├── giab.truthset.paths.tsv │ │ ├── prepare_stratification_regions.R │ │ └── rename_chr_vcf.py │ │ ├── snakemake_config_chm13.yaml │ │ ├── snakemake_config_giab1-2-5.yaml │ │ ├── snakemake_config_hg002.yaml │ │ ├── snakemake_config_lifted.yaml │ │ ├── snakemake_config_lifted_cmrg.yaml │ │ ├── snarls-stats.R │ │ └── terra-files │ │ ├── CHM13.path_list.txt │ │ ├── GRCh38.path_list.txt │ │ ├── bwa-deepvariant-chm13.json │ │ ├── bwa_deepvariant.wdl │ │ ├── giraffe-deepvariant-chm13_pangenome-chm13_projection.json │ │ ├── giraffe-deepvariant-chm13_pangenome-grch38_projection.json │ │ └── giraffe-deepvariant-grch38_pangenome-grch38_projection.json ├── pangenome.md ├── progressive.md ├── running-in-aws.md ├── sa_refgraph_hackathon_2023.md ├── updating-alignments.md ├── yeast-pg-chrI.full.draw.png ├── yeast-pg-chrI.full.viz.png ├── yeast-pg-chrII.full.viz.png ├── yeast-pg-chunk-view.png └── yeast-pg-chunk-viz.png ├── examples ├── 10way-mhc.txt ├── evolverMammals.txt ├── evolverPrimates.txt ├── par1_cb.txt ├── par1_hcb.txt ├── par1_hcbg.txt └── yeastPangenome.txt ├── hal ├── Makefile ├── __init__.py ├── impl │ ├── fasta.c │ └── hal.c ├── inc │ └── hal.h └── tests │ └── allTests.c ├── include.mk ├── pipeline ├── Makefile ├── cactus_consolidated.c ├── docker_test_script.py ├── impl │ ├── convertAlignmentCoordinates.c │ └── traverseFlowers.c ├── inc │ ├── convertAlignmentCoordinates.h │ └── traverseFlowers.h └── tests │ └── allTests.c ├── preprocessor ├── Makefile ├── cactus_analyseAssembly.c ├── cactus_filterSmallFastaSequences.py ├── cactus_makeAlphaNumericHeaders.py ├── cactus_redPrefilter.c ├── cactus_sanitizeFastaHeaders.c ├── cactus_softmask2hardmask.c └── lastzRepeatMasking │ ├── Makefile │ ├── cactus_covered_intervals.c │ ├── cactus_fasta_fragments.py │ └── cactus_fasta_softmask_intervals.py ├── pytest.ini ├── reference ├── Makefile ├── __init__.py ├── impl │ ├── addReferenceCoordinates.c │ ├── blockMLString.c │ ├── buildReference.c │ ├── getReferenceSequences.c │ └── recursiveThreadBuilder.c ├── inc │ ├── addReferenceCoordinates.h │ ├── blockMLString.h │ ├── cactusReference.h │ └── recursiveThreadBuilder.h └── tests │ ├── addReferenceCoordinatesTest.c │ ├── allTests.c │ ├── buildReferenceTest.c │ └── recursiveThreadBuilderTest.c ├── runtime └── wrapper.sh ├── setup.py ├── setup ├── Makefile ├── __init__.py ├── impl │ └── setup.c └── inc │ └── cactus_setup.h ├── src ├── __init__.py └── cactus │ ├── __init__.py │ ├── attcc-alpha.knm │ ├── bar │ └── cactus_barTest.py │ ├── blast │ ├── __init__.py │ └── cactus_blast.py │ ├── cactus_progressive_config.xml │ ├── hal │ ├── __init__.py │ └── cactus_halTest.py │ ├── maf │ ├── __init__.py │ ├── cactus_hal2chains.py │ ├── cactus_hal2maf.py │ └── cactus_maf2bigmaf.py │ ├── paf │ ├── __init__.py │ ├── last_scoring.py │ ├── local_alignment.py │ ├── paf.py │ └── pafTest.py │ ├── pipeline │ ├── __init__.py │ ├── cactus_evolverTest.py │ ├── cactus_workflow.py │ └── cactus_workflowTest.py │ ├── preprocessor │ ├── __init__.py │ ├── cactus_preprocessor.py │ ├── cactus_preprocessorTest.py │ ├── checkUniqueHeaders.py │ ├── cutHeaders.py │ ├── dnabrnnMasking.py │ ├── fastanMasking.py │ ├── fileMasking.py │ ├── lastzRepeatMasking │ │ ├── __init__.py │ │ ├── cactus_lastzRepeatMask.py │ │ └── cactus_lastzRepeatMaskTest.py │ ├── preprocessorTest.py │ ├── redMasking.py │ └── unmasking.py │ ├── progressive │ ├── __init__.py │ ├── cactus_constructFromIntermediates.py │ ├── cactus_prepare.py │ ├── cactus_progressive.py │ ├── cactus_progressiveTest.py │ ├── cactus_terra_helper.py │ ├── multiCactusTree.py │ ├── multiCactusTreeTest.py │ ├── outgroup.py │ ├── outgroupTest.py │ ├── progressive_decomposition.py │ └── seqFile.py │ ├── reference │ ├── __init__.py │ └── cactus_referenceTest.py │ ├── refmap │ ├── __init__.py │ ├── apply_dipcall_bed_filter.py │ ├── cactus_graphmap.py │ ├── cactus_graphmap_join.py │ ├── cactus_graphmap_split.py │ ├── cactus_minigraph.py │ ├── cactus_pangenome.py │ ├── cactus_refmap.py │ ├── fasta_preprocessing.py │ └── paf_to_lastz.py │ ├── setup │ ├── __init__.py │ └── cactus_align.py │ ├── shared │ ├── __init__.py │ ├── common.py │ ├── commonTest.py │ ├── configWrapper.py │ └── test.py │ └── update │ ├── __init__.py │ └── cactus_update_prepare.py ├── test ├── evolverMammals-default.comp.xml ├── evolverPrimates-default.comp.xml └── evolverTest.py └── toil-requirement.txt /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/.gitignore -------------------------------------------------------------------------------- /.gitlab-ci.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/.gitlab-ci.yml -------------------------------------------------------------------------------- /.gitmodules: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/.gitmodules -------------------------------------------------------------------------------- /.travis_old.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/.travis_old.yml -------------------------------------------------------------------------------- /BIN-INSTALL.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/BIN-INSTALL.md -------------------------------------------------------------------------------- /DEVELOPMENT.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/DEVELOPMENT.md -------------------------------------------------------------------------------- /Dockerfile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/Dockerfile -------------------------------------------------------------------------------- /Dockerfile.ci-base: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/Dockerfile.ci-base -------------------------------------------------------------------------------- /Dockerfile.kegalign: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/Dockerfile.kegalign -------------------------------------------------------------------------------- /LICENSE.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/LICENSE.txt -------------------------------------------------------------------------------- /Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/Makefile -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/README.md -------------------------------------------------------------------------------- /ReleaseNotes.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/ReleaseNotes.md -------------------------------------------------------------------------------- /api/Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/api/Makefile -------------------------------------------------------------------------------- /api/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/api/__init__.py -------------------------------------------------------------------------------- /api/impl/cactusBlock.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/api/impl/cactusBlock.c -------------------------------------------------------------------------------- /api/impl/cactusBlockPrivate.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/api/impl/cactusBlockPrivate.h -------------------------------------------------------------------------------- /api/impl/cactusCap.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/api/impl/cactusCap.c -------------------------------------------------------------------------------- /api/impl/cactusCapPrivate.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/api/impl/cactusCapPrivate.h -------------------------------------------------------------------------------- /api/impl/cactusChain.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/api/impl/cactusChain.c -------------------------------------------------------------------------------- /api/impl/cactusChainPrivate.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/api/impl/cactusChainPrivate.h -------------------------------------------------------------------------------- /api/impl/cactusDisk.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/api/impl/cactusDisk.c -------------------------------------------------------------------------------- /api/impl/cactusDiskPrivate.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/api/impl/cactusDiskPrivate.h -------------------------------------------------------------------------------- /api/impl/cactusEnd.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/api/impl/cactusEnd.c -------------------------------------------------------------------------------- /api/impl/cactusEndPrivate.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/api/impl/cactusEndPrivate.h -------------------------------------------------------------------------------- /api/impl/cactusEvent.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/api/impl/cactusEvent.c -------------------------------------------------------------------------------- /api/impl/cactusEventPrivate.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/api/impl/cactusEventPrivate.h -------------------------------------------------------------------------------- /api/impl/cactusEventTree.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/api/impl/cactusEventTree.c -------------------------------------------------------------------------------- /api/impl/cactusEventTreePrivate.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/api/impl/cactusEventTreePrivate.h -------------------------------------------------------------------------------- /api/impl/cactusFlower.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/api/impl/cactusFlower.c -------------------------------------------------------------------------------- /api/impl/cactusFlowerPrivate.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/api/impl/cactusFlowerPrivate.h -------------------------------------------------------------------------------- /api/impl/cactusGlobalsPrivate.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/api/impl/cactusGlobalsPrivate.h -------------------------------------------------------------------------------- /api/impl/cactusGroup.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/api/impl/cactusGroup.c -------------------------------------------------------------------------------- /api/impl/cactusGroupPrivate.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/api/impl/cactusGroupPrivate.h -------------------------------------------------------------------------------- /api/impl/cactusLink.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/api/impl/cactusLink.c -------------------------------------------------------------------------------- /api/impl/cactusLinkPrivate.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/api/impl/cactusLinkPrivate.h -------------------------------------------------------------------------------- /api/impl/cactusMisc.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/api/impl/cactusMisc.c -------------------------------------------------------------------------------- /api/impl/cactusSegment.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/api/impl/cactusSegment.c -------------------------------------------------------------------------------- /api/impl/cactusSegmentPrivate.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/api/impl/cactusSegmentPrivate.h -------------------------------------------------------------------------------- /api/impl/cactusSequence.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/api/impl/cactusSequence.c -------------------------------------------------------------------------------- /api/impl/cactusSequencePrivate.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/api/impl/cactusSequencePrivate.h -------------------------------------------------------------------------------- /api/impl/cactusTestCommon.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/api/impl/cactusTestCommon.c -------------------------------------------------------------------------------- /api/impl/cactus_params_parser.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/api/impl/cactus_params_parser.c -------------------------------------------------------------------------------- /api/inc/cactus.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/api/inc/cactus.h -------------------------------------------------------------------------------- /api/inc/cactusBlock.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/api/inc/cactusBlock.h -------------------------------------------------------------------------------- /api/inc/cactusCap.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/api/inc/cactusCap.h -------------------------------------------------------------------------------- /api/inc/cactusChain.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/api/inc/cactusChain.h -------------------------------------------------------------------------------- /api/inc/cactusDisk.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/api/inc/cactusDisk.h -------------------------------------------------------------------------------- /api/inc/cactusEnd.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/api/inc/cactusEnd.h -------------------------------------------------------------------------------- /api/inc/cactusEvent.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/api/inc/cactusEvent.h -------------------------------------------------------------------------------- /api/inc/cactusEventTree.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/api/inc/cactusEventTree.h -------------------------------------------------------------------------------- /api/inc/cactusFlower.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/api/inc/cactusFlower.h -------------------------------------------------------------------------------- /api/inc/cactusGlobals.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/api/inc/cactusGlobals.h -------------------------------------------------------------------------------- /api/inc/cactusGroup.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/api/inc/cactusGroup.h -------------------------------------------------------------------------------- /api/inc/cactusLink.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/api/inc/cactusLink.h -------------------------------------------------------------------------------- /api/inc/cactusMisc.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/api/inc/cactusMisc.h -------------------------------------------------------------------------------- /api/inc/cactusSegment.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/api/inc/cactusSegment.h -------------------------------------------------------------------------------- /api/inc/cactusSequence.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/api/inc/cactusSequence.h -------------------------------------------------------------------------------- /api/inc/cactusTestCommon.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/api/inc/cactusTestCommon.h -------------------------------------------------------------------------------- /api/inc/cactus_params_parser.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/api/inc/cactus_params_parser.h -------------------------------------------------------------------------------- /api/tests/allTests.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/api/tests/allTests.c -------------------------------------------------------------------------------- /api/tests/cactusBlockTest.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/api/tests/cactusBlockTest.c -------------------------------------------------------------------------------- /api/tests/cactusBlocksTestShared.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/api/tests/cactusBlocksTestShared.h -------------------------------------------------------------------------------- /api/tests/cactusCapTest.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/api/tests/cactusCapTest.c -------------------------------------------------------------------------------- /api/tests/cactusChainTest.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/api/tests/cactusChainTest.c -------------------------------------------------------------------------------- /api/tests/cactusChainsTestShared.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/api/tests/cactusChainsTestShared.h -------------------------------------------------------------------------------- /api/tests/cactusDiskTest.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/api/tests/cactusDiskTest.c -------------------------------------------------------------------------------- /api/tests/cactusEndTest.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/api/tests/cactusEndTest.c -------------------------------------------------------------------------------- /api/tests/cactusEndsTestShared.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/api/tests/cactusEndsTestShared.h -------------------------------------------------------------------------------- /api/tests/cactusEventTest.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/api/tests/cactusEventTest.c -------------------------------------------------------------------------------- /api/tests/cactusEventTreeTest.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/api/tests/cactusEventTreeTest.c -------------------------------------------------------------------------------- /api/tests/cactusFlowerTest.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/api/tests/cactusFlowerTest.c -------------------------------------------------------------------------------- /api/tests/cactusGroupTest.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/api/tests/cactusGroupTest.c -------------------------------------------------------------------------------- /api/tests/cactusLinkTest.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/api/tests/cactusLinkTest.c -------------------------------------------------------------------------------- /api/tests/cactusMiscTest.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/api/tests/cactusMiscTest.c -------------------------------------------------------------------------------- /api/tests/cactusParamsTest.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/api/tests/cactusParamsTest.c -------------------------------------------------------------------------------- /api/tests/cactusSegmentTest.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/api/tests/cactusSegmentTest.c -------------------------------------------------------------------------------- /api/tests/cactusSequenceTest.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/api/tests/cactusSequenceTest.c -------------------------------------------------------------------------------- /bar/Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/bar/Makefile -------------------------------------------------------------------------------- /bar/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/bar/__init__.py -------------------------------------------------------------------------------- /bar/impl/adjacencySequences.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/bar/impl/adjacencySequences.c -------------------------------------------------------------------------------- /bar/impl/bar.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/bar/impl/bar.c -------------------------------------------------------------------------------- /bar/impl/endAligner.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/bar/impl/endAligner.c -------------------------------------------------------------------------------- /bar/impl/flowerAligner.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/bar/impl/flowerAligner.c -------------------------------------------------------------------------------- /bar/impl/poaBarAligner.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/bar/impl/poaBarAligner.c -------------------------------------------------------------------------------- /bar/impl/rescue.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/bar/impl/rescue.c -------------------------------------------------------------------------------- /bar/inc/adjacencySequences.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/bar/inc/adjacencySequences.h -------------------------------------------------------------------------------- /bar/inc/endAligner.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/bar/inc/endAligner.h -------------------------------------------------------------------------------- /bar/inc/flowerAligner.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/bar/inc/flowerAligner.h -------------------------------------------------------------------------------- /bar/inc/poaBarAligner.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/bar/inc/poaBarAligner.h -------------------------------------------------------------------------------- /bar/inc/rescue.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/bar/inc/rescue.h -------------------------------------------------------------------------------- /bar/tests/adjacencySequencesTest.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/bar/tests/adjacencySequencesTest.c -------------------------------------------------------------------------------- /bar/tests/allTests.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/bar/tests/allTests.c -------------------------------------------------------------------------------- /bar/tests/endAlignerTest.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/bar/tests/endAlignerTest.c -------------------------------------------------------------------------------- /bar/tests/flowerAlignerTest.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/bar/tests/flowerAlignerTest.c -------------------------------------------------------------------------------- /bar/tests/flowersShared.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/bar/tests/flowersShared.h -------------------------------------------------------------------------------- /bar/tests/poaBarTest.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/bar/tests/poaBarTest.c -------------------------------------------------------------------------------- /bar/tests/rescueTest.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/bar/tests/rescueTest.c -------------------------------------------------------------------------------- /caf/Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/caf/Makefile -------------------------------------------------------------------------------- /caf/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/caf/__init__.py -------------------------------------------------------------------------------- /caf/impl/addAdjacencies.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/caf/impl/addAdjacencies.c -------------------------------------------------------------------------------- /caf/impl/annealing.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/caf/impl/annealing.c -------------------------------------------------------------------------------- /caf/impl/cactus_setup.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/caf/impl/cactus_setup.c -------------------------------------------------------------------------------- /caf/impl/caf.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/caf/impl/caf.c -------------------------------------------------------------------------------- /caf/impl/filtering.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/caf/impl/filtering.c -------------------------------------------------------------------------------- /caf/impl/finishing.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/caf/impl/finishing.c -------------------------------------------------------------------------------- /caf/impl/giantComponent.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/caf/impl/giantComponent.c -------------------------------------------------------------------------------- /caf/impl/melting.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/caf/impl/melting.c -------------------------------------------------------------------------------- /caf/impl/phylogeny.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/caf/impl/phylogeny.c -------------------------------------------------------------------------------- /caf/impl/pinchIterator.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/caf/impl/pinchIterator.c -------------------------------------------------------------------------------- /caf/impl/pinchToCactus.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/caf/impl/pinchToCactus.c -------------------------------------------------------------------------------- /caf/inc/stCaf.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/caf/inc/stCaf.h -------------------------------------------------------------------------------- /caf/inc/stCafPhylogeny.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/caf/inc/stCafPhylogeny.h -------------------------------------------------------------------------------- /caf/inc/stGiantComponent.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/caf/inc/stGiantComponent.h -------------------------------------------------------------------------------- /caf/inc/stPinchIterator.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/caf/inc/stPinchIterator.h -------------------------------------------------------------------------------- /caf/tests/allTests.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/caf/tests/allTests.c -------------------------------------------------------------------------------- /caf/tests/annealingTest.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/caf/tests/annealingTest.c -------------------------------------------------------------------------------- /caf/tests/filteringTest.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/caf/tests/filteringTest.c -------------------------------------------------------------------------------- /caf/tests/giantComponentTest.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/caf/tests/giantComponentTest.c -------------------------------------------------------------------------------- /caf/tests/phylogenyTests.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/caf/tests/phylogenyTests.c -------------------------------------------------------------------------------- /caf/tests/pinchIteratorTest.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/caf/tests/pinchIteratorTest.c -------------------------------------------------------------------------------- /caf/tests/recoverableChainsTest.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/caf/tests/recoverableChainsTest.c -------------------------------------------------------------------------------- /conftest.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/conftest.py -------------------------------------------------------------------------------- /doc/INSTALL.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/doc/INSTALL.txt -------------------------------------------------------------------------------- /doc/README.pages: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/doc/README.pages -------------------------------------------------------------------------------- /doc/README.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/doc/README.pdf -------------------------------------------------------------------------------- /doc/add-genome-fig-github.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/doc/add-genome-fig-github.png -------------------------------------------------------------------------------- /doc/cactus-update-prepare.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/doc/cactus-update-prepare.md -------------------------------------------------------------------------------- /doc/grch38-alt-pg-lrc_kir.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/doc/grch38-alt-pg-lrc_kir.png -------------------------------------------------------------------------------- /doc/grch38-alt-pg-mhc.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/doc/grch38-alt-pg-mhc.png -------------------------------------------------------------------------------- /doc/mc-pangenomes/10-chicken-pg-2022-09-23-commands.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/doc/mc-pangenomes/10-chicken-pg-2022-09-23-commands.md -------------------------------------------------------------------------------- /doc/mc-pangenomes/10-chicken-pg-2022-09-23-seqfile.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/doc/mc-pangenomes/10-chicken-pg-2022-09-23-seqfile.txt -------------------------------------------------------------------------------- /doc/mc-pangenomes/10-chicken-pg-2023-06-27-commands.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/doc/mc-pangenomes/10-chicken-pg-2023-06-27-commands.md -------------------------------------------------------------------------------- /doc/mc-pangenomes/10-chicken-pg-2023-06-27-seqfile.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/doc/mc-pangenomes/10-chicken-pg-2023-06-27-seqfile.txt -------------------------------------------------------------------------------- /doc/mc-pangenomes/10-t2t-apes-mc-2023v2.README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/doc/mc-pangenomes/10-t2t-apes-mc-2023v2.README.md -------------------------------------------------------------------------------- /doc/mc-pangenomes/10-t2t-apes-mc-2023v2.seqfile.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/doc/mc-pangenomes/10-t2t-apes-mc-2023v2.seqfile.txt -------------------------------------------------------------------------------- /doc/mc-pangenomes/16-fly-pg-2022-05-26-commands.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/doc/mc-pangenomes/16-fly-pg-2022-05-26-commands.md -------------------------------------------------------------------------------- /doc/mc-pangenomes/16-fly-pg-2022-05-26-seqfile.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/doc/mc-pangenomes/16-fly-pg-2022-05-26-seqfile.txt -------------------------------------------------------------------------------- /doc/mc-pangenomes/16-fly-pg-2023-08-25-commands.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/doc/mc-pangenomes/16-fly-pg-2023-08-25-commands.md -------------------------------------------------------------------------------- /doc/mc-pangenomes/16-fly-pg-2023-08-25-seqfile.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/doc/mc-pangenomes/16-fly-pg-2023-08-25-seqfile.txt -------------------------------------------------------------------------------- /doc/mc-pangenomes/17-soybean-pg-2022-09-26-commands.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/doc/mc-pangenomes/17-soybean-pg-2022-09-26-commands.md -------------------------------------------------------------------------------- /doc/mc-pangenomes/17-soybean-pg-2022-09-26-seqfile.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/doc/mc-pangenomes/17-soybean-pg-2022-09-26-seqfile.txt -------------------------------------------------------------------------------- /doc/mc-pangenomes/30-mouse-pg-2022-09-23-commands.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/doc/mc-pangenomes/30-mouse-pg-2022-09-23-commands.md -------------------------------------------------------------------------------- /doc/mc-pangenomes/30-mouse-pg-2022-09-23-seqfile.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/doc/mc-pangenomes/30-mouse-pg-2022-09-23-seqfile.txt -------------------------------------------------------------------------------- /doc/mc-pangenomes/4-t2t-orangs-mc-2023v2.README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/doc/mc-pangenomes/4-t2t-orangs-mc-2023v2.README.md -------------------------------------------------------------------------------- /doc/mc-pangenomes/4-t2t-orangs-mc-2023v2.seqfile.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/doc/mc-pangenomes/4-t2t-orangs-mc-2023v2.seqfile.txt -------------------------------------------------------------------------------- /doc/mc-pangenomes/5-cow-pg-2022-09-22-commands.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/doc/mc-pangenomes/5-cow-pg-2022-09-22-commands.md -------------------------------------------------------------------------------- /doc/mc-pangenomes/5-cow-pg-2022-09-22-seqfile.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/doc/mc-pangenomes/5-cow-pg-2022-09-22-seqfile.txt -------------------------------------------------------------------------------- /doc/mc-pangenomes/5-cow-pg-2023-03-31-commands.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/doc/mc-pangenomes/5-cow-pg-2023-03-31-commands.md -------------------------------------------------------------------------------- /doc/mc-pangenomes/5-cow-pg-2023-03-31-seqfile.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/doc/mc-pangenomes/5-cow-pg-2023-03-31-seqfile.txt -------------------------------------------------------------------------------- /doc/mc-pangenomes/9-dog-pg-2022-09-23-commands.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/doc/mc-pangenomes/9-dog-pg-2022-09-23-commands.md -------------------------------------------------------------------------------- /doc/mc-pangenomes/9-dog-pg-2022-09-23-seqfile.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/doc/mc-pangenomes/9-dog-pg-2022-09-23-seqfile.txt -------------------------------------------------------------------------------- /doc/mc-pangenomes/9-dog-pg-2023-06-27-commands.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/doc/mc-pangenomes/9-dog-pg-2023-06-27-commands.md -------------------------------------------------------------------------------- /doc/mc-pangenomes/9-dog-pg-2023-06-27-seqfile.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/doc/mc-pangenomes/9-dog-pg-2023-06-27-seqfile.txt -------------------------------------------------------------------------------- /doc/mc-pangenomes/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/doc/mc-pangenomes/README.md -------------------------------------------------------------------------------- /doc/mc-pangenomes/grch38-alts-pg-2023-04-13-commands.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/doc/mc-pangenomes/grch38-alts-pg-2023-04-13-commands.md -------------------------------------------------------------------------------- /doc/mc-pangenomes/grch38-alts-pg-2023-04-13-seqfile.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/doc/mc-pangenomes/grch38-alts-pg-2023-04-13-seqfile.txt -------------------------------------------------------------------------------- /doc/mc-pangenomes/hprc-v1.1-mc-input-contigs.bed: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/doc/mc-pangenomes/hprc-v1.1-mc-input-contigs.bed -------------------------------------------------------------------------------- /doc/mc-pangenomes/hprc-v1.1-mc.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/doc/mc-pangenomes/hprc-v1.1-mc.md -------------------------------------------------------------------------------- /doc/mc-pangenomes/hprc-v1.1-mc.seqfile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/doc/mc-pangenomes/hprc-v1.1-mc.seqfile -------------------------------------------------------------------------------- /doc/mc-paper/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/doc/mc-paper/README.md -------------------------------------------------------------------------------- /doc/mc-paper/fly-sra.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/doc/mc-paper/fly-sra.tsv -------------------------------------------------------------------------------- /doc/mc-paper/fly/Dockerfile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/doc/mc-paper/fly/Dockerfile -------------------------------------------------------------------------------- /doc/mc-paper/fly/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/doc/mc-paper/fly/README.md -------------------------------------------------------------------------------- /doc/mc-paper/fly/Snakefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/doc/mc-paper/fly/Snakefile -------------------------------------------------------------------------------- /doc/mc-paper/fly/Snakefile_aws: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/doc/mc-paper/fly/Snakefile_aws -------------------------------------------------------------------------------- /doc/mc-paper/fly/annotate-repeats.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/doc/mc-paper/fly/annotate-repeats.R -------------------------------------------------------------------------------- /doc/mc-paper/fly/cluster-svs.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/doc/mc-paper/fly/cluster-svs.R -------------------------------------------------------------------------------- /doc/mc-paper/fly/compare-freebayes-calls-hetrate.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/doc/mc-paper/fly/compare-freebayes-calls-hetrate.R -------------------------------------------------------------------------------- /doc/mc-paper/fly/compare-freebayes-calls.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/doc/mc-paper/fly/compare-freebayes-calls.R -------------------------------------------------------------------------------- /doc/mc-paper/fly/mapstats-analysis.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/doc/mc-paper/fly/mapstats-analysis.R -------------------------------------------------------------------------------- /doc/mc-paper/fly/scripts/compute_mapping_stats.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/doc/mc-paper/fly/scripts/compute_mapping_stats.py -------------------------------------------------------------------------------- /doc/mc-paper/fly/scripts/decompose_graph_variants.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/doc/mc-paper/fly/scripts/decompose_graph_variants.py -------------------------------------------------------------------------------- /doc/mc-paper/fly/scripts/decompose_graph_variants_simple.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/doc/mc-paper/fly/scripts/decompose_graph_variants_simple.py -------------------------------------------------------------------------------- /doc/mc-paper/fly/scripts/drop_inconsistent_sites.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/doc/mc-paper/fly/scripts/drop_inconsistent_sites.py -------------------------------------------------------------------------------- /doc/mc-paper/fly/scripts/freebayes_stats.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/doc/mc-paper/fly/scripts/freebayes_stats.R -------------------------------------------------------------------------------- /doc/mc-paper/fly/scripts/read_svs.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/doc/mc-paper/fly/scripts/read_svs.R -------------------------------------------------------------------------------- /doc/mc-paper/fly/scripts/remove_duplicates.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/doc/mc-paper/fly/scripts/remove_duplicates.py -------------------------------------------------------------------------------- /doc/mc-paper/fly/scripts/rename_chr_vcf.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/doc/mc-paper/fly/scripts/rename_chr_vcf.py -------------------------------------------------------------------------------- /doc/mc-paper/fly/snakemake_log.compare_freebayes_calls.log: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/doc/mc-paper/fly/snakemake_log.compare_freebayes_calls.log -------------------------------------------------------------------------------- /doc/mc-paper/fly/snakemake_log.decompose_pangenome.log: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/doc/mc-paper/fly/snakemake_log.decompose_pangenome.log -------------------------------------------------------------------------------- /doc/mc-paper/fly/snakemake_log.decompose_vg_calls.log: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/doc/mc-paper/fly/snakemake_log.decompose_vg_calls.log -------------------------------------------------------------------------------- /doc/mc-paper/fly/snakemake_log.mapping_stats_dm6_bwa.log: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/doc/mc-paper/fly/snakemake_log.mapping_stats_dm6_bwa.log -------------------------------------------------------------------------------- /doc/mc-paper/fly/snakemake_log.mapping_stats_mc_giraffe.log: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/doc/mc-paper/fly/snakemake_log.mapping_stats_mc_giraffe.log -------------------------------------------------------------------------------- /doc/mc-paper/fly/snakemake_log.merge_freebayes_dm6_bwa_calls.log: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/doc/mc-paper/fly/snakemake_log.merge_freebayes_dm6_bwa_calls.log -------------------------------------------------------------------------------- /doc/mc-paper/fly/snakemake_log.merge_freebayes_mc_giraffe_calls.log: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/doc/mc-paper/fly/snakemake_log.merge_freebayes_mc_giraffe_calls.log -------------------------------------------------------------------------------- /doc/mc-paper/fly/svs-analysis.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/doc/mc-paper/fly/svs-analysis.R -------------------------------------------------------------------------------- /doc/mc-paper/hprc/GRCh38-f1g-90-mc-jun1.minigraph.split.log.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/doc/mc-paper/hprc/GRCh38-f1g-90-mc-jun1.minigraph.split.log.gz -------------------------------------------------------------------------------- /doc/mc-paper/hprc/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/doc/mc-paper/hprc/README.md -------------------------------------------------------------------------------- /doc/mc-paper/hprc/Snakefile_eval_chm13: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/doc/mc-paper/hprc/Snakefile_eval_chm13 -------------------------------------------------------------------------------- /doc/mc-paper/hprc/Snakefile_eval_grch38: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/doc/mc-paper/hprc/Snakefile_eval_grch38 -------------------------------------------------------------------------------- /doc/mc-paper/hprc/Snakefile_mapstats: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/doc/mc-paper/hprc/Snakefile_mapstats -------------------------------------------------------------------------------- /doc/mc-paper/hprc/calls-evaluation-exploration.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/doc/mc-paper/hprc/calls-evaluation-exploration.R -------------------------------------------------------------------------------- /doc/mc-paper/hprc/chm13-f1g-90-mc-jun1.minigraph.split.log.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/doc/mc-paper/hprc/chm13-f1g-90-mc-jun1.minigraph.split.log.gz -------------------------------------------------------------------------------- /doc/mc-paper/hprc/contig.inclusion.stats.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/doc/mc-paper/hprc/contig.inclusion.stats.R -------------------------------------------------------------------------------- /doc/mc-paper/hprc/eval-stratification-grch38-chm13.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/doc/mc-paper/hprc/eval-stratification-grch38-chm13.R -------------------------------------------------------------------------------- /doc/mc-paper/hprc/graphs-pangenie.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/doc/mc-paper/hprc/graphs-pangenie.R -------------------------------------------------------------------------------- /doc/mc-paper/hprc/mapstats-analysis.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/doc/mc-paper/hprc/mapstats-analysis.R -------------------------------------------------------------------------------- /doc/mc-paper/hprc/resources/compute_mapping_stats.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/doc/mc-paper/hprc/resources/compute_mapping_stats.py -------------------------------------------------------------------------------- /doc/mc-paper/hprc/resources/compute_mapping_stats_gaf.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/doc/mc-paper/hprc/resources/compute_mapping_stats_gaf.py -------------------------------------------------------------------------------- /doc/mc-paper/hprc/resources/compute_mapping_stats_jq.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/doc/mc-paper/hprc/resources/compute_mapping_stats_jq.py -------------------------------------------------------------------------------- /doc/mc-paper/hprc/resources/eval-roc-summary.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/doc/mc-paper/hprc/resources/eval-roc-summary.R -------------------------------------------------------------------------------- /doc/mc-paper/hprc/resources/eval-summary.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/doc/mc-paper/hprc/resources/eval-summary.R -------------------------------------------------------------------------------- /doc/mc-paper/hprc/resources/get_stratification_on_sample.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/doc/mc-paper/hprc/resources/get_stratification_on_sample.R -------------------------------------------------------------------------------- /doc/mc-paper/hprc/resources/giab.truthset.paths.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/doc/mc-paper/hprc/resources/giab.truthset.paths.tsv -------------------------------------------------------------------------------- /doc/mc-paper/hprc/resources/prepare_stratification_regions.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/doc/mc-paper/hprc/resources/prepare_stratification_regions.R -------------------------------------------------------------------------------- /doc/mc-paper/hprc/resources/rename_chr_vcf.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/doc/mc-paper/hprc/resources/rename_chr_vcf.py -------------------------------------------------------------------------------- /doc/mc-paper/hprc/snakemake_config_chm13.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/doc/mc-paper/hprc/snakemake_config_chm13.yaml -------------------------------------------------------------------------------- /doc/mc-paper/hprc/snakemake_config_giab1-2-5.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/doc/mc-paper/hprc/snakemake_config_giab1-2-5.yaml -------------------------------------------------------------------------------- /doc/mc-paper/hprc/snakemake_config_hg002.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/doc/mc-paper/hprc/snakemake_config_hg002.yaml -------------------------------------------------------------------------------- /doc/mc-paper/hprc/snakemake_config_lifted.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/doc/mc-paper/hprc/snakemake_config_lifted.yaml -------------------------------------------------------------------------------- /doc/mc-paper/hprc/snakemake_config_lifted_cmrg.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/doc/mc-paper/hprc/snakemake_config_lifted_cmrg.yaml -------------------------------------------------------------------------------- /doc/mc-paper/hprc/snarls-stats.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/doc/mc-paper/hprc/snarls-stats.R -------------------------------------------------------------------------------- /doc/mc-paper/hprc/terra-files/CHM13.path_list.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/doc/mc-paper/hprc/terra-files/CHM13.path_list.txt -------------------------------------------------------------------------------- /doc/mc-paper/hprc/terra-files/GRCh38.path_list.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/doc/mc-paper/hprc/terra-files/GRCh38.path_list.txt -------------------------------------------------------------------------------- /doc/mc-paper/hprc/terra-files/bwa-deepvariant-chm13.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/doc/mc-paper/hprc/terra-files/bwa-deepvariant-chm13.json -------------------------------------------------------------------------------- /doc/mc-paper/hprc/terra-files/bwa_deepvariant.wdl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/doc/mc-paper/hprc/terra-files/bwa_deepvariant.wdl -------------------------------------------------------------------------------- /doc/mc-paper/hprc/terra-files/giraffe-deepvariant-chm13_pangenome-chm13_projection.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/doc/mc-paper/hprc/terra-files/giraffe-deepvariant-chm13_pangenome-chm13_projection.json -------------------------------------------------------------------------------- /doc/mc-paper/hprc/terra-files/giraffe-deepvariant-chm13_pangenome-grch38_projection.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/doc/mc-paper/hprc/terra-files/giraffe-deepvariant-chm13_pangenome-grch38_projection.json -------------------------------------------------------------------------------- /doc/mc-paper/hprc/terra-files/giraffe-deepvariant-grch38_pangenome-grch38_projection.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/doc/mc-paper/hprc/terra-files/giraffe-deepvariant-grch38_pangenome-grch38_projection.json -------------------------------------------------------------------------------- /doc/pangenome.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/doc/pangenome.md -------------------------------------------------------------------------------- /doc/progressive.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/doc/progressive.md -------------------------------------------------------------------------------- /doc/running-in-aws.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/doc/running-in-aws.md -------------------------------------------------------------------------------- /doc/sa_refgraph_hackathon_2023.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/doc/sa_refgraph_hackathon_2023.md -------------------------------------------------------------------------------- /doc/updating-alignments.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/doc/updating-alignments.md -------------------------------------------------------------------------------- /doc/yeast-pg-chrI.full.draw.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/doc/yeast-pg-chrI.full.draw.png -------------------------------------------------------------------------------- /doc/yeast-pg-chrI.full.viz.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/doc/yeast-pg-chrI.full.viz.png -------------------------------------------------------------------------------- /doc/yeast-pg-chrII.full.viz.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/doc/yeast-pg-chrII.full.viz.png -------------------------------------------------------------------------------- /doc/yeast-pg-chunk-view.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/doc/yeast-pg-chunk-view.png -------------------------------------------------------------------------------- /doc/yeast-pg-chunk-viz.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/doc/yeast-pg-chunk-viz.png -------------------------------------------------------------------------------- /examples/10way-mhc.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/examples/10way-mhc.txt -------------------------------------------------------------------------------- /examples/evolverMammals.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/examples/evolverMammals.txt -------------------------------------------------------------------------------- /examples/evolverPrimates.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/examples/evolverPrimates.txt -------------------------------------------------------------------------------- /examples/par1_cb.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/examples/par1_cb.txt -------------------------------------------------------------------------------- /examples/par1_hcb.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/examples/par1_hcb.txt -------------------------------------------------------------------------------- /examples/par1_hcbg.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/examples/par1_hcbg.txt -------------------------------------------------------------------------------- /examples/yeastPangenome.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/examples/yeastPangenome.txt -------------------------------------------------------------------------------- /hal/Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/hal/Makefile -------------------------------------------------------------------------------- /hal/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /hal/impl/fasta.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/hal/impl/fasta.c -------------------------------------------------------------------------------- /hal/impl/hal.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/hal/impl/hal.c -------------------------------------------------------------------------------- /hal/inc/hal.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/hal/inc/hal.h -------------------------------------------------------------------------------- /hal/tests/allTests.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/hal/tests/allTests.c -------------------------------------------------------------------------------- /include.mk: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/include.mk -------------------------------------------------------------------------------- /pipeline/Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/pipeline/Makefile -------------------------------------------------------------------------------- /pipeline/cactus_consolidated.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/pipeline/cactus_consolidated.c -------------------------------------------------------------------------------- /pipeline/docker_test_script.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/pipeline/docker_test_script.py -------------------------------------------------------------------------------- /pipeline/impl/convertAlignmentCoordinates.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/pipeline/impl/convertAlignmentCoordinates.c -------------------------------------------------------------------------------- /pipeline/impl/traverseFlowers.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/pipeline/impl/traverseFlowers.c -------------------------------------------------------------------------------- /pipeline/inc/convertAlignmentCoordinates.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/pipeline/inc/convertAlignmentCoordinates.h -------------------------------------------------------------------------------- /pipeline/inc/traverseFlowers.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/pipeline/inc/traverseFlowers.h -------------------------------------------------------------------------------- /pipeline/tests/allTests.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/pipeline/tests/allTests.c -------------------------------------------------------------------------------- /preprocessor/Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/preprocessor/Makefile -------------------------------------------------------------------------------- /preprocessor/cactus_analyseAssembly.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/preprocessor/cactus_analyseAssembly.c -------------------------------------------------------------------------------- /preprocessor/cactus_filterSmallFastaSequences.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/preprocessor/cactus_filterSmallFastaSequences.py -------------------------------------------------------------------------------- /preprocessor/cactus_makeAlphaNumericHeaders.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/preprocessor/cactus_makeAlphaNumericHeaders.py -------------------------------------------------------------------------------- /preprocessor/cactus_redPrefilter.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/preprocessor/cactus_redPrefilter.c -------------------------------------------------------------------------------- /preprocessor/cactus_sanitizeFastaHeaders.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/preprocessor/cactus_sanitizeFastaHeaders.c -------------------------------------------------------------------------------- /preprocessor/cactus_softmask2hardmask.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/preprocessor/cactus_softmask2hardmask.c -------------------------------------------------------------------------------- /preprocessor/lastzRepeatMasking/Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/preprocessor/lastzRepeatMasking/Makefile -------------------------------------------------------------------------------- /preprocessor/lastzRepeatMasking/cactus_covered_intervals.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/preprocessor/lastzRepeatMasking/cactus_covered_intervals.c -------------------------------------------------------------------------------- /preprocessor/lastzRepeatMasking/cactus_fasta_fragments.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/preprocessor/lastzRepeatMasking/cactus_fasta_fragments.py -------------------------------------------------------------------------------- /preprocessor/lastzRepeatMasking/cactus_fasta_softmask_intervals.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/preprocessor/lastzRepeatMasking/cactus_fasta_softmask_intervals.py -------------------------------------------------------------------------------- /pytest.ini: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/pytest.ini -------------------------------------------------------------------------------- /reference/Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/reference/Makefile -------------------------------------------------------------------------------- /reference/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/reference/__init__.py -------------------------------------------------------------------------------- /reference/impl/addReferenceCoordinates.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/reference/impl/addReferenceCoordinates.c -------------------------------------------------------------------------------- /reference/impl/blockMLString.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/reference/impl/blockMLString.c -------------------------------------------------------------------------------- /reference/impl/buildReference.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/reference/impl/buildReference.c -------------------------------------------------------------------------------- /reference/impl/getReferenceSequences.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/reference/impl/getReferenceSequences.c -------------------------------------------------------------------------------- /reference/impl/recursiveThreadBuilder.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/reference/impl/recursiveThreadBuilder.c -------------------------------------------------------------------------------- /reference/inc/addReferenceCoordinates.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/reference/inc/addReferenceCoordinates.h -------------------------------------------------------------------------------- /reference/inc/blockMLString.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/reference/inc/blockMLString.h -------------------------------------------------------------------------------- /reference/inc/cactusReference.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/reference/inc/cactusReference.h -------------------------------------------------------------------------------- /reference/inc/recursiveThreadBuilder.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/reference/inc/recursiveThreadBuilder.h -------------------------------------------------------------------------------- /reference/tests/addReferenceCoordinatesTest.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/reference/tests/addReferenceCoordinatesTest.c -------------------------------------------------------------------------------- /reference/tests/allTests.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/reference/tests/allTests.c -------------------------------------------------------------------------------- /reference/tests/buildReferenceTest.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/reference/tests/buildReferenceTest.c -------------------------------------------------------------------------------- /reference/tests/recursiveThreadBuilderTest.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/reference/tests/recursiveThreadBuilderTest.c -------------------------------------------------------------------------------- /runtime/wrapper.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/runtime/wrapper.sh -------------------------------------------------------------------------------- /setup.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/setup.py -------------------------------------------------------------------------------- /setup/Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/setup/Makefile -------------------------------------------------------------------------------- /setup/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/setup/__init__.py -------------------------------------------------------------------------------- /setup/impl/setup.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/setup/impl/setup.c -------------------------------------------------------------------------------- /setup/inc/cactus_setup.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/setup/inc/cactus_setup.h -------------------------------------------------------------------------------- /src/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /src/cactus/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /src/cactus/attcc-alpha.knm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/src/cactus/attcc-alpha.knm -------------------------------------------------------------------------------- /src/cactus/bar/cactus_barTest.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/src/cactus/bar/cactus_barTest.py -------------------------------------------------------------------------------- /src/cactus/blast/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/src/cactus/blast/__init__.py -------------------------------------------------------------------------------- /src/cactus/blast/cactus_blast.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/src/cactus/blast/cactus_blast.py -------------------------------------------------------------------------------- /src/cactus/cactus_progressive_config.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/src/cactus/cactus_progressive_config.xml -------------------------------------------------------------------------------- /src/cactus/hal/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /src/cactus/hal/cactus_halTest.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/src/cactus/hal/cactus_halTest.py -------------------------------------------------------------------------------- /src/cactus/maf/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /src/cactus/maf/cactus_hal2chains.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/src/cactus/maf/cactus_hal2chains.py -------------------------------------------------------------------------------- /src/cactus/maf/cactus_hal2maf.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/src/cactus/maf/cactus_hal2maf.py -------------------------------------------------------------------------------- /src/cactus/maf/cactus_maf2bigmaf.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/src/cactus/maf/cactus_maf2bigmaf.py -------------------------------------------------------------------------------- /src/cactus/paf/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /src/cactus/paf/last_scoring.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/src/cactus/paf/last_scoring.py -------------------------------------------------------------------------------- /src/cactus/paf/local_alignment.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/src/cactus/paf/local_alignment.py -------------------------------------------------------------------------------- /src/cactus/paf/paf.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/src/cactus/paf/paf.py -------------------------------------------------------------------------------- /src/cactus/paf/pafTest.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/src/cactus/paf/pafTest.py -------------------------------------------------------------------------------- /src/cactus/pipeline/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /src/cactus/pipeline/cactus_evolverTest.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/src/cactus/pipeline/cactus_evolverTest.py -------------------------------------------------------------------------------- /src/cactus/pipeline/cactus_workflow.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/src/cactus/pipeline/cactus_workflow.py -------------------------------------------------------------------------------- /src/cactus/pipeline/cactus_workflowTest.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/src/cactus/pipeline/cactus_workflowTest.py -------------------------------------------------------------------------------- /src/cactus/preprocessor/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/src/cactus/preprocessor/__init__.py -------------------------------------------------------------------------------- /src/cactus/preprocessor/cactus_preprocessor.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/src/cactus/preprocessor/cactus_preprocessor.py -------------------------------------------------------------------------------- /src/cactus/preprocessor/cactus_preprocessorTest.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/src/cactus/preprocessor/cactus_preprocessorTest.py -------------------------------------------------------------------------------- /src/cactus/preprocessor/checkUniqueHeaders.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/src/cactus/preprocessor/checkUniqueHeaders.py -------------------------------------------------------------------------------- /src/cactus/preprocessor/cutHeaders.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/src/cactus/preprocessor/cutHeaders.py -------------------------------------------------------------------------------- /src/cactus/preprocessor/dnabrnnMasking.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/src/cactus/preprocessor/dnabrnnMasking.py -------------------------------------------------------------------------------- /src/cactus/preprocessor/fastanMasking.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/src/cactus/preprocessor/fastanMasking.py -------------------------------------------------------------------------------- /src/cactus/preprocessor/fileMasking.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/src/cactus/preprocessor/fileMasking.py -------------------------------------------------------------------------------- /src/cactus/preprocessor/lastzRepeatMasking/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/src/cactus/preprocessor/lastzRepeatMasking/__init__.py -------------------------------------------------------------------------------- /src/cactus/preprocessor/lastzRepeatMasking/cactus_lastzRepeatMask.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/src/cactus/preprocessor/lastzRepeatMasking/cactus_lastzRepeatMask.py -------------------------------------------------------------------------------- /src/cactus/preprocessor/lastzRepeatMasking/cactus_lastzRepeatMaskTest.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/src/cactus/preprocessor/lastzRepeatMasking/cactus_lastzRepeatMaskTest.py -------------------------------------------------------------------------------- /src/cactus/preprocessor/preprocessorTest.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/src/cactus/preprocessor/preprocessorTest.py -------------------------------------------------------------------------------- /src/cactus/preprocessor/redMasking.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/src/cactus/preprocessor/redMasking.py -------------------------------------------------------------------------------- /src/cactus/preprocessor/unmasking.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/src/cactus/preprocessor/unmasking.py -------------------------------------------------------------------------------- /src/cactus/progressive/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/src/cactus/progressive/__init__.py -------------------------------------------------------------------------------- /src/cactus/progressive/cactus_constructFromIntermediates.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/src/cactus/progressive/cactus_constructFromIntermediates.py -------------------------------------------------------------------------------- /src/cactus/progressive/cactus_prepare.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/src/cactus/progressive/cactus_prepare.py -------------------------------------------------------------------------------- /src/cactus/progressive/cactus_progressive.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/src/cactus/progressive/cactus_progressive.py -------------------------------------------------------------------------------- /src/cactus/progressive/cactus_progressiveTest.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/src/cactus/progressive/cactus_progressiveTest.py -------------------------------------------------------------------------------- /src/cactus/progressive/cactus_terra_helper.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/src/cactus/progressive/cactus_terra_helper.py -------------------------------------------------------------------------------- /src/cactus/progressive/multiCactusTree.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/src/cactus/progressive/multiCactusTree.py -------------------------------------------------------------------------------- /src/cactus/progressive/multiCactusTreeTest.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/src/cactus/progressive/multiCactusTreeTest.py -------------------------------------------------------------------------------- /src/cactus/progressive/outgroup.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/src/cactus/progressive/outgroup.py -------------------------------------------------------------------------------- /src/cactus/progressive/outgroupTest.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/src/cactus/progressive/outgroupTest.py -------------------------------------------------------------------------------- /src/cactus/progressive/progressive_decomposition.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/src/cactus/progressive/progressive_decomposition.py -------------------------------------------------------------------------------- /src/cactus/progressive/seqFile.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/src/cactus/progressive/seqFile.py -------------------------------------------------------------------------------- /src/cactus/reference/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /src/cactus/reference/cactus_referenceTest.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/src/cactus/reference/cactus_referenceTest.py -------------------------------------------------------------------------------- /src/cactus/refmap/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/src/cactus/refmap/__init__.py -------------------------------------------------------------------------------- /src/cactus/refmap/apply_dipcall_bed_filter.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/src/cactus/refmap/apply_dipcall_bed_filter.py -------------------------------------------------------------------------------- /src/cactus/refmap/cactus_graphmap.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/src/cactus/refmap/cactus_graphmap.py -------------------------------------------------------------------------------- /src/cactus/refmap/cactus_graphmap_join.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/src/cactus/refmap/cactus_graphmap_join.py -------------------------------------------------------------------------------- /src/cactus/refmap/cactus_graphmap_split.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/src/cactus/refmap/cactus_graphmap_split.py -------------------------------------------------------------------------------- /src/cactus/refmap/cactus_minigraph.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/src/cactus/refmap/cactus_minigraph.py -------------------------------------------------------------------------------- /src/cactus/refmap/cactus_pangenome.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/src/cactus/refmap/cactus_pangenome.py -------------------------------------------------------------------------------- /src/cactus/refmap/cactus_refmap.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/src/cactus/refmap/cactus_refmap.py -------------------------------------------------------------------------------- /src/cactus/refmap/fasta_preprocessing.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/src/cactus/refmap/fasta_preprocessing.py -------------------------------------------------------------------------------- /src/cactus/refmap/paf_to_lastz.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/src/cactus/refmap/paf_to_lastz.py -------------------------------------------------------------------------------- /src/cactus/setup/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /src/cactus/setup/cactus_align.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/src/cactus/setup/cactus_align.py -------------------------------------------------------------------------------- /src/cactus/shared/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/src/cactus/shared/__init__.py -------------------------------------------------------------------------------- /src/cactus/shared/common.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/src/cactus/shared/common.py -------------------------------------------------------------------------------- /src/cactus/shared/commonTest.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/src/cactus/shared/commonTest.py -------------------------------------------------------------------------------- /src/cactus/shared/configWrapper.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/src/cactus/shared/configWrapper.py -------------------------------------------------------------------------------- /src/cactus/shared/test.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/src/cactus/shared/test.py -------------------------------------------------------------------------------- /src/cactus/update/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /src/cactus/update/cactus_update_prepare.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/src/cactus/update/cactus_update_prepare.py -------------------------------------------------------------------------------- /test/evolverMammals-default.comp.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/test/evolverMammals-default.comp.xml -------------------------------------------------------------------------------- /test/evolverPrimates-default.comp.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/test/evolverPrimates-default.comp.xml -------------------------------------------------------------------------------- /test/evolverTest.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/HEAD/test/evolverTest.py -------------------------------------------------------------------------------- /toil-requirement.txt: -------------------------------------------------------------------------------- 1 | backports.zoneinfo[tzdata];python_version<"3.9" 2 | toil[aws]==9.1.2 3 | --------------------------------------------------------------------------------