├── .gitignore ├── .travis.yml ├── LICENSE ├── README.md ├── doc ├── Makefile ├── _static │ └── images │ │ ├── age-logo.jpg │ │ ├── age-vusage.png │ │ ├── framework.png │ │ ├── hsct-logo.jpg │ │ ├── hsct-stackplot.png │ │ ├── modules │ │ ├── annotate-aaprofile.png │ │ ├── basic-fancyspectra.png │ │ ├── basic-fancyvj.png │ │ ├── basic-segmentusage.png │ │ ├── basic-spectrav.png │ │ ├── diversity-qstat.png │ │ ├── diversity-rarefaction.png │ │ ├── intersect-batch-circos.png │ │ ├── intersect-batch-dendro.png │ │ ├── intersect-batch-mds.png │ │ ├── intersect-batch-perms.png │ │ ├── intersect-pair-scatter.png │ │ ├── intersect-pair-stack.png │ │ ├── intersect-seq-heatplot.png │ │ ├── intersect-seq-stackplot.png │ │ ├── intersect-seq-summary.png │ │ ├── join-venn.png │ │ └── test-clusters.png │ │ ├── ms-logo.jpg │ │ ├── ms-rarefaction.png │ │ ├── vdjviz.png │ │ └── vdjviz1.png ├── annotate.rst ├── basic.rst ├── browser.rst ├── conf.py ├── diversity.rst ├── examples.rst ├── index.rst ├── input.rst ├── install.rst ├── intro.rst ├── modules.rst ├── operate.rst ├── overlap.rst ├── preprocess.rst ├── usage.rst ├── util.rst └── vdjviz.rst ├── gradle └── wrapper │ ├── gradle-wrapper.jar │ └── gradle-wrapper.properties ├── gradlew ├── gradlew.bat ├── jitpack.yaml ├── src ├── main │ ├── groovy │ │ └── com │ │ │ └── antigenomics │ │ │ └── vdjtools │ │ │ ├── VdjTools.groovy │ │ │ ├── VdjUtil.groovy │ │ │ ├── annotate │ │ │ ├── AaPropertyAnnotator.groovy │ │ │ ├── Annotate.groovy │ │ │ ├── BaseAnnotator.groovy │ │ │ ├── CalcCdrAaStats.groovy │ │ │ ├── CalcDegreeStats.groovy │ │ │ ├── ClonotypeAnnotator.groovy │ │ │ ├── DegreeStatisticsAnnotator.groovy │ │ │ ├── KnownAminoAcidProperties.groovy │ │ │ ├── KnownAnnotators.groovy │ │ │ ├── KnownCdr3Regions.groovy │ │ │ ├── SampleAnnotator.groovy │ │ │ └── SegmentsToFamilies.groovy │ │ │ ├── basic │ │ │ ├── BasicStats.groovy │ │ │ ├── CalcBasicStats.groovy │ │ │ ├── CalcSegmentUsage.groovy │ │ │ ├── CalcSpectratype.groovy │ │ │ ├── FancySpectratype.groovy │ │ │ ├── Histogram.groovy │ │ │ ├── InsertHist.groovy │ │ │ ├── NdnHist.groovy │ │ │ ├── PlotFancySpectratype.groovy │ │ │ ├── PlotFancyVJUsage.groovy │ │ │ ├── PlotSpectratypeV.groovy │ │ │ ├── SegmentUsage.groovy │ │ │ ├── Spectratype.groovy │ │ │ └── SpectratypeV.groovy │ │ │ ├── diversity │ │ │ ├── CalcDiversityStats.groovy │ │ │ ├── Chao2Estimator.groovy │ │ │ ├── ChaoEstimator.groovy │ │ │ ├── DiversityEstimate.groovy │ │ │ ├── DiversityEstimator.groovy │ │ │ ├── DiversityIndex.groovy │ │ │ ├── EstimationMethod.groovy │ │ │ ├── ExactEstimator.groovy │ │ │ ├── FrequencyTable.groovy │ │ │ ├── PlotQuantileStats.groovy │ │ │ ├── QuantileStats.groovy │ │ │ ├── Rarefaction.groovy │ │ │ ├── RarefactionPlot.groovy │ │ │ ├── ResamplingEstimator.groovy │ │ │ ├── RichnessEstimateType.groovy │ │ │ └── SpeciesRichness.groovy │ │ │ ├── io │ │ │ ├── DummySampleConnection.groovy │ │ │ ├── FileInputStreamFactory.groovy │ │ │ ├── InputStreamFactory.groovy │ │ │ ├── SampleConnection.groovy │ │ │ ├── SampleFileConnection.groovy │ │ │ ├── SampleStreamConnection.groovy │ │ │ ├── SampleWriter.groovy │ │ │ └── parser │ │ │ │ ├── BaseParser.groovy │ │ │ │ ├── ClonotypeStreamParser.groovy │ │ │ │ ├── ImSeqParser.groovy │ │ │ │ ├── ImgtHighVQuestParser.groovy │ │ │ │ ├── ImmunoSeqParser.groovy │ │ │ │ ├── ImmunoSeqV2Parser.groovy │ │ │ │ ├── MiGecParser.groovy │ │ │ │ ├── MiTcrParser.groovy │ │ │ │ ├── MiXcrParser.groovy │ │ │ │ ├── MigMapParser.groovy │ │ │ │ ├── RtcrParser.groovy │ │ │ │ └── VidjilParser.groovy │ │ │ ├── misc │ │ │ ├── CommonUtil.groovy │ │ │ ├── Convert.groovy │ │ │ ├── ExecUtil.groovy │ │ │ ├── FilterMetadata.groovy │ │ │ ├── RInstall.groovy │ │ │ ├── RUtil.groovy │ │ │ ├── Software.groovy │ │ │ └── SplitMetadata.groovy │ │ │ ├── operate │ │ │ ├── JoinSamples.groovy │ │ │ └── PoolSamples.groovy │ │ │ ├── overlap │ │ │ ├── CalcPairwiseDistances.groovy │ │ │ ├── ClusterSamples.groovy │ │ │ ├── Overlap.groovy │ │ │ ├── OverlapEvaluator.groovy │ │ │ ├── OverlapMetric.groovy │ │ │ ├── OverlapMetricNormalization.groovy │ │ │ ├── OverlapPair.groovy │ │ │ ├── OverlapType.groovy │ │ │ ├── PairwiseOverlap.groovy │ │ │ ├── TestClusters.groovy │ │ │ ├── TrackClonotypes.groovy │ │ │ └── permutations │ │ │ │ ├── ContFactorClusterStats.groovy │ │ │ │ └── DiscreteFactorClusterStats.groovy │ │ │ ├── preprocess │ │ │ ├── ApplySampleAsFilter.groovy │ │ │ ├── Correct.groovy │ │ │ ├── Decontaminate.groovy │ │ │ ├── DownSample.groovy │ │ │ ├── DownSampler.groovy │ │ │ ├── FilterByFrequency.groovy │ │ │ ├── FilterBySegment.groovy │ │ │ ├── FilterNonFunctional.groovy │ │ │ ├── Sampler.groovy │ │ │ ├── SelectTop.groovy │ │ │ ├── TopCountSampler.groovy │ │ │ ├── TopQuantileSampler.groovy │ │ │ └── TopSampler.groovy │ │ │ └── sample │ │ │ ├── SampleCollection.groovy │ │ │ ├── SamplePair.groovy │ │ │ ├── SampleStatistics.groovy │ │ │ └── metadata │ │ │ ├── BlankMetadataEntryFilter.groovy │ │ │ ├── MetadataColumnInfo.groovy │ │ │ ├── MetadataColumnType.groovy │ │ │ ├── MetadataEntry.groovy │ │ │ ├── MetadataEntryExpressionFilter.groovy │ │ │ ├── MetadataEntryFilter.groovy │ │ │ ├── MetadataTable.groovy │ │ │ ├── MetadataUtil.groovy │ │ │ ├── SampleMetadata.groovy │ │ │ └── SampleMetadataFilter.groovy │ ├── java │ │ └── com │ │ │ └── antigenomics │ │ │ └── vdjtools │ │ │ ├── ClonotypeWrapper.java │ │ │ ├── ClonotypeWrapperContainer.java │ │ │ ├── Countable.java │ │ │ ├── annotate │ │ │ ├── AaProperty.java │ │ │ ├── AaPropertySummary.java │ │ │ ├── AaPropertySummaryEvaluator.java │ │ │ ├── Cdr3ContactEstimate.java │ │ │ ├── SimpleAaProperty.java │ │ │ └── partitioning │ │ │ │ ├── Cdr3Center.java │ │ │ │ ├── Cdr3Region.java │ │ │ │ ├── DGermline.java │ │ │ │ ├── DJJunction.java │ │ │ │ ├── FullCdr3.java │ │ │ │ ├── JGermline.java │ │ │ │ ├── SequenceRegion.java │ │ │ │ ├── VDJunction.java │ │ │ │ ├── VGermline.java │ │ │ │ └── VJJunction.java │ │ │ ├── graph │ │ │ ├── ClonotypeGroup.java │ │ │ ├── ClonotypeGroupingFactory.java │ │ │ ├── DegreeStatistics.java │ │ │ ├── DegreeStatisticsCalculator.java │ │ │ ├── DummyClonotypeGroup.java │ │ │ ├── DummyClonotypeGroupingFactory.java │ │ │ ├── GroupingSummary.java │ │ │ ├── VClonotypeGroup.java │ │ │ ├── VClonotypeGroupingFactory.java │ │ │ ├── VJClonotypeGroup.java │ │ │ ├── VJClonotypeGroupingFactory.java │ │ │ ├── VJLClonotypeGroup.java │ │ │ └── VJLClonotypeGroupingFactory.java │ │ │ ├── join │ │ │ ├── ClonotypeKeyGen.java │ │ │ ├── CompositeJoinFilter.java │ │ │ ├── JoinFilter.java │ │ │ ├── JointClonotype.java │ │ │ ├── JointSample.java │ │ │ ├── OccurrenceJoinFilter.java │ │ │ ├── SampleSpecificJoinFilter.java │ │ │ ├── SampleSpecificOccurrenceJoinFilter.java │ │ │ └── key │ │ │ │ ├── AaKey.java │ │ │ │ ├── AaNotNtKey.java │ │ │ │ ├── AaVJKey.java │ │ │ │ ├── AaVKey.java │ │ │ │ ├── ClonotypeKey.java │ │ │ │ ├── NtKey.java │ │ │ │ ├── NtVJKey.java │ │ │ │ ├── NtVKey.java │ │ │ │ └── StrictKey.java │ │ │ ├── misc │ │ │ ├── AtomicDouble.java │ │ │ ├── AtomicDoubleArray.java │ │ │ ├── LinkedListExt.java │ │ │ ├── MathUtil.java │ │ │ ├── Segment.java │ │ │ ├── SegmentFactory.java │ │ │ └── StatUtil.java │ │ │ ├── pool │ │ │ ├── ClonotypeAggregator.java │ │ │ ├── ClonotypeAggregatorFactory.java │ │ │ ├── MaxClonotypeAggregator.java │ │ │ ├── MaxClonotypeAggregatorFactory.java │ │ │ ├── PooledSample.java │ │ │ ├── RatioFilter.java │ │ │ ├── SampleAggregator.java │ │ │ ├── StoringClonotypeAggregator.java │ │ │ └── StoringClonotypeAggregatorFactory.java │ │ │ ├── preprocess │ │ │ └── Corrector.java │ │ │ └── sample │ │ │ ├── BlankClonotypeFilter.java │ │ │ ├── Chain.java │ │ │ ├── Clonotype.java │ │ │ ├── ClonotypeConverter.java │ │ │ ├── ClonotypeFilter.java │ │ │ ├── CompositeClonotypeFilter.java │ │ │ ├── CountFilter.java │ │ │ ├── DFilter.java │ │ │ ├── FrequencyFilter.java │ │ │ ├── FunctionalClonotypeFilter.java │ │ │ ├── IntersectionClonotypeFilter.java │ │ │ ├── JFilter.java │ │ │ ├── QuantileFilter.java │ │ │ ├── Sample.java │ │ │ ├── SegmentConverter.java │ │ │ ├── SegmentFilter.java │ │ │ ├── SequenceMatchFilter.java │ │ │ └── VFilter.java │ └── resources │ │ ├── profile │ │ ├── aa_property_table.txt │ │ └── cdr3contact.txt │ │ ├── rscripts │ │ ├── cdr3aa_profile.r │ │ ├── cluster_permutations_plot.r │ │ ├── cluster_samples.r │ │ ├── fancy_spectratype.r │ │ ├── install.r │ │ ├── intersect_pair_area.r │ │ ├── intersect_pair_area_v2.r │ │ ├── intersect_pair_scatter.r │ │ ├── join_venn.r │ │ ├── pairwise_distance_plot.r │ │ ├── plot_time_series.r │ │ ├── quantile_stats.r │ │ ├── rarefaction_curve.r │ │ ├── test.r │ │ ├── tracking_heatcourse.r │ │ ├── tracking_similarity_map.r │ │ ├── tracking_stackplot.r │ │ ├── vexpr_plot.r │ │ └── vj_pairing_plot.r │ │ └── vj_families.txt └── test │ ├── groovy │ └── com │ │ └── antigenomics │ │ └── vdjtools │ │ ├── TestUtil.groovy │ │ ├── annotate │ │ ├── AnnotateTest.groovy │ │ └── CdrAaStatsTest.groovy │ │ ├── basic │ │ ├── BasicStatsTest.groovy │ │ ├── FancySpectratypeTest.groovy │ │ ├── SegmentUsageTest.groovy │ │ ├── SpectratypeTest.groovy │ │ └── SpectratypeVTest.groovy │ │ ├── diversity │ │ ├── ExactEstimatorTest.groovy │ │ └── FrequencyTableGenerator.groovy │ │ ├── io │ │ ├── SampleAnnotationExportTest.groovy │ │ └── SampleLoadTest.groovy │ │ └── overlap │ │ └── DistanceMeasureTest.groovy │ ├── java │ └── com │ │ └── antigenomics │ │ └── vdjtools │ │ └── Dummy.java │ └── resources │ └── samples │ ├── empty.txt │ ├── imgthighvquest.txt.gz │ ├── immunoseq.txt.gz │ ├── immunoseq_1.txt.gz │ ├── immunoseqv2.txt.gz │ ├── imseq.txt.gz │ ├── migec.txt.gz │ ├── migmap.txt.gz │ ├── mitcr.txt.gz │ ├── mixcr.171.txt.gz │ ├── mixcr.21.txt.gz │ ├── mixcr.3.txt.gz │ ├── mixcr.fl.txt.gz │ ├── mixcr.txt.gz │ ├── rtcr.txt.gz │ ├── vdjdb.txt.gz │ ├── vdjtools.txt.gz │ ├── vdjtoolsrenorm.txt.gz │ └── vidjil.txt.gz ├── travis.post.sh ├── vdjdb.test.txt └── vdjtools /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/.gitignore -------------------------------------------------------------------------------- /.travis.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/.travis.yml -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/README.md -------------------------------------------------------------------------------- /doc/Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/doc/Makefile -------------------------------------------------------------------------------- /doc/_static/images/age-logo.jpg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/doc/_static/images/age-logo.jpg -------------------------------------------------------------------------------- /doc/_static/images/age-vusage.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/doc/_static/images/age-vusage.png -------------------------------------------------------------------------------- /doc/_static/images/framework.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/doc/_static/images/framework.png -------------------------------------------------------------------------------- /doc/_static/images/hsct-logo.jpg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/doc/_static/images/hsct-logo.jpg -------------------------------------------------------------------------------- /doc/_static/images/hsct-stackplot.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/doc/_static/images/hsct-stackplot.png -------------------------------------------------------------------------------- /doc/_static/images/modules/annotate-aaprofile.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/doc/_static/images/modules/annotate-aaprofile.png -------------------------------------------------------------------------------- /doc/_static/images/modules/basic-fancyspectra.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/doc/_static/images/modules/basic-fancyspectra.png -------------------------------------------------------------------------------- /doc/_static/images/modules/basic-fancyvj.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/doc/_static/images/modules/basic-fancyvj.png -------------------------------------------------------------------------------- /doc/_static/images/modules/basic-segmentusage.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/doc/_static/images/modules/basic-segmentusage.png -------------------------------------------------------------------------------- /doc/_static/images/modules/basic-spectrav.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/doc/_static/images/modules/basic-spectrav.png -------------------------------------------------------------------------------- /doc/_static/images/modules/diversity-qstat.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/doc/_static/images/modules/diversity-qstat.png -------------------------------------------------------------------------------- /doc/_static/images/modules/diversity-rarefaction.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/doc/_static/images/modules/diversity-rarefaction.png -------------------------------------------------------------------------------- /doc/_static/images/modules/intersect-batch-circos.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/doc/_static/images/modules/intersect-batch-circos.png -------------------------------------------------------------------------------- /doc/_static/images/modules/intersect-batch-dendro.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/doc/_static/images/modules/intersect-batch-dendro.png -------------------------------------------------------------------------------- /doc/_static/images/modules/intersect-batch-mds.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/doc/_static/images/modules/intersect-batch-mds.png -------------------------------------------------------------------------------- /doc/_static/images/modules/intersect-batch-perms.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/doc/_static/images/modules/intersect-batch-perms.png -------------------------------------------------------------------------------- /doc/_static/images/modules/intersect-pair-scatter.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/doc/_static/images/modules/intersect-pair-scatter.png -------------------------------------------------------------------------------- /doc/_static/images/modules/intersect-pair-stack.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/doc/_static/images/modules/intersect-pair-stack.png -------------------------------------------------------------------------------- /doc/_static/images/modules/intersect-seq-heatplot.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/doc/_static/images/modules/intersect-seq-heatplot.png -------------------------------------------------------------------------------- /doc/_static/images/modules/intersect-seq-stackplot.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/doc/_static/images/modules/intersect-seq-stackplot.png -------------------------------------------------------------------------------- /doc/_static/images/modules/intersect-seq-summary.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/doc/_static/images/modules/intersect-seq-summary.png -------------------------------------------------------------------------------- /doc/_static/images/modules/join-venn.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/doc/_static/images/modules/join-venn.png -------------------------------------------------------------------------------- /doc/_static/images/modules/test-clusters.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/doc/_static/images/modules/test-clusters.png -------------------------------------------------------------------------------- /doc/_static/images/ms-logo.jpg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/doc/_static/images/ms-logo.jpg -------------------------------------------------------------------------------- /doc/_static/images/ms-rarefaction.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/doc/_static/images/ms-rarefaction.png -------------------------------------------------------------------------------- /doc/_static/images/vdjviz.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/doc/_static/images/vdjviz.png -------------------------------------------------------------------------------- /doc/_static/images/vdjviz1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/doc/_static/images/vdjviz1.png -------------------------------------------------------------------------------- /doc/annotate.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/doc/annotate.rst -------------------------------------------------------------------------------- /doc/basic.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/doc/basic.rst -------------------------------------------------------------------------------- /doc/browser.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/doc/browser.rst -------------------------------------------------------------------------------- /doc/conf.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/doc/conf.py -------------------------------------------------------------------------------- /doc/diversity.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/doc/diversity.rst -------------------------------------------------------------------------------- /doc/examples.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/doc/examples.rst -------------------------------------------------------------------------------- /doc/index.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/doc/index.rst -------------------------------------------------------------------------------- /doc/input.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/doc/input.rst -------------------------------------------------------------------------------- /doc/install.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/doc/install.rst -------------------------------------------------------------------------------- /doc/intro.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/doc/intro.rst -------------------------------------------------------------------------------- /doc/modules.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/doc/modules.rst -------------------------------------------------------------------------------- /doc/operate.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/doc/operate.rst -------------------------------------------------------------------------------- /doc/overlap.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/doc/overlap.rst -------------------------------------------------------------------------------- /doc/preprocess.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/doc/preprocess.rst -------------------------------------------------------------------------------- /doc/usage.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/doc/usage.rst -------------------------------------------------------------------------------- /doc/util.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/doc/util.rst -------------------------------------------------------------------------------- /doc/vdjviz.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/doc/vdjviz.rst -------------------------------------------------------------------------------- /gradle/wrapper/gradle-wrapper.jar: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/gradle/wrapper/gradle-wrapper.jar -------------------------------------------------------------------------------- /gradle/wrapper/gradle-wrapper.properties: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/gradle/wrapper/gradle-wrapper.properties -------------------------------------------------------------------------------- /gradlew: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/gradlew -------------------------------------------------------------------------------- /gradlew.bat: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/gradlew.bat -------------------------------------------------------------------------------- /jitpack.yaml: -------------------------------------------------------------------------------- 1 | jdk: 2 | - openjdk10 -------------------------------------------------------------------------------- /src/main/groovy/com/antigenomics/vdjtools/VdjTools.groovy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/groovy/com/antigenomics/vdjtools/VdjTools.groovy -------------------------------------------------------------------------------- /src/main/groovy/com/antigenomics/vdjtools/VdjUtil.groovy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/groovy/com/antigenomics/vdjtools/VdjUtil.groovy -------------------------------------------------------------------------------- /src/main/groovy/com/antigenomics/vdjtools/annotate/AaPropertyAnnotator.groovy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/groovy/com/antigenomics/vdjtools/annotate/AaPropertyAnnotator.groovy -------------------------------------------------------------------------------- /src/main/groovy/com/antigenomics/vdjtools/annotate/Annotate.groovy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/groovy/com/antigenomics/vdjtools/annotate/Annotate.groovy -------------------------------------------------------------------------------- /src/main/groovy/com/antigenomics/vdjtools/annotate/BaseAnnotator.groovy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/groovy/com/antigenomics/vdjtools/annotate/BaseAnnotator.groovy -------------------------------------------------------------------------------- /src/main/groovy/com/antigenomics/vdjtools/annotate/CalcCdrAaStats.groovy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/groovy/com/antigenomics/vdjtools/annotate/CalcCdrAaStats.groovy -------------------------------------------------------------------------------- /src/main/groovy/com/antigenomics/vdjtools/annotate/CalcDegreeStats.groovy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/groovy/com/antigenomics/vdjtools/annotate/CalcDegreeStats.groovy -------------------------------------------------------------------------------- /src/main/groovy/com/antigenomics/vdjtools/annotate/ClonotypeAnnotator.groovy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/groovy/com/antigenomics/vdjtools/annotate/ClonotypeAnnotator.groovy -------------------------------------------------------------------------------- /src/main/groovy/com/antigenomics/vdjtools/annotate/DegreeStatisticsAnnotator.groovy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/groovy/com/antigenomics/vdjtools/annotate/DegreeStatisticsAnnotator.groovy -------------------------------------------------------------------------------- /src/main/groovy/com/antigenomics/vdjtools/annotate/KnownAminoAcidProperties.groovy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/groovy/com/antigenomics/vdjtools/annotate/KnownAminoAcidProperties.groovy -------------------------------------------------------------------------------- /src/main/groovy/com/antigenomics/vdjtools/annotate/KnownAnnotators.groovy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/groovy/com/antigenomics/vdjtools/annotate/KnownAnnotators.groovy -------------------------------------------------------------------------------- /src/main/groovy/com/antigenomics/vdjtools/annotate/KnownCdr3Regions.groovy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/groovy/com/antigenomics/vdjtools/annotate/KnownCdr3Regions.groovy -------------------------------------------------------------------------------- /src/main/groovy/com/antigenomics/vdjtools/annotate/SampleAnnotator.groovy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/groovy/com/antigenomics/vdjtools/annotate/SampleAnnotator.groovy -------------------------------------------------------------------------------- /src/main/groovy/com/antigenomics/vdjtools/annotate/SegmentsToFamilies.groovy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/groovy/com/antigenomics/vdjtools/annotate/SegmentsToFamilies.groovy -------------------------------------------------------------------------------- /src/main/groovy/com/antigenomics/vdjtools/basic/BasicStats.groovy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/groovy/com/antigenomics/vdjtools/basic/BasicStats.groovy -------------------------------------------------------------------------------- /src/main/groovy/com/antigenomics/vdjtools/basic/CalcBasicStats.groovy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/groovy/com/antigenomics/vdjtools/basic/CalcBasicStats.groovy -------------------------------------------------------------------------------- /src/main/groovy/com/antigenomics/vdjtools/basic/CalcSegmentUsage.groovy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/groovy/com/antigenomics/vdjtools/basic/CalcSegmentUsage.groovy -------------------------------------------------------------------------------- /src/main/groovy/com/antigenomics/vdjtools/basic/CalcSpectratype.groovy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/groovy/com/antigenomics/vdjtools/basic/CalcSpectratype.groovy -------------------------------------------------------------------------------- /src/main/groovy/com/antigenomics/vdjtools/basic/FancySpectratype.groovy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/groovy/com/antigenomics/vdjtools/basic/FancySpectratype.groovy -------------------------------------------------------------------------------- /src/main/groovy/com/antigenomics/vdjtools/basic/Histogram.groovy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/groovy/com/antigenomics/vdjtools/basic/Histogram.groovy -------------------------------------------------------------------------------- /src/main/groovy/com/antigenomics/vdjtools/basic/InsertHist.groovy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/groovy/com/antigenomics/vdjtools/basic/InsertHist.groovy -------------------------------------------------------------------------------- /src/main/groovy/com/antigenomics/vdjtools/basic/NdnHist.groovy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/groovy/com/antigenomics/vdjtools/basic/NdnHist.groovy -------------------------------------------------------------------------------- /src/main/groovy/com/antigenomics/vdjtools/basic/PlotFancySpectratype.groovy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/groovy/com/antigenomics/vdjtools/basic/PlotFancySpectratype.groovy -------------------------------------------------------------------------------- /src/main/groovy/com/antigenomics/vdjtools/basic/PlotFancyVJUsage.groovy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/groovy/com/antigenomics/vdjtools/basic/PlotFancyVJUsage.groovy -------------------------------------------------------------------------------- /src/main/groovy/com/antigenomics/vdjtools/basic/PlotSpectratypeV.groovy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/groovy/com/antigenomics/vdjtools/basic/PlotSpectratypeV.groovy -------------------------------------------------------------------------------- /src/main/groovy/com/antigenomics/vdjtools/basic/SegmentUsage.groovy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/groovy/com/antigenomics/vdjtools/basic/SegmentUsage.groovy -------------------------------------------------------------------------------- /src/main/groovy/com/antigenomics/vdjtools/basic/Spectratype.groovy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/groovy/com/antigenomics/vdjtools/basic/Spectratype.groovy -------------------------------------------------------------------------------- /src/main/groovy/com/antigenomics/vdjtools/basic/SpectratypeV.groovy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/groovy/com/antigenomics/vdjtools/basic/SpectratypeV.groovy -------------------------------------------------------------------------------- /src/main/groovy/com/antigenomics/vdjtools/diversity/CalcDiversityStats.groovy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/groovy/com/antigenomics/vdjtools/diversity/CalcDiversityStats.groovy -------------------------------------------------------------------------------- /src/main/groovy/com/antigenomics/vdjtools/diversity/Chao2Estimator.groovy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/groovy/com/antigenomics/vdjtools/diversity/Chao2Estimator.groovy -------------------------------------------------------------------------------- /src/main/groovy/com/antigenomics/vdjtools/diversity/ChaoEstimator.groovy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/groovy/com/antigenomics/vdjtools/diversity/ChaoEstimator.groovy -------------------------------------------------------------------------------- /src/main/groovy/com/antigenomics/vdjtools/diversity/DiversityEstimate.groovy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/groovy/com/antigenomics/vdjtools/diversity/DiversityEstimate.groovy -------------------------------------------------------------------------------- /src/main/groovy/com/antigenomics/vdjtools/diversity/DiversityEstimator.groovy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/groovy/com/antigenomics/vdjtools/diversity/DiversityEstimator.groovy -------------------------------------------------------------------------------- /src/main/groovy/com/antigenomics/vdjtools/diversity/DiversityIndex.groovy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/groovy/com/antigenomics/vdjtools/diversity/DiversityIndex.groovy -------------------------------------------------------------------------------- /src/main/groovy/com/antigenomics/vdjtools/diversity/EstimationMethod.groovy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/groovy/com/antigenomics/vdjtools/diversity/EstimationMethod.groovy -------------------------------------------------------------------------------- /src/main/groovy/com/antigenomics/vdjtools/diversity/ExactEstimator.groovy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/groovy/com/antigenomics/vdjtools/diversity/ExactEstimator.groovy -------------------------------------------------------------------------------- /src/main/groovy/com/antigenomics/vdjtools/diversity/FrequencyTable.groovy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/groovy/com/antigenomics/vdjtools/diversity/FrequencyTable.groovy -------------------------------------------------------------------------------- /src/main/groovy/com/antigenomics/vdjtools/diversity/PlotQuantileStats.groovy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/groovy/com/antigenomics/vdjtools/diversity/PlotQuantileStats.groovy -------------------------------------------------------------------------------- /src/main/groovy/com/antigenomics/vdjtools/diversity/QuantileStats.groovy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/groovy/com/antigenomics/vdjtools/diversity/QuantileStats.groovy -------------------------------------------------------------------------------- /src/main/groovy/com/antigenomics/vdjtools/diversity/Rarefaction.groovy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/groovy/com/antigenomics/vdjtools/diversity/Rarefaction.groovy -------------------------------------------------------------------------------- /src/main/groovy/com/antigenomics/vdjtools/diversity/RarefactionPlot.groovy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/groovy/com/antigenomics/vdjtools/diversity/RarefactionPlot.groovy -------------------------------------------------------------------------------- /src/main/groovy/com/antigenomics/vdjtools/diversity/ResamplingEstimator.groovy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/groovy/com/antigenomics/vdjtools/diversity/ResamplingEstimator.groovy -------------------------------------------------------------------------------- /src/main/groovy/com/antigenomics/vdjtools/diversity/RichnessEstimateType.groovy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/groovy/com/antigenomics/vdjtools/diversity/RichnessEstimateType.groovy -------------------------------------------------------------------------------- /src/main/groovy/com/antigenomics/vdjtools/diversity/SpeciesRichness.groovy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/groovy/com/antigenomics/vdjtools/diversity/SpeciesRichness.groovy -------------------------------------------------------------------------------- /src/main/groovy/com/antigenomics/vdjtools/io/DummySampleConnection.groovy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/groovy/com/antigenomics/vdjtools/io/DummySampleConnection.groovy -------------------------------------------------------------------------------- /src/main/groovy/com/antigenomics/vdjtools/io/FileInputStreamFactory.groovy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/groovy/com/antigenomics/vdjtools/io/FileInputStreamFactory.groovy -------------------------------------------------------------------------------- /src/main/groovy/com/antigenomics/vdjtools/io/InputStreamFactory.groovy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/groovy/com/antigenomics/vdjtools/io/InputStreamFactory.groovy -------------------------------------------------------------------------------- /src/main/groovy/com/antigenomics/vdjtools/io/SampleConnection.groovy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/groovy/com/antigenomics/vdjtools/io/SampleConnection.groovy -------------------------------------------------------------------------------- /src/main/groovy/com/antigenomics/vdjtools/io/SampleFileConnection.groovy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/groovy/com/antigenomics/vdjtools/io/SampleFileConnection.groovy -------------------------------------------------------------------------------- /src/main/groovy/com/antigenomics/vdjtools/io/SampleStreamConnection.groovy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/groovy/com/antigenomics/vdjtools/io/SampleStreamConnection.groovy -------------------------------------------------------------------------------- /src/main/groovy/com/antigenomics/vdjtools/io/SampleWriter.groovy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/groovy/com/antigenomics/vdjtools/io/SampleWriter.groovy -------------------------------------------------------------------------------- /src/main/groovy/com/antigenomics/vdjtools/io/parser/BaseParser.groovy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/groovy/com/antigenomics/vdjtools/io/parser/BaseParser.groovy -------------------------------------------------------------------------------- /src/main/groovy/com/antigenomics/vdjtools/io/parser/ClonotypeStreamParser.groovy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/groovy/com/antigenomics/vdjtools/io/parser/ClonotypeStreamParser.groovy -------------------------------------------------------------------------------- /src/main/groovy/com/antigenomics/vdjtools/io/parser/ImSeqParser.groovy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/groovy/com/antigenomics/vdjtools/io/parser/ImSeqParser.groovy -------------------------------------------------------------------------------- /src/main/groovy/com/antigenomics/vdjtools/io/parser/ImgtHighVQuestParser.groovy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/groovy/com/antigenomics/vdjtools/io/parser/ImgtHighVQuestParser.groovy -------------------------------------------------------------------------------- /src/main/groovy/com/antigenomics/vdjtools/io/parser/ImmunoSeqParser.groovy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/groovy/com/antigenomics/vdjtools/io/parser/ImmunoSeqParser.groovy -------------------------------------------------------------------------------- /src/main/groovy/com/antigenomics/vdjtools/io/parser/ImmunoSeqV2Parser.groovy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/groovy/com/antigenomics/vdjtools/io/parser/ImmunoSeqV2Parser.groovy -------------------------------------------------------------------------------- /src/main/groovy/com/antigenomics/vdjtools/io/parser/MiGecParser.groovy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/groovy/com/antigenomics/vdjtools/io/parser/MiGecParser.groovy -------------------------------------------------------------------------------- /src/main/groovy/com/antigenomics/vdjtools/io/parser/MiTcrParser.groovy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/groovy/com/antigenomics/vdjtools/io/parser/MiTcrParser.groovy -------------------------------------------------------------------------------- /src/main/groovy/com/antigenomics/vdjtools/io/parser/MiXcrParser.groovy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/groovy/com/antigenomics/vdjtools/io/parser/MiXcrParser.groovy -------------------------------------------------------------------------------- /src/main/groovy/com/antigenomics/vdjtools/io/parser/MigMapParser.groovy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/groovy/com/antigenomics/vdjtools/io/parser/MigMapParser.groovy -------------------------------------------------------------------------------- /src/main/groovy/com/antigenomics/vdjtools/io/parser/RtcrParser.groovy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/groovy/com/antigenomics/vdjtools/io/parser/RtcrParser.groovy -------------------------------------------------------------------------------- /src/main/groovy/com/antigenomics/vdjtools/io/parser/VidjilParser.groovy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/groovy/com/antigenomics/vdjtools/io/parser/VidjilParser.groovy -------------------------------------------------------------------------------- /src/main/groovy/com/antigenomics/vdjtools/misc/CommonUtil.groovy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/groovy/com/antigenomics/vdjtools/misc/CommonUtil.groovy -------------------------------------------------------------------------------- /src/main/groovy/com/antigenomics/vdjtools/misc/Convert.groovy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/groovy/com/antigenomics/vdjtools/misc/Convert.groovy -------------------------------------------------------------------------------- /src/main/groovy/com/antigenomics/vdjtools/misc/ExecUtil.groovy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/groovy/com/antigenomics/vdjtools/misc/ExecUtil.groovy -------------------------------------------------------------------------------- /src/main/groovy/com/antigenomics/vdjtools/misc/FilterMetadata.groovy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/groovy/com/antigenomics/vdjtools/misc/FilterMetadata.groovy -------------------------------------------------------------------------------- /src/main/groovy/com/antigenomics/vdjtools/misc/RInstall.groovy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/groovy/com/antigenomics/vdjtools/misc/RInstall.groovy -------------------------------------------------------------------------------- /src/main/groovy/com/antigenomics/vdjtools/misc/RUtil.groovy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/groovy/com/antigenomics/vdjtools/misc/RUtil.groovy -------------------------------------------------------------------------------- /src/main/groovy/com/antigenomics/vdjtools/misc/Software.groovy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/groovy/com/antigenomics/vdjtools/misc/Software.groovy -------------------------------------------------------------------------------- /src/main/groovy/com/antigenomics/vdjtools/misc/SplitMetadata.groovy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/groovy/com/antigenomics/vdjtools/misc/SplitMetadata.groovy -------------------------------------------------------------------------------- /src/main/groovy/com/antigenomics/vdjtools/operate/JoinSamples.groovy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/groovy/com/antigenomics/vdjtools/operate/JoinSamples.groovy -------------------------------------------------------------------------------- /src/main/groovy/com/antigenomics/vdjtools/operate/PoolSamples.groovy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/groovy/com/antigenomics/vdjtools/operate/PoolSamples.groovy -------------------------------------------------------------------------------- /src/main/groovy/com/antigenomics/vdjtools/overlap/CalcPairwiseDistances.groovy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/groovy/com/antigenomics/vdjtools/overlap/CalcPairwiseDistances.groovy -------------------------------------------------------------------------------- /src/main/groovy/com/antigenomics/vdjtools/overlap/ClusterSamples.groovy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/groovy/com/antigenomics/vdjtools/overlap/ClusterSamples.groovy -------------------------------------------------------------------------------- /src/main/groovy/com/antigenomics/vdjtools/overlap/Overlap.groovy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/groovy/com/antigenomics/vdjtools/overlap/Overlap.groovy -------------------------------------------------------------------------------- /src/main/groovy/com/antigenomics/vdjtools/overlap/OverlapEvaluator.groovy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/groovy/com/antigenomics/vdjtools/overlap/OverlapEvaluator.groovy -------------------------------------------------------------------------------- /src/main/groovy/com/antigenomics/vdjtools/overlap/OverlapMetric.groovy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/groovy/com/antigenomics/vdjtools/overlap/OverlapMetric.groovy -------------------------------------------------------------------------------- /src/main/groovy/com/antigenomics/vdjtools/overlap/OverlapMetricNormalization.groovy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/groovy/com/antigenomics/vdjtools/overlap/OverlapMetricNormalization.groovy -------------------------------------------------------------------------------- /src/main/groovy/com/antigenomics/vdjtools/overlap/OverlapPair.groovy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/groovy/com/antigenomics/vdjtools/overlap/OverlapPair.groovy -------------------------------------------------------------------------------- /src/main/groovy/com/antigenomics/vdjtools/overlap/OverlapType.groovy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/groovy/com/antigenomics/vdjtools/overlap/OverlapType.groovy -------------------------------------------------------------------------------- /src/main/groovy/com/antigenomics/vdjtools/overlap/PairwiseOverlap.groovy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/groovy/com/antigenomics/vdjtools/overlap/PairwiseOverlap.groovy -------------------------------------------------------------------------------- /src/main/groovy/com/antigenomics/vdjtools/overlap/TestClusters.groovy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/groovy/com/antigenomics/vdjtools/overlap/TestClusters.groovy -------------------------------------------------------------------------------- /src/main/groovy/com/antigenomics/vdjtools/overlap/TrackClonotypes.groovy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/groovy/com/antigenomics/vdjtools/overlap/TrackClonotypes.groovy -------------------------------------------------------------------------------- /src/main/groovy/com/antigenomics/vdjtools/overlap/permutations/ContFactorClusterStats.groovy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/groovy/com/antigenomics/vdjtools/overlap/permutations/ContFactorClusterStats.groovy -------------------------------------------------------------------------------- /src/main/groovy/com/antigenomics/vdjtools/overlap/permutations/DiscreteFactorClusterStats.groovy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/groovy/com/antigenomics/vdjtools/overlap/permutations/DiscreteFactorClusterStats.groovy -------------------------------------------------------------------------------- /src/main/groovy/com/antigenomics/vdjtools/preprocess/ApplySampleAsFilter.groovy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/groovy/com/antigenomics/vdjtools/preprocess/ApplySampleAsFilter.groovy -------------------------------------------------------------------------------- /src/main/groovy/com/antigenomics/vdjtools/preprocess/Correct.groovy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/groovy/com/antigenomics/vdjtools/preprocess/Correct.groovy -------------------------------------------------------------------------------- /src/main/groovy/com/antigenomics/vdjtools/preprocess/Decontaminate.groovy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/groovy/com/antigenomics/vdjtools/preprocess/Decontaminate.groovy -------------------------------------------------------------------------------- /src/main/groovy/com/antigenomics/vdjtools/preprocess/DownSample.groovy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/groovy/com/antigenomics/vdjtools/preprocess/DownSample.groovy -------------------------------------------------------------------------------- /src/main/groovy/com/antigenomics/vdjtools/preprocess/DownSampler.groovy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/groovy/com/antigenomics/vdjtools/preprocess/DownSampler.groovy -------------------------------------------------------------------------------- /src/main/groovy/com/antigenomics/vdjtools/preprocess/FilterByFrequency.groovy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/groovy/com/antigenomics/vdjtools/preprocess/FilterByFrequency.groovy -------------------------------------------------------------------------------- /src/main/groovy/com/antigenomics/vdjtools/preprocess/FilterBySegment.groovy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/groovy/com/antigenomics/vdjtools/preprocess/FilterBySegment.groovy -------------------------------------------------------------------------------- /src/main/groovy/com/antigenomics/vdjtools/preprocess/FilterNonFunctional.groovy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/groovy/com/antigenomics/vdjtools/preprocess/FilterNonFunctional.groovy -------------------------------------------------------------------------------- /src/main/groovy/com/antigenomics/vdjtools/preprocess/Sampler.groovy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/groovy/com/antigenomics/vdjtools/preprocess/Sampler.groovy -------------------------------------------------------------------------------- /src/main/groovy/com/antigenomics/vdjtools/preprocess/SelectTop.groovy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/groovy/com/antigenomics/vdjtools/preprocess/SelectTop.groovy -------------------------------------------------------------------------------- /src/main/groovy/com/antigenomics/vdjtools/preprocess/TopCountSampler.groovy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/groovy/com/antigenomics/vdjtools/preprocess/TopCountSampler.groovy -------------------------------------------------------------------------------- /src/main/groovy/com/antigenomics/vdjtools/preprocess/TopQuantileSampler.groovy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/groovy/com/antigenomics/vdjtools/preprocess/TopQuantileSampler.groovy -------------------------------------------------------------------------------- /src/main/groovy/com/antigenomics/vdjtools/preprocess/TopSampler.groovy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/groovy/com/antigenomics/vdjtools/preprocess/TopSampler.groovy -------------------------------------------------------------------------------- /src/main/groovy/com/antigenomics/vdjtools/sample/SampleCollection.groovy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/groovy/com/antigenomics/vdjtools/sample/SampleCollection.groovy -------------------------------------------------------------------------------- /src/main/groovy/com/antigenomics/vdjtools/sample/SamplePair.groovy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/groovy/com/antigenomics/vdjtools/sample/SamplePair.groovy -------------------------------------------------------------------------------- /src/main/groovy/com/antigenomics/vdjtools/sample/SampleStatistics.groovy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/groovy/com/antigenomics/vdjtools/sample/SampleStatistics.groovy -------------------------------------------------------------------------------- /src/main/groovy/com/antigenomics/vdjtools/sample/metadata/BlankMetadataEntryFilter.groovy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/groovy/com/antigenomics/vdjtools/sample/metadata/BlankMetadataEntryFilter.groovy -------------------------------------------------------------------------------- /src/main/groovy/com/antigenomics/vdjtools/sample/metadata/MetadataColumnInfo.groovy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/groovy/com/antigenomics/vdjtools/sample/metadata/MetadataColumnInfo.groovy -------------------------------------------------------------------------------- /src/main/groovy/com/antigenomics/vdjtools/sample/metadata/MetadataColumnType.groovy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/groovy/com/antigenomics/vdjtools/sample/metadata/MetadataColumnType.groovy -------------------------------------------------------------------------------- /src/main/groovy/com/antigenomics/vdjtools/sample/metadata/MetadataEntry.groovy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/groovy/com/antigenomics/vdjtools/sample/metadata/MetadataEntry.groovy -------------------------------------------------------------------------------- /src/main/groovy/com/antigenomics/vdjtools/sample/metadata/MetadataEntryExpressionFilter.groovy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/groovy/com/antigenomics/vdjtools/sample/metadata/MetadataEntryExpressionFilter.groovy -------------------------------------------------------------------------------- /src/main/groovy/com/antigenomics/vdjtools/sample/metadata/MetadataEntryFilter.groovy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/groovy/com/antigenomics/vdjtools/sample/metadata/MetadataEntryFilter.groovy -------------------------------------------------------------------------------- /src/main/groovy/com/antigenomics/vdjtools/sample/metadata/MetadataTable.groovy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/groovy/com/antigenomics/vdjtools/sample/metadata/MetadataTable.groovy -------------------------------------------------------------------------------- /src/main/groovy/com/antigenomics/vdjtools/sample/metadata/MetadataUtil.groovy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/groovy/com/antigenomics/vdjtools/sample/metadata/MetadataUtil.groovy -------------------------------------------------------------------------------- /src/main/groovy/com/antigenomics/vdjtools/sample/metadata/SampleMetadata.groovy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/groovy/com/antigenomics/vdjtools/sample/metadata/SampleMetadata.groovy -------------------------------------------------------------------------------- /src/main/groovy/com/antigenomics/vdjtools/sample/metadata/SampleMetadataFilter.groovy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/groovy/com/antigenomics/vdjtools/sample/metadata/SampleMetadataFilter.groovy -------------------------------------------------------------------------------- /src/main/java/com/antigenomics/vdjtools/ClonotypeWrapper.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/java/com/antigenomics/vdjtools/ClonotypeWrapper.java -------------------------------------------------------------------------------- /src/main/java/com/antigenomics/vdjtools/ClonotypeWrapperContainer.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/java/com/antigenomics/vdjtools/ClonotypeWrapperContainer.java -------------------------------------------------------------------------------- /src/main/java/com/antigenomics/vdjtools/Countable.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/java/com/antigenomics/vdjtools/Countable.java -------------------------------------------------------------------------------- /src/main/java/com/antigenomics/vdjtools/annotate/AaProperty.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/java/com/antigenomics/vdjtools/annotate/AaProperty.java -------------------------------------------------------------------------------- /src/main/java/com/antigenomics/vdjtools/annotate/AaPropertySummary.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/java/com/antigenomics/vdjtools/annotate/AaPropertySummary.java -------------------------------------------------------------------------------- /src/main/java/com/antigenomics/vdjtools/annotate/AaPropertySummaryEvaluator.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/java/com/antigenomics/vdjtools/annotate/AaPropertySummaryEvaluator.java -------------------------------------------------------------------------------- /src/main/java/com/antigenomics/vdjtools/annotate/Cdr3ContactEstimate.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/java/com/antigenomics/vdjtools/annotate/Cdr3ContactEstimate.java -------------------------------------------------------------------------------- /src/main/java/com/antigenomics/vdjtools/annotate/SimpleAaProperty.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/java/com/antigenomics/vdjtools/annotate/SimpleAaProperty.java -------------------------------------------------------------------------------- /src/main/java/com/antigenomics/vdjtools/annotate/partitioning/Cdr3Center.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/java/com/antigenomics/vdjtools/annotate/partitioning/Cdr3Center.java -------------------------------------------------------------------------------- /src/main/java/com/antigenomics/vdjtools/annotate/partitioning/Cdr3Region.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/java/com/antigenomics/vdjtools/annotate/partitioning/Cdr3Region.java -------------------------------------------------------------------------------- /src/main/java/com/antigenomics/vdjtools/annotate/partitioning/DGermline.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/java/com/antigenomics/vdjtools/annotate/partitioning/DGermline.java -------------------------------------------------------------------------------- /src/main/java/com/antigenomics/vdjtools/annotate/partitioning/DJJunction.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/java/com/antigenomics/vdjtools/annotate/partitioning/DJJunction.java -------------------------------------------------------------------------------- /src/main/java/com/antigenomics/vdjtools/annotate/partitioning/FullCdr3.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/java/com/antigenomics/vdjtools/annotate/partitioning/FullCdr3.java -------------------------------------------------------------------------------- /src/main/java/com/antigenomics/vdjtools/annotate/partitioning/JGermline.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/java/com/antigenomics/vdjtools/annotate/partitioning/JGermline.java -------------------------------------------------------------------------------- /src/main/java/com/antigenomics/vdjtools/annotate/partitioning/SequenceRegion.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/java/com/antigenomics/vdjtools/annotate/partitioning/SequenceRegion.java -------------------------------------------------------------------------------- /src/main/java/com/antigenomics/vdjtools/annotate/partitioning/VDJunction.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/java/com/antigenomics/vdjtools/annotate/partitioning/VDJunction.java -------------------------------------------------------------------------------- /src/main/java/com/antigenomics/vdjtools/annotate/partitioning/VGermline.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/java/com/antigenomics/vdjtools/annotate/partitioning/VGermline.java -------------------------------------------------------------------------------- /src/main/java/com/antigenomics/vdjtools/annotate/partitioning/VJJunction.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/java/com/antigenomics/vdjtools/annotate/partitioning/VJJunction.java -------------------------------------------------------------------------------- /src/main/java/com/antigenomics/vdjtools/graph/ClonotypeGroup.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/java/com/antigenomics/vdjtools/graph/ClonotypeGroup.java -------------------------------------------------------------------------------- /src/main/java/com/antigenomics/vdjtools/graph/ClonotypeGroupingFactory.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/java/com/antigenomics/vdjtools/graph/ClonotypeGroupingFactory.java -------------------------------------------------------------------------------- /src/main/java/com/antigenomics/vdjtools/graph/DegreeStatistics.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/java/com/antigenomics/vdjtools/graph/DegreeStatistics.java -------------------------------------------------------------------------------- /src/main/java/com/antigenomics/vdjtools/graph/DegreeStatisticsCalculator.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/java/com/antigenomics/vdjtools/graph/DegreeStatisticsCalculator.java -------------------------------------------------------------------------------- /src/main/java/com/antigenomics/vdjtools/graph/DummyClonotypeGroup.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/java/com/antigenomics/vdjtools/graph/DummyClonotypeGroup.java -------------------------------------------------------------------------------- /src/main/java/com/antigenomics/vdjtools/graph/DummyClonotypeGroupingFactory.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/java/com/antigenomics/vdjtools/graph/DummyClonotypeGroupingFactory.java -------------------------------------------------------------------------------- /src/main/java/com/antigenomics/vdjtools/graph/GroupingSummary.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/java/com/antigenomics/vdjtools/graph/GroupingSummary.java -------------------------------------------------------------------------------- /src/main/java/com/antigenomics/vdjtools/graph/VClonotypeGroup.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/java/com/antigenomics/vdjtools/graph/VClonotypeGroup.java -------------------------------------------------------------------------------- /src/main/java/com/antigenomics/vdjtools/graph/VClonotypeGroupingFactory.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/java/com/antigenomics/vdjtools/graph/VClonotypeGroupingFactory.java -------------------------------------------------------------------------------- /src/main/java/com/antigenomics/vdjtools/graph/VJClonotypeGroup.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/java/com/antigenomics/vdjtools/graph/VJClonotypeGroup.java -------------------------------------------------------------------------------- /src/main/java/com/antigenomics/vdjtools/graph/VJClonotypeGroupingFactory.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/java/com/antigenomics/vdjtools/graph/VJClonotypeGroupingFactory.java -------------------------------------------------------------------------------- /src/main/java/com/antigenomics/vdjtools/graph/VJLClonotypeGroup.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/java/com/antigenomics/vdjtools/graph/VJLClonotypeGroup.java -------------------------------------------------------------------------------- /src/main/java/com/antigenomics/vdjtools/graph/VJLClonotypeGroupingFactory.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/java/com/antigenomics/vdjtools/graph/VJLClonotypeGroupingFactory.java -------------------------------------------------------------------------------- /src/main/java/com/antigenomics/vdjtools/join/ClonotypeKeyGen.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/java/com/antigenomics/vdjtools/join/ClonotypeKeyGen.java -------------------------------------------------------------------------------- /src/main/java/com/antigenomics/vdjtools/join/CompositeJoinFilter.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/java/com/antigenomics/vdjtools/join/CompositeJoinFilter.java -------------------------------------------------------------------------------- /src/main/java/com/antigenomics/vdjtools/join/JoinFilter.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/java/com/antigenomics/vdjtools/join/JoinFilter.java -------------------------------------------------------------------------------- /src/main/java/com/antigenomics/vdjtools/join/JointClonotype.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/java/com/antigenomics/vdjtools/join/JointClonotype.java -------------------------------------------------------------------------------- /src/main/java/com/antigenomics/vdjtools/join/JointSample.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/java/com/antigenomics/vdjtools/join/JointSample.java -------------------------------------------------------------------------------- /src/main/java/com/antigenomics/vdjtools/join/OccurrenceJoinFilter.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/java/com/antigenomics/vdjtools/join/OccurrenceJoinFilter.java -------------------------------------------------------------------------------- /src/main/java/com/antigenomics/vdjtools/join/SampleSpecificJoinFilter.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/java/com/antigenomics/vdjtools/join/SampleSpecificJoinFilter.java -------------------------------------------------------------------------------- /src/main/java/com/antigenomics/vdjtools/join/SampleSpecificOccurrenceJoinFilter.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/java/com/antigenomics/vdjtools/join/SampleSpecificOccurrenceJoinFilter.java -------------------------------------------------------------------------------- /src/main/java/com/antigenomics/vdjtools/join/key/AaKey.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/java/com/antigenomics/vdjtools/join/key/AaKey.java -------------------------------------------------------------------------------- /src/main/java/com/antigenomics/vdjtools/join/key/AaNotNtKey.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/java/com/antigenomics/vdjtools/join/key/AaNotNtKey.java -------------------------------------------------------------------------------- /src/main/java/com/antigenomics/vdjtools/join/key/AaVJKey.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/java/com/antigenomics/vdjtools/join/key/AaVJKey.java -------------------------------------------------------------------------------- /src/main/java/com/antigenomics/vdjtools/join/key/AaVKey.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/java/com/antigenomics/vdjtools/join/key/AaVKey.java -------------------------------------------------------------------------------- /src/main/java/com/antigenomics/vdjtools/join/key/ClonotypeKey.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/java/com/antigenomics/vdjtools/join/key/ClonotypeKey.java -------------------------------------------------------------------------------- /src/main/java/com/antigenomics/vdjtools/join/key/NtKey.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/java/com/antigenomics/vdjtools/join/key/NtKey.java -------------------------------------------------------------------------------- /src/main/java/com/antigenomics/vdjtools/join/key/NtVJKey.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/java/com/antigenomics/vdjtools/join/key/NtVJKey.java -------------------------------------------------------------------------------- /src/main/java/com/antigenomics/vdjtools/join/key/NtVKey.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/java/com/antigenomics/vdjtools/join/key/NtVKey.java -------------------------------------------------------------------------------- /src/main/java/com/antigenomics/vdjtools/join/key/StrictKey.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/java/com/antigenomics/vdjtools/join/key/StrictKey.java -------------------------------------------------------------------------------- /src/main/java/com/antigenomics/vdjtools/misc/AtomicDouble.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/java/com/antigenomics/vdjtools/misc/AtomicDouble.java -------------------------------------------------------------------------------- /src/main/java/com/antigenomics/vdjtools/misc/AtomicDoubleArray.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/java/com/antigenomics/vdjtools/misc/AtomicDoubleArray.java -------------------------------------------------------------------------------- /src/main/java/com/antigenomics/vdjtools/misc/LinkedListExt.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/java/com/antigenomics/vdjtools/misc/LinkedListExt.java -------------------------------------------------------------------------------- /src/main/java/com/antigenomics/vdjtools/misc/MathUtil.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/java/com/antigenomics/vdjtools/misc/MathUtil.java -------------------------------------------------------------------------------- /src/main/java/com/antigenomics/vdjtools/misc/Segment.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/java/com/antigenomics/vdjtools/misc/Segment.java -------------------------------------------------------------------------------- /src/main/java/com/antigenomics/vdjtools/misc/SegmentFactory.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/java/com/antigenomics/vdjtools/misc/SegmentFactory.java -------------------------------------------------------------------------------- /src/main/java/com/antigenomics/vdjtools/misc/StatUtil.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/java/com/antigenomics/vdjtools/misc/StatUtil.java -------------------------------------------------------------------------------- /src/main/java/com/antigenomics/vdjtools/pool/ClonotypeAggregator.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/java/com/antigenomics/vdjtools/pool/ClonotypeAggregator.java -------------------------------------------------------------------------------- /src/main/java/com/antigenomics/vdjtools/pool/ClonotypeAggregatorFactory.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/java/com/antigenomics/vdjtools/pool/ClonotypeAggregatorFactory.java -------------------------------------------------------------------------------- /src/main/java/com/antigenomics/vdjtools/pool/MaxClonotypeAggregator.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/java/com/antigenomics/vdjtools/pool/MaxClonotypeAggregator.java -------------------------------------------------------------------------------- /src/main/java/com/antigenomics/vdjtools/pool/MaxClonotypeAggregatorFactory.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/java/com/antigenomics/vdjtools/pool/MaxClonotypeAggregatorFactory.java -------------------------------------------------------------------------------- /src/main/java/com/antigenomics/vdjtools/pool/PooledSample.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/java/com/antigenomics/vdjtools/pool/PooledSample.java -------------------------------------------------------------------------------- /src/main/java/com/antigenomics/vdjtools/pool/RatioFilter.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/java/com/antigenomics/vdjtools/pool/RatioFilter.java -------------------------------------------------------------------------------- /src/main/java/com/antigenomics/vdjtools/pool/SampleAggregator.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/java/com/antigenomics/vdjtools/pool/SampleAggregator.java -------------------------------------------------------------------------------- /src/main/java/com/antigenomics/vdjtools/pool/StoringClonotypeAggregator.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/java/com/antigenomics/vdjtools/pool/StoringClonotypeAggregator.java -------------------------------------------------------------------------------- /src/main/java/com/antigenomics/vdjtools/pool/StoringClonotypeAggregatorFactory.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/java/com/antigenomics/vdjtools/pool/StoringClonotypeAggregatorFactory.java -------------------------------------------------------------------------------- /src/main/java/com/antigenomics/vdjtools/preprocess/Corrector.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/java/com/antigenomics/vdjtools/preprocess/Corrector.java -------------------------------------------------------------------------------- /src/main/java/com/antigenomics/vdjtools/sample/BlankClonotypeFilter.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/java/com/antigenomics/vdjtools/sample/BlankClonotypeFilter.java -------------------------------------------------------------------------------- /src/main/java/com/antigenomics/vdjtools/sample/Chain.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/java/com/antigenomics/vdjtools/sample/Chain.java -------------------------------------------------------------------------------- /src/main/java/com/antigenomics/vdjtools/sample/Clonotype.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/java/com/antigenomics/vdjtools/sample/Clonotype.java -------------------------------------------------------------------------------- /src/main/java/com/antigenomics/vdjtools/sample/ClonotypeConverter.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/java/com/antigenomics/vdjtools/sample/ClonotypeConverter.java -------------------------------------------------------------------------------- /src/main/java/com/antigenomics/vdjtools/sample/ClonotypeFilter.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/java/com/antigenomics/vdjtools/sample/ClonotypeFilter.java -------------------------------------------------------------------------------- /src/main/java/com/antigenomics/vdjtools/sample/CompositeClonotypeFilter.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/java/com/antigenomics/vdjtools/sample/CompositeClonotypeFilter.java -------------------------------------------------------------------------------- /src/main/java/com/antigenomics/vdjtools/sample/CountFilter.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/java/com/antigenomics/vdjtools/sample/CountFilter.java -------------------------------------------------------------------------------- /src/main/java/com/antigenomics/vdjtools/sample/DFilter.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/java/com/antigenomics/vdjtools/sample/DFilter.java -------------------------------------------------------------------------------- /src/main/java/com/antigenomics/vdjtools/sample/FrequencyFilter.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/java/com/antigenomics/vdjtools/sample/FrequencyFilter.java -------------------------------------------------------------------------------- /src/main/java/com/antigenomics/vdjtools/sample/FunctionalClonotypeFilter.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/java/com/antigenomics/vdjtools/sample/FunctionalClonotypeFilter.java -------------------------------------------------------------------------------- /src/main/java/com/antigenomics/vdjtools/sample/IntersectionClonotypeFilter.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/java/com/antigenomics/vdjtools/sample/IntersectionClonotypeFilter.java -------------------------------------------------------------------------------- /src/main/java/com/antigenomics/vdjtools/sample/JFilter.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/java/com/antigenomics/vdjtools/sample/JFilter.java -------------------------------------------------------------------------------- /src/main/java/com/antigenomics/vdjtools/sample/QuantileFilter.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/java/com/antigenomics/vdjtools/sample/QuantileFilter.java -------------------------------------------------------------------------------- /src/main/java/com/antigenomics/vdjtools/sample/Sample.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/java/com/antigenomics/vdjtools/sample/Sample.java -------------------------------------------------------------------------------- /src/main/java/com/antigenomics/vdjtools/sample/SegmentConverter.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/java/com/antigenomics/vdjtools/sample/SegmentConverter.java -------------------------------------------------------------------------------- /src/main/java/com/antigenomics/vdjtools/sample/SegmentFilter.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/java/com/antigenomics/vdjtools/sample/SegmentFilter.java -------------------------------------------------------------------------------- /src/main/java/com/antigenomics/vdjtools/sample/SequenceMatchFilter.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/java/com/antigenomics/vdjtools/sample/SequenceMatchFilter.java -------------------------------------------------------------------------------- /src/main/java/com/antigenomics/vdjtools/sample/VFilter.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/java/com/antigenomics/vdjtools/sample/VFilter.java -------------------------------------------------------------------------------- /src/main/resources/profile/aa_property_table.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/resources/profile/aa_property_table.txt -------------------------------------------------------------------------------- /src/main/resources/profile/cdr3contact.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/resources/profile/cdr3contact.txt -------------------------------------------------------------------------------- /src/main/resources/rscripts/cdr3aa_profile.r: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/resources/rscripts/cdr3aa_profile.r -------------------------------------------------------------------------------- /src/main/resources/rscripts/cluster_permutations_plot.r: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/resources/rscripts/cluster_permutations_plot.r -------------------------------------------------------------------------------- /src/main/resources/rscripts/cluster_samples.r: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/resources/rscripts/cluster_samples.r -------------------------------------------------------------------------------- /src/main/resources/rscripts/fancy_spectratype.r: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/resources/rscripts/fancy_spectratype.r -------------------------------------------------------------------------------- /src/main/resources/rscripts/install.r: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/resources/rscripts/install.r -------------------------------------------------------------------------------- /src/main/resources/rscripts/intersect_pair_area.r: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/resources/rscripts/intersect_pair_area.r -------------------------------------------------------------------------------- /src/main/resources/rscripts/intersect_pair_area_v2.r: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/resources/rscripts/intersect_pair_area_v2.r -------------------------------------------------------------------------------- /src/main/resources/rscripts/intersect_pair_scatter.r: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/resources/rscripts/intersect_pair_scatter.r -------------------------------------------------------------------------------- /src/main/resources/rscripts/join_venn.r: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/resources/rscripts/join_venn.r -------------------------------------------------------------------------------- /src/main/resources/rscripts/pairwise_distance_plot.r: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/resources/rscripts/pairwise_distance_plot.r -------------------------------------------------------------------------------- /src/main/resources/rscripts/plot_time_series.r: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/resources/rscripts/plot_time_series.r -------------------------------------------------------------------------------- /src/main/resources/rscripts/quantile_stats.r: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/resources/rscripts/quantile_stats.r -------------------------------------------------------------------------------- /src/main/resources/rscripts/rarefaction_curve.r: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/resources/rscripts/rarefaction_curve.r -------------------------------------------------------------------------------- /src/main/resources/rscripts/test.r: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/resources/rscripts/test.r -------------------------------------------------------------------------------- /src/main/resources/rscripts/tracking_heatcourse.r: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/resources/rscripts/tracking_heatcourse.r -------------------------------------------------------------------------------- /src/main/resources/rscripts/tracking_similarity_map.r: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/resources/rscripts/tracking_similarity_map.r -------------------------------------------------------------------------------- /src/main/resources/rscripts/tracking_stackplot.r: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/resources/rscripts/tracking_stackplot.r -------------------------------------------------------------------------------- /src/main/resources/rscripts/vexpr_plot.r: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/resources/rscripts/vexpr_plot.r -------------------------------------------------------------------------------- /src/main/resources/rscripts/vj_pairing_plot.r: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/resources/rscripts/vj_pairing_plot.r -------------------------------------------------------------------------------- /src/main/resources/vj_families.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/main/resources/vj_families.txt -------------------------------------------------------------------------------- /src/test/groovy/com/antigenomics/vdjtools/TestUtil.groovy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/test/groovy/com/antigenomics/vdjtools/TestUtil.groovy -------------------------------------------------------------------------------- /src/test/groovy/com/antigenomics/vdjtools/annotate/AnnotateTest.groovy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/test/groovy/com/antigenomics/vdjtools/annotate/AnnotateTest.groovy -------------------------------------------------------------------------------- /src/test/groovy/com/antigenomics/vdjtools/annotate/CdrAaStatsTest.groovy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/test/groovy/com/antigenomics/vdjtools/annotate/CdrAaStatsTest.groovy -------------------------------------------------------------------------------- /src/test/groovy/com/antigenomics/vdjtools/basic/BasicStatsTest.groovy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/test/groovy/com/antigenomics/vdjtools/basic/BasicStatsTest.groovy -------------------------------------------------------------------------------- /src/test/groovy/com/antigenomics/vdjtools/basic/FancySpectratypeTest.groovy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/test/groovy/com/antigenomics/vdjtools/basic/FancySpectratypeTest.groovy -------------------------------------------------------------------------------- /src/test/groovy/com/antigenomics/vdjtools/basic/SegmentUsageTest.groovy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/test/groovy/com/antigenomics/vdjtools/basic/SegmentUsageTest.groovy -------------------------------------------------------------------------------- /src/test/groovy/com/antigenomics/vdjtools/basic/SpectratypeTest.groovy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/test/groovy/com/antigenomics/vdjtools/basic/SpectratypeTest.groovy -------------------------------------------------------------------------------- /src/test/groovy/com/antigenomics/vdjtools/basic/SpectratypeVTest.groovy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/test/groovy/com/antigenomics/vdjtools/basic/SpectratypeVTest.groovy -------------------------------------------------------------------------------- /src/test/groovy/com/antigenomics/vdjtools/diversity/ExactEstimatorTest.groovy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/test/groovy/com/antigenomics/vdjtools/diversity/ExactEstimatorTest.groovy -------------------------------------------------------------------------------- /src/test/groovy/com/antigenomics/vdjtools/diversity/FrequencyTableGenerator.groovy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/test/groovy/com/antigenomics/vdjtools/diversity/FrequencyTableGenerator.groovy -------------------------------------------------------------------------------- /src/test/groovy/com/antigenomics/vdjtools/io/SampleAnnotationExportTest.groovy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/test/groovy/com/antigenomics/vdjtools/io/SampleAnnotationExportTest.groovy -------------------------------------------------------------------------------- /src/test/groovy/com/antigenomics/vdjtools/io/SampleLoadTest.groovy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/test/groovy/com/antigenomics/vdjtools/io/SampleLoadTest.groovy -------------------------------------------------------------------------------- /src/test/groovy/com/antigenomics/vdjtools/overlap/DistanceMeasureTest.groovy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/test/groovy/com/antigenomics/vdjtools/overlap/DistanceMeasureTest.groovy -------------------------------------------------------------------------------- /src/test/java/com/antigenomics/vdjtools/Dummy.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/test/java/com/antigenomics/vdjtools/Dummy.java -------------------------------------------------------------------------------- /src/test/resources/samples/empty.txt: -------------------------------------------------------------------------------- 1 | #header -------------------------------------------------------------------------------- /src/test/resources/samples/imgthighvquest.txt.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/test/resources/samples/imgthighvquest.txt.gz -------------------------------------------------------------------------------- /src/test/resources/samples/immunoseq.txt.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/test/resources/samples/immunoseq.txt.gz -------------------------------------------------------------------------------- /src/test/resources/samples/immunoseq_1.txt.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/test/resources/samples/immunoseq_1.txt.gz -------------------------------------------------------------------------------- /src/test/resources/samples/immunoseqv2.txt.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/test/resources/samples/immunoseqv2.txt.gz -------------------------------------------------------------------------------- /src/test/resources/samples/imseq.txt.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/test/resources/samples/imseq.txt.gz -------------------------------------------------------------------------------- /src/test/resources/samples/migec.txt.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/test/resources/samples/migec.txt.gz -------------------------------------------------------------------------------- /src/test/resources/samples/migmap.txt.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/test/resources/samples/migmap.txt.gz -------------------------------------------------------------------------------- /src/test/resources/samples/mitcr.txt.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/test/resources/samples/mitcr.txt.gz -------------------------------------------------------------------------------- /src/test/resources/samples/mixcr.171.txt.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/test/resources/samples/mixcr.171.txt.gz -------------------------------------------------------------------------------- /src/test/resources/samples/mixcr.21.txt.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/test/resources/samples/mixcr.21.txt.gz -------------------------------------------------------------------------------- /src/test/resources/samples/mixcr.3.txt.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/test/resources/samples/mixcr.3.txt.gz -------------------------------------------------------------------------------- /src/test/resources/samples/mixcr.fl.txt.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/test/resources/samples/mixcr.fl.txt.gz -------------------------------------------------------------------------------- /src/test/resources/samples/mixcr.txt.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/test/resources/samples/mixcr.txt.gz -------------------------------------------------------------------------------- /src/test/resources/samples/rtcr.txt.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/test/resources/samples/rtcr.txt.gz -------------------------------------------------------------------------------- /src/test/resources/samples/vdjdb.txt.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/test/resources/samples/vdjdb.txt.gz -------------------------------------------------------------------------------- /src/test/resources/samples/vdjtools.txt.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/test/resources/samples/vdjtools.txt.gz -------------------------------------------------------------------------------- /src/test/resources/samples/vdjtoolsrenorm.txt.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/test/resources/samples/vdjtoolsrenorm.txt.gz -------------------------------------------------------------------------------- /src/test/resources/samples/vidjil.txt.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/src/test/resources/samples/vidjil.txt.gz -------------------------------------------------------------------------------- /travis.post.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/travis.post.sh -------------------------------------------------------------------------------- /vdjdb.test.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/vdjdb.test.txt -------------------------------------------------------------------------------- /vdjtools: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikessh/vdjtools/HEAD/vdjtools --------------------------------------------------------------------------------