Biodata Tools

org.opencb.biodata : biodata-tools

5 usages
  1. Download JAR / Source Code / Javadoc
  2. View Java Class Source Code in JAR file
  3. View Javadoc in JAR file

Download JAR / Source / Javadoc

Version Date Download
2.1.2 Sep 30, 2021
2.1.1 Jul 24, 2021
2.1.0 Jun 16, 2021
2.0.5 Mar 09, 2021
2.0.4 Dec 31, 2020
2.0.3 Oct 06, 2020
2.0.2 Sep 24, 2020
2.0.1 Aug 03, 2020
2.0.0 Jun 02, 2020
1.5.5 Feb 25, 2021
1.5.4 Feb 17, 2021
1.5.3 Aug 27, 2020
1.5.2 Feb 19, 2020
1.5.1 Sep 19, 2019
1.5.0 Jun 13, 2019
1.4.5 Nov 03, 2019
1.4.4 Apr 04, 2019
1.4.3 Mar 18, 2019
1.4.2 Dec 01, 2018
1.4.1 Sep 01, 2018
1.4.0 Aug 23, 2018
1.3.3 Jun 13, 2019
1.3.2 Feb 08, 2018
1.3.1 Dec 06, 2017
1.3.0 Nov 20, 2017
1.2.3 Aug 02, 2018
1.2.2 Nov 20, 2017
1.2.1 Sep 15, 2017
1.2.0 Jul 28, 2017
1.1.2 Jun 04, 2017
1.1.1 May 31, 2017
1.1.0 May 22, 2017
1.0.1 May 15, 2017
1.0.0 Mar 17, 2017
0.9.1 Mar 17, 2017
0.9.0 Jan 11, 2017
0.8.5 Oct 26, 2016
0.8.4 Oct 05, 2016
0.8.3 Sep 22, 2016
0.8.2 Sep 20, 2016
0.8.1 Sep 16, 2016
0.8.0 Aug 31, 2016
0.7.4 Oct 05, 2016
0.7.3 Sep 22, 2016
0.7.2 Sep 20, 2016
0.7.1 Jul 30, 2016
0.7.0 Jul 30, 2016
0.6.0 Apr 05, 2016
0.5.1 Sep 18, 2015
0.5.0 Sep 08, 2015
0.4.5 Mar 03, 2016
0.4.4 Jul 29, 2015
0.4.3 May 08, 2015
0.4.2 Apr 20, 2015

View Java Class Source Code in JAR file

  1. Download JD-GUI to open JAR file and explore Java source code file (.class .java)
  2. Click menu "File → Open File..." or just drag-and-drop the JAR file in the JD-GUI window biodata-tools-2.1.2-sources.jar file or biodata-tools-2.1.2.jar file.
    Once you open a JAR file, all the java classes in the JAR file will be displayed.
org/
org/opencb/
org/opencb/biodata/
org/opencb/biodata/tools/
org/opencb/biodata/tools/alignment/
org/opencb/biodata/tools/alignment/exceptions/
org/opencb/biodata/tools/alignment/converters/
org/opencb/biodata/tools/alignment/filters/
org/opencb/biodata/tools/alignment/coverage/
org/opencb/biodata/tools/alignment/iterators/
org/opencb/biodata/tools/alignment/stats/
org/opencb/biodata/tools/sequence/
org/opencb/biodata/tools/commons/
org/opencb/biodata/tools/pedigree/
org/opencb/biodata/tools/feature/
org/opencb/biodata/tools/clinical/
org/opencb/biodata/tools/variant/
org/opencb/biodata/tools/variant/metadata/
org/opencb/biodata/tools/variant/exceptions/
org/opencb/biodata/tools/variant/converters/
org/opencb/biodata/tools/variant/converters/avro/
org/opencb/biodata/tools/variant/converters/ga4gh/
org/opencb/biodata/tools/variant/converters/ga4gh/factories/
org/opencb/biodata/tools/variant/converters/proto/
org/opencb/biodata/tools/variant/filters/
org/opencb/biodata/tools/variant/algorithm/
org/opencb/biodata/tools/variant/writers/
org/opencb/biodata/tools/variant/merge/
org/opencb/biodata/tools/variant/simulator/
org/opencb/biodata/tools/variant/iterators/
org/opencb/biodata/tools/variant/scores/
org/opencb/biodata/tools/variant/stats/
org/opencb/biodata/tools/variant/stats/writer/
org/opencb/biodata/tools/variant/normalizer/
org/opencb/biodata/tools/variant/normalizer/extensions/
org/opencb/biodata/tools/alignment/exceptions/AlignmentCoverageException.java
org/opencb/biodata/tools/alignment/converters/SAMRecordToAvroReadAlignmentBiConverter.java
org/opencb/biodata/tools/alignment/converters/SAMRecordToProtoReadAlignmentBiConverter$1.java
org/opencb/biodata/tools/alignment/converters/AlignmentBiConverter.java
org/opencb/biodata/tools/alignment/converters/SAMRecordToProtoReadAlignmentBiConverter.java
org/opencb/biodata/tools/alignment/converters/SAMRecordToAvroReadAlignmentBiConverter$1.java
org/opencb/biodata/tools/alignment/filters/ReadAlignmentFilters.java
org/opencb/biodata/tools/alignment/filters/SamRecordFilters.java
org/opencb/biodata/tools/alignment/filters/AlignmentFilters.java
org/opencb/biodata/tools/alignment/BamUtils$1.java
org/opencb/biodata/tools/alignment/BamManager.java
org/opencb/biodata/tools/alignment/coverage/RegionCoverageCalculator.java
org/opencb/biodata/tools/alignment/coverage/SamRecordRegionCoverageCalculator.java
org/opencb/biodata/tools/alignment/coverage/AvroRegionCoverageCalculator$1.java
org/opencb/biodata/tools/alignment/coverage/AvroRegionCoverageCalculator.java
org/opencb/biodata/tools/alignment/AlignmentOptions.java
org/opencb/biodata/tools/alignment/iterators/SAMRecordToProtoReadAlignmentBamIterator.java
org/opencb/biodata/tools/alignment/iterators/SAMRecordToAvroReadAlignmentBamIterator.java
org/opencb/biodata/tools/alignment/iterators/AvroFileIterator.java
org/opencb/biodata/tools/alignment/iterators/BamIterator.java
org/opencb/biodata/tools/alignment/iterators/SamRecordBamIterator.java
org/opencb/biodata/tools/alignment/BamUtils.java
org/opencb/biodata/tools/alignment/stats/SamRecordAlignmentGlobalStatsCalculator$1.java
org/opencb/biodata/tools/alignment/stats/ProtoAlignmentGlobalStatsCalculator$1.java
org/opencb/biodata/tools/alignment/stats/SequenceStatsCalculator.java
org/opencb/biodata/tools/alignment/stats/SequenceKmers.java
org/opencb/biodata/tools/alignment/stats/AlignmentGlobalStatsCalculator$CIGAR.java
org/opencb/biodata/tools/alignment/stats/SequenceKmersCalculator.java
org/opencb/biodata/tools/alignment/stats/AlignmentGlobalStats.java
org/opencb/biodata/tools/alignment/stats/ProtoAlignmentGlobalStatsCalculator.java
org/opencb/biodata/tools/alignment/stats/AlignmentGlobalStatsCalculator.java
org/opencb/biodata/tools/alignment/stats/SamRecordAlignmentGlobalStatsCalculator.java
org/opencb/biodata/tools/alignment/stats/AvroAlignmentGlobalStatsCalculator$1.java
org/opencb/biodata/tools/alignment/stats/SequenceInfo.java
org/opencb/biodata/tools/alignment/stats/AvroAlignmentGlobalStatsCalculator.java
org/opencb/biodata/tools/alignment/stats/SequenceStats.java
org/opencb/biodata/tools/sequence/FastqRecordToReadBiConverter.java
org/opencb/biodata/tools/sequence/FastaIndexManager.java
org/opencb/biodata/tools/sequence/FastaIndex.java
org/opencb/biodata/tools/sequence/SequenceAdaptor.java
org/opencb/biodata/tools/sequence/SamtoolsFastaIndex.java
org/opencb/biodata/tools/commons/CommonsFilters.java
org/opencb/biodata/tools/commons/ChunkFrequencyManager.java
org/opencb/biodata/tools/commons/Converter.java
org/opencb/biodata/tools/commons/BiConverter.java
org/opencb/biodata/tools/commons/ChunkFrequencyManager$ChunkFrequency.java
org/opencb/biodata/tools/pedigree/MendelianError$GenotypeCode.java
org/opencb/biodata/tools/pedigree/MendelianError.java
org/opencb/biodata/tools/pedigree/ModeOfInheritance.java
org/opencb/biodata/tools/feature/BedManager.java
org/opencb/biodata/tools/feature/WigUtils.java
org/opencb/biodata/tools/feature/BigWigManager.java
org/opencb/biodata/tools/feature/FeatureManager.java
org/opencb/biodata/tools/clinical/DefaultClinicalVariantCreator.java
org/opencb/biodata/tools/clinical/DiseasePanelParsers.java
org/opencb/biodata/tools/clinical/TieringClinicalVariantCreator.java
org/opencb/biodata/tools/clinical/ClinicalVariantCreator.java
org/opencb/biodata/tools/clinical/TeamClinicalVariantCreator.java
org/opencb/biodata/tools/variant/VariantNormalizer$VariantNormalizerConfig.java
org/opencb/biodata/tools/variant/metadata/VariantMetadataManager.java
org/opencb/biodata/tools/variant/metadata/VariantMetadataUtils.java
org/opencb/biodata/tools/variant/VariantVcfHtsjdkReader$1.java
org/opencb/biodata/tools/variant/VariantNormalizer.java
org/opencb/biodata/tools/variant/exceptions/VariantNormalizerException.java
org/opencb/biodata/tools/variant/converters/avro/VariantStatsToTsvConverter.java
org/opencb/biodata/tools/variant/converters/avro/VariantStatsToPopulationFrequencyConverter.java
org/opencb/biodata/tools/variant/converters/avro/VariantStudyMetadataToVCFHeaderConverter.java
org/opencb/biodata/tools/variant/converters/avro/VariantContextToVariantConverter.java
org/opencb/biodata/tools/variant/converters/avro/VCFHeaderToVariantFileHeaderConverter.java
org/opencb/biodata/tools/variant/converters/avro/VCFHeaderToAvroVcfHeaderConverter.java
org/opencb/biodata/tools/variant/converters/avro/VariantAvroToVariantContextConverter.java
org/opencb/biodata/tools/variant/converters/avro/VariantSourceToVCFHeaderConverter.java
org/opencb/biodata/tools/variant/converters/avro/VariantFileHeaderToVCFHeaderConverter.java
org/opencb/biodata/tools/variant/converters/ga4gh/Ga4ghVariantSetConverter.java
org/opencb/biodata/tools/variant/converters/ga4gh/Ga4ghCallSetConverter.java
org/opencb/biodata/tools/variant/converters/ga4gh/factories/AvroGa4GhVariantFactory.java
org/opencb/biodata/tools/variant/converters/ga4gh/factories/ProtoGa4GhVariantFactory.java
org/opencb/biodata/tools/variant/converters/ga4gh/factories/Ga4ghVariantFactory.java
org/opencb/biodata/tools/variant/converters/ga4gh/Ga4ghVariantConverter.java
org/opencb/biodata/tools/variant/converters/VCFExporter.java
org/opencb/biodata/tools/variant/converters/proto/VariantProtoToVariantContextConverter.java
org/opencb/biodata/tools/variant/converters/proto/VariantContextToVariantProtoConverter.java
org/opencb/biodata/tools/variant/converters/proto/VariantAvroToVariantProtoConverter.java
org/opencb/biodata/tools/variant/converters/proto/VcfSliceToVariantListConverter.java
org/opencb/biodata/tools/variant/converters/proto/VcfRecordProtoToVariantConverter.java
org/opencb/biodata/tools/variant/converters/proto/VariantToVcfSliceConverter.java
org/opencb/biodata/tools/variant/converters/proto/VcfRecordProtoToVariantConverter$1.java
org/opencb/biodata/tools/variant/converters/proto/VariantToProtoVcfRecord.java
org/opencb/biodata/tools/variant/converters/VariantContextConverter.java
org/opencb/biodata/tools/variant/filters/VariantAvroFilters.java
org/opencb/biodata/tools/variant/filters/VariantFilters.java
org/opencb/biodata/tools/variant/filters/VariantProtoFilters.java
org/opencb/biodata/tools/variant/filters/VariantContextFilters.java
org/opencb/biodata/tools/variant/VariantOptions.java
org/opencb/biodata/tools/variant/VariantNormalizer$1.java
org/opencb/biodata/tools/variant/VariantDeduplicationTask$DuplicatedVariantsResolver.java
org/opencb/biodata/tools/variant/VariantDeduplicationTask$CircularSortedArrayQueue.java
org/opencb/biodata/tools/variant/algorithm/IdentityByStateClustering$SamplePairConsumer.java
org/opencb/biodata/tools/variant/algorithm/IdentityByDescentClustering.java
org/opencb/biodata/tools/variant/algorithm/IdentityByStateClustering.java
org/opencb/biodata/tools/variant/VariantSorterTask.java
org/opencb/biodata/tools/variant/VcfFileReader$1.java
org/opencb/biodata/tools/variant/VariantDeduplicationTask.java
org/opencb/biodata/tools/variant/VariantJsonReader.java
org/opencb/biodata/tools/variant/VcfManager.java
org/opencb/biodata/tools/variant/writers/EnsemblVepOutputWriter.java
org/opencb/biodata/tools/variant/merge/VariantAlternateRearranger$Configuration.java
org/opencb/biodata/tools/variant/merge/VariantMerger.java
org/opencb/biodata/tools/variant/merge/VariantMerger$1.java
org/opencb/biodata/tools/variant/merge/VariantAlternateRearranger$1.java
org/opencb/biodata/tools/variant/merge/VariantAlternateRearranger.java
org/opencb/biodata/tools/variant/simulator/VariantSimulatorConfiguration.java
org/opencb/biodata/tools/variant/simulator/VariantSimulator.java
org/opencb/biodata/tools/variant/LeftAligner$LeftAlignmentWindow.java
org/opencb/biodata/tools/variant/VcfUtils.java
org/opencb/biodata/tools/variant/iterators/VariantContextToProtoVariantVcfIterator.java
org/opencb/biodata/tools/variant/iterators/VariantContextToAvroVariantVcfIterator.java
org/opencb/biodata/tools/variant/iterators/VcfIterator.java
org/opencb/biodata/tools/variant/iterators/VariantContextVcfIterator.java
org/opencb/biodata/tools/variant/VariantReferenceBlockCreatorTask.java
org/opencb/biodata/tools/variant/VariantVcfHtsjdkReader.java
org/opencb/biodata/tools/variant/scores/HardyWeinbergScoreCalculatorTask.java
org/opencb/biodata/tools/variant/scores/AcmgVariantClassifier.java
org/opencb/biodata/tools/variant/stats/VariantStatsCalculator$1.java
org/opencb/biodata/tools/variant/stats/VariantAggregatedEVSStatsCalculator.java
org/opencb/biodata/tools/variant/stats/VariantStatsCalculator.java
org/opencb/biodata/tools/variant/stats/AggregationUtils.java
org/opencb/biodata/tools/variant/stats/VariantAggregatedExacStatsCalculator.java
org/opencb/biodata/tools/variant/stats/VariantAggregatedStatsCalculator.java
org/opencb/biodata/tools/variant/stats/VariantSetStatsCalculator.java
org/opencb/biodata/tools/variant/stats/VariantStatsPedigree.java
org/opencb/biodata/tools/variant/stats/SampleVariantStatsCalculator.java
org/opencb/biodata/tools/variant/stats/writer/VariantStatsTsvExporter.java
org/opencb/biodata/tools/variant/stats/writer/VariantStatsPopulationFrequencyExporter.java
org/opencb/biodata/tools/variant/VcfFileReader.java
org/opencb/biodata/tools/variant/normalizer/extensions/VafVariantNormalizerExtension.java
org/opencb/biodata/tools/variant/normalizer/extensions/VariantNormalizerExtensionFileToSample.java
org/opencb/biodata/tools/variant/normalizer/extensions/VariantNormalizerExtensionFactory.java
org/opencb/biodata/tools/variant/normalizer/extensions/SvVariantNormalizerExtension.java
org/opencb/biodata/tools/variant/normalizer/extensions/CustomNormalizerExtension.java
org/opencb/biodata/tools/variant/normalizer/extensions/VariantNormalizerExtension.java
org/opencb/biodata/tools/variant/LeftAligner.java
org/opencb/biodata/tools/variant/VariantNormalizer$VariantKeyFields.java
META-INF/maven/
META-INF/maven/org.opencb.biodata/
META-INF/maven/org.opencb.biodata/biodata-tools/
META-INF/maven/org.opencb.biodata/biodata-tools/pom.xml
META-INF/maven/org.opencb.biodata/biodata-tools/pom.properties

View Javadoc in JAR file

  1. Download WinRAR to extract JAR file.
  2. Navigate to biodata-tools-2.1.2-javadoc.jar you want to extract in File Explorer.
  3. Right-click biodata-tools-2.1.2-sources.jar file → Select "Extract Here" in the drop-down context menu.
  4. Navigate to biodata-tools-2.1.2-javadoc extracted folder in File Explorer.
  5. Open index.html file with your Browser to view the contents of the javadoc HTML files.