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master
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AddLogStatements
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BRUTest
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CTBuilder
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ak_AddOrReplaceReadGroups_test
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ak_Annotator
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ak_CalculateReadGroupChecksum_tests
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ak_CigarUtils_tests
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ak_CollectBaseDistributionByCycle_tests
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ak_CollectQualityYieldMetrics_test
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ak_CollectWgsMetrics_test
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ak_LeftAlignIndels
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ak_LiftOverIntervalList_test
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ak_MeanQualityByCycle_spark2
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ak_MisencodedBaseQualityReadTransformer
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ak_QualityScoreDistribution_tests
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ak_ReadLikelihoodCalculationEngine
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ak_ReplaceSamHeader_test
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ak_VariantAnnotatorEngine
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ak_add_cloudera
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ak_add_google
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ak_analyzeCovariates
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ak_apply_vqsr_onTranchesBranch
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ak_bqsr_NPE
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ak_bqsr_multiple_site_lists
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ak_bqsr_part2
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ak_bqsr_pipeline_test
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ak_clipReads
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ak_clone
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ak_clp_test
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ak_codecs
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ak_copyright
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ak_countBases_spark
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ak_countReads_spark
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ak_countReads_spark_moreTests
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ak_coverage_spark
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ak_dataflow_codereading
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ak_dead_code_removal
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ak_delete_BamToBfq
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ak_delete_code_not_being_ported_from_picard
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ak_diamonds
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ak_diff_engine
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ak_disable_broken_picard_tests
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ak_enable_ReadCovariatesUnitTest
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ak_exampleVariantWalker
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ak_feature_input
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ak_flagstat_spark
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ak_gatreport
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ak_genotyper
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ak_good_read_filter
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ak_hc_assemblygraph
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ak_improve_testing_coverage
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ak_left_tail_bqsr
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ak_log4j2_xml
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ak_logging_info_in_readme
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ak_malformed_read_filter
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ak_mark_duplicates
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ak_meanqualitybycycle_tests
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ak_pairhmm
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ak_pileup_work
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ak_printReadsOptionsAndTests
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ak_printReads_spark
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ak_readClipperUnitTests
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ak_read_additional_filters
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ak_readme_on_testing
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ak_remove_multiThreading_from_ExtractIlluminaBarcodes
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ak_remove_readFilterTest
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ak_replaceCustomGamma_withApache
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ak_simplify_covariates
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ak_small_readme_edits
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ak_snacks
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ak_some_code_cleanup
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ak_sparkToolName
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ak_splitNCigarReads
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ak_test_LeftAlignIndels
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ak_validate_variants
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ak_variant_filtration
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ak_variant_recalibrator
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ak_variant_walker
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ak_vqsr_tranche_doc
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ak_vqsr_tranches
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ak_vqsr_variant_data_management
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ak_warnings
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ak_wellformed_filter_tests
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akiezun-README-guidelines
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akiezun-readme-style_tweaks
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bh_prune_vcf
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cn_filter_reads
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cn_gatk_read
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cn_haplotype_bamwriter
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cn_log4j_picard
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cn_read_filters
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cn_select_variants
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cn_set_log4j_level
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cn_split_reads
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cs_basicqcmetrics
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da_auth
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da_copy_deps
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da_credential_factory
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da_credentials
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da_dataflow_version_bump
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da_genomics_pipeline_deps
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da_hook_up_mark_dupes
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da_keyed_transforms
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da_less_brittle_dataflow_tests
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da_mark_dupes_fusion_fun
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da_mark_dupes_refactor
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da_playground2
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da_read_pipeline
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da_spark_integration
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da_spark_integration_test
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da_spark_local
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da_spark_mark_dupes
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da_spark_markdupes
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da_spark_skeleton
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da_spark_tuning
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da_variant_start
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db_covariance
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db_genotyper_logarithms
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db_kill_median
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db_natural_log
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db_target_collection
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dek_CollectJumpingLibraryMetrics_IT
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dek_CollectTargetedPcrMetrics_IT
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dek_RenameSampleInVCF_test
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dek_normalizeFasta_IT
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dr_activate_cloud_tests_for_real
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dr_add_dbsnp_vcf_for_chr1
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dr_add_intellij_setup_to_readme
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dr_add_large_test_files_with_git-lfs
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dr_add_tests_to_ref_api_source
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dr_add_yarn_executor_overhead
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dr_artificialreadutils_specify_contig_in_artificial_uuid_methods
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dr_authenticated_pipeline_options_test_helper
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dr_change_logging_level
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dr_clarify_testing_requirements_for_tools
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dr_customize_reference_window_in_dataflow_sharding
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dr_disable_parallel_tests
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dr_disentangle_spark_and_dataflow
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dr_dummy_feature
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dr_dynamic_window_in_referencecontext
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dr_expose_feature_headers
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dr_extract_readssource_class
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dr_feature_support
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dr_feature_traversal_by_intervals
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dr_featureinput_tostring
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dr_features_as_intervals
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dr_fix_featuredatasource_caching
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dr_fix_gradle_fatjar
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dr_fix_ioutils_createtempfile
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dr_fix_sequence_dict_check_in_bqsr_dataflow
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dr_gatkcoder_test
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dr_gatksparktool
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dr_handle_reads_that_consume_no_ref_bases_in_readwalkers
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dr_initial_traversal_engine
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dr_interval_walker
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dr_lb_spark_bqsr
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dr_lb_spark_bqsr_bak
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dr_lb_spark_test
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dr_make_context_objects_non_optional
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dr_more_contigs_in_artificialreadutils
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dr_move_simpleinterval_to_hellbender
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dr_output_logging_messages_during_engine_initialization
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dr_port_tools_to_readwalker_interface
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dr_read_adapter_equals_tweak
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dr_read_common_interfaces
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dr_reenable_broken_bqsr_test
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dr_refactor_exceptions
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dr_relax_sequence_dictionary_checks
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dr_remove_com_sun_import
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dr_remove_protective_copies_from_spark_bqsr
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dr_rename_sam_utils_package
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dr_rev_htsjdk_to_1.132
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dr_rev_htsjdk_to_1.139
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dr_rev_htsjkd_to_1.138
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dr_spark_pipeline_markdupes_sharding_fix
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dr_stub_reads_pipelineTest
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dr_test_cram_with_intervals
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ek_comment_802
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ek_countreads_590
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ek_craminttests_675
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ek_cramreference_606
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ek_cramreference_677
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ek_fixtests_659
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ek_fixwarnings_359_377
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ek_locatable_559
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ek_npe_273
-
ek_refdict_802
-
ek_seqdict_101
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ek_unmapped_766
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ek_wordcount_537
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expand_dataflow_test_contigs
-
firstCheckin
-
fix_gradle_one_more_time
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gvda_authorlist_sorting
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gvda_current_gatk_links
-
issue-948-option-duplicate-reads-exomereadcounts
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jp_ApiMeansNoSecrets
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jp_ApplyBQSR
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jp_ApplyBQSRCloud2
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jp_BaseRecalOutputs
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jp_CEU_test_data
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jp_CloudTests
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jp_DFBR_cloud
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jp_DF_BaseRecalibrator
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jp_FewReadsWriter
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jp_ReadSourceStringency
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jp_RecalibrationTablesMerger
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jp_adding_first_test
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jp_apply_skel_rebased
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jp_badtype_repro
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jp_bigger_apiref
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jp_binarysearch
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jp_bqsr_newtest
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jp_bqsr_skel_rerebased
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jp_consistentWhitespace
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jp_enable_working_tests
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jp_fixFatJar
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jp_fix_BaseRecal_test
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jp_fix_refapisource
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jp_fix_secrets
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jp_intervalsskiplist
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jp_perf_apply2
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jp_perf_br
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jp_perf_markdups
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jp_readstest
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jp_sam2gatk
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jp_skel_01
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jp_skel_03
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jp_start_with_mandatory_tests
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jp_start_with_mandatory_tests_rebased
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jp_start_with_mandatory_tests_rebased2
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jp_testReadWrite
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jp_uprev_genomics-dataflow
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jpm_bqsr
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jt_typo
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ks_print_reads_by_read_group
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lb_add_key_for_travis
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lb_add_packing_command
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lb_add_rm_rf_shutdownhook_for_da
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lb_bqsr_scaling_tweaks
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lb_change_cran_mirror
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lb_codeship
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lb_coveralls
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lb_dataflow
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lb_dataflow_dependencies
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lb_delete_commandlineparse_exception
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lb_delete_compare_metrics
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lb_delete_illumina_test_data
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lb_delete_unused_classes_relating_to_MarkDuplicates
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lb_dockerizing_for_execution_service
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lb_enable_circle_ci
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lb_error_message_when_R_doesnt_exist
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lb_exception_hidden_by_onShutdown_exception
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lb_expose_test_classes
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lb_fix_137_truncate_names_with_whitespace
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lb_fix_ambigous_parse_with_optional_args
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lb_fix_bqsr_concurrency_issue
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lb_fix_build_failure_from_no_git
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lb_fix_default_collections
-
lb_fix_documentation_error
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lb_fix_last_4_warnings
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lb_fix_monstrous_error_message
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lb_fix_required_collections
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lb_fix_travis_button
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lb_gatktool_argument_collection_enhancement
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lb_hide_secret_key
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lb_htsjdk_to_130
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lb_improve_cli_output_for_collections
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lb_improve_parsing_errors
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lb_improved_R_installation
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lb_insertSizeMetricDataflow
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lb_java_logger_levels
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lb_killing_warnings_again
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lb_limit_circle_ci_gradle_memory
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lb_lower_git_lfs_usage
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lb_lsystem
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lb_mail_test_result
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lb_make_working_cloud_tests_mandatory
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lb_mavenization
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lb_minor_utils_cleanups
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lb_misencoded_base_test_update
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lb_move_placement_of_travis_wait
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lb_move_testSortingFile_somewhere_sensible
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lb_move_unreliable_test_to_dataflow_todo
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lb_only_download_gsalib_when_needed
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lb_optimize_GATKRead_getLength
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lb_option_to_run_all_tests
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lb_output_failed_tests
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lb_parallel_tests
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lb_port_gvcfwriter
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lb_r_installation_refactoring
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lb_r_output_improvement
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lb_reduce_test_time_for_SplitNCigarReads
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lb_reinstate_transformers_and_filters
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lb_remove_deprecated
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lb_remove_encrypted_key_for_now
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lb_remove_min_max_elems_cli
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lb_remove_sudo
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lb_remove_the_vampire_that_haunts_valentine
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lb_remove_unecessary_gradle_download
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lb_remove_unused_genotypeutils
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lb_rename_option
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lb_rename_usage_short
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lb_replace_TestPipeline_with_GatkTestPipeline
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lb_replace_file_create_temp_file
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lb_return_values
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lb_scale_back_R
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lb_scaling
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lb_simple_interval_constructor
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lb_sort_dependencies
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lb_stop_creating_test_file_in_basedir
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lb_suppress_warnings
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lb_test_speedup
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lb_transfer
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lb_travis_container_build
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lb_travis_lfs
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lb_unix_style_options
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lb_update_ReadSource_for_public_consumption
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lb_update_dependencies
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lb_update_gradle_to_2.7
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lb_update_htsjdk
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lb_update_license_to_bsd
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lb_update_sam_header
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lb_update_to_central_htsjdk
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lb_update_to_snapshot_google_http
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lb_updating_dataflow_sdk_and_others
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lb_upload_test_reports
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lb_version_number
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lbergelson-readme-update
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mds_cleanup_picard_package
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mds_fix_compare_sams
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mds_fix_picard_issues
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mds_migrate_picard_sam
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mds_picard_sam_2
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mds_port_all_the_things
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mds_resync_picard_sam
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mds_update_integration_test
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mds_vectorize_coveralls_badge
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tn_mark_duplicates
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tw_hadoop_bam_writer
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tw_hadoop_references
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tw_hadoop_unmapped_reads
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tw_hadoop_use_seq_dict
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tw_hadoop_variants
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tw_local_base_recalibrator_test
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tw_parallelism_comment
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tw_r_groups
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tw_shared_spark_context
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tw_spark_fix_adam_deps
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tw_spark_mark_dupes_sharded
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tw_spark_markdupes
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tw_spark_markdupes_optimization
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tw_spark_sam_record_optimization
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tw_spark_shadowjar_fix
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tw_spark_sort_bam
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tw_spark_test_group
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tw_test
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tw_ul_spark_bqsr
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ul_parquet_io
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ul_random_uuid_bdg
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vrr_exome_depth
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vrr_exons_from_file
-
vrr_feature_iterators
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vrr_help_generation_on_enum_options_change_toSring_to_name
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vrr_mark_duplicates_erc
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vrr_pcov_erc
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vrr_remove_genomeloc_from_erc
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wb_copyright
CHANGE BRANCH
x
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master
- AddLogStatements
- BRUTest
- CTBuilder
- ak_AddOrReplaceReadGroups_test
- ak_Annotator
- ak_CalculateReadGroupChecksum_tests
- ak_CigarUtils_tests
- ak_CollectBaseDistributionByCycle_tests
- ak_CollectQualityYieldMetrics_test
- ak_CollectWgsMetrics_test
- ak_LeftAlignIndels
- ak_LiftOverIntervalList_test
- ak_MeanQualityByCycle_spark2
- ak_MisencodedBaseQualityReadTransformer
- ak_QualityScoreDistribution_tests
- ak_ReadLikelihoodCalculationEngine
- ak_ReplaceSamHeader_test
- ak_VariantAnnotatorEngine
- ak_add_cloudera
- ak_add_google
- ak_analyzeCovariates
- ak_apply_vqsr_onTranchesBranch
- ak_bqsr_NPE
- ak_bqsr_multiple_site_lists
- ak_bqsr_part2
- ak_bqsr_pipeline_test
- ak_clipReads
- ak_clone
- ak_clp_test
- ak_codecs
- ak_copyright
- ak_countBases_spark
- ak_countReads_spark
- ak_countReads_spark_moreTests
- ak_coverage_spark
- ak_dataflow_codereading
- ak_dead_code_removal
- ak_delete_BamToBfq
- ak_delete_code_not_being_ported_from_picard
- ak_diamonds
- ak_diff_engine
- ak_disable_broken_picard_tests
- ak_enable_ReadCovariatesUnitTest
- ak_exampleVariantWalker
- ak_feature_input
- ak_flagstat_spark
- ak_gatreport
- ak_genotyper
- ak_good_read_filter
- ak_hc_assemblygraph
- ak_improve_testing_coverage
- ak_left_tail_bqsr
- ak_log4j2_xml
- ak_logging_info_in_readme
- ak_malformed_read_filter
- ak_mark_duplicates
- ak_meanqualitybycycle_tests
- ak_pairhmm
- ak_pileup_work
- ak_printReadsOptionsAndTests
- ak_printReads_spark
- ak_readClipperUnitTests
- ak_read_additional_filters
- ak_readme_on_testing
- ak_remove_multiThreading_from_ExtractIlluminaBarcodes
- ak_remove_readFilterTest
- ak_replaceCustomGamma_withApache
- ak_simplify_covariates
- ak_small_readme_edits
- ak_snacks
- ak_some_code_cleanup
- ak_sparkToolName
- ak_splitNCigarReads
- ak_test_LeftAlignIndels
- ak_validate_variants
- ak_variant_filtration
- ak_variant_recalibrator
- ak_variant_walker
- ak_vqsr_tranche_doc
- ak_vqsr_tranches
- ak_vqsr_variant_data_management
- ak_warnings
- ak_wellformed_filter_tests
- akiezun-README-guidelines
- akiezun-readme-style_tweaks
- bh_prune_vcf
- cn_filter_reads
- cn_gatk_read
- cn_haplotype_bamwriter
- cn_log4j_picard
- cn_read_filters
- cn_select_variants
- cn_set_log4j_level
- cn_split_reads
- cs_basicqcmetrics
- da_auth
- da_copy_deps
- da_credential_factory
- da_credentials
- da_dataflow_version_bump
- da_genomics_pipeline_deps
- da_hook_up_mark_dupes
- da_keyed_transforms
- da_less_brittle_dataflow_tests
- da_mark_dupes_fusion_fun
- da_mark_dupes_refactor
- da_playground2
- da_read_pipeline
- da_spark_integration
- da_spark_integration_test
- da_spark_local
- da_spark_mark_dupes
- da_spark_markdupes
- da_spark_skeleton
- da_spark_tuning
- da_variant_start
- db_covariance
- db_genotyper_logarithms
- db_kill_median
- db_natural_log
- db_target_collection
- dek_CollectJumpingLibraryMetrics_IT
- dek_CollectTargetedPcrMetrics_IT
- dek_RenameSampleInVCF_test
- dek_normalizeFasta_IT
- dr_activate_cloud_tests_for_real
- dr_add_dbsnp_vcf_for_chr1
- dr_add_intellij_setup_to_readme
- dr_add_large_test_files_with_git-lfs
- dr_add_tests_to_ref_api_source
- dr_add_yarn_executor_overhead
- dr_artificialreadutils_specify_contig_in_artificial_uuid_methods
- dr_authenticated_pipeline_options_test_helper
- dr_change_logging_level
- dr_clarify_testing_requirements_for_tools
- dr_customize_reference_window_in_dataflow_sharding
- dr_disable_parallel_tests
- dr_disentangle_spark_and_dataflow
- dr_dummy_feature
- dr_dynamic_window_in_referencecontext
- dr_expose_feature_headers
- dr_extract_readssource_class
- dr_feature_support
- dr_feature_traversal_by_intervals
- dr_featureinput_tostring
- dr_features_as_intervals
- dr_fix_featuredatasource_caching
- dr_fix_gradle_fatjar
- dr_fix_ioutils_createtempfile
- dr_fix_sequence_dict_check_in_bqsr_dataflow
- dr_gatkcoder_test
- dr_gatksparktool
- dr_handle_reads_that_consume_no_ref_bases_in_readwalkers
- dr_initial_traversal_engine
- dr_interval_walker
- dr_lb_spark_bqsr
- dr_lb_spark_bqsr_bak
- dr_lb_spark_test
- dr_make_context_objects_non_optional
- dr_more_contigs_in_artificialreadutils
- dr_move_simpleinterval_to_hellbender
- dr_output_logging_messages_during_engine_initialization
- dr_port_tools_to_readwalker_interface
- dr_read_adapter_equals_tweak
- dr_read_common_interfaces
- dr_reenable_broken_bqsr_test
- dr_refactor_exceptions
- dr_relax_sequence_dictionary_checks
- dr_remove_com_sun_import
- dr_remove_protective_copies_from_spark_bqsr
- dr_rename_sam_utils_package
- dr_rev_htsjdk_to_1.132
- dr_rev_htsjdk_to_1.139
- dr_rev_htsjkd_to_1.138
- dr_spark_pipeline_markdupes_sharding_fix
- dr_stub_reads_pipelineTest
- dr_test_cram_with_intervals
- ek_comment_802
- ek_countreads_590
- ek_craminttests_675
- ek_cramreference_606
- ek_cramreference_677
- ek_fixtests_659
- ek_fixwarnings_359_377
- ek_locatable_559
- ek_npe_273
- ek_refdict_802
- ek_seqdict_101
- ek_unmapped_766
- ek_wordcount_537
- expand_dataflow_test_contigs
- firstCheckin
- fix_gradle_one_more_time
- gvda_authorlist_sorting
- gvda_current_gatk_links
- issue-948-option-duplicate-reads-exomereadcounts
- jp_ApiMeansNoSecrets
- jp_ApplyBQSR
- jp_ApplyBQSRCloud2
- jp_BaseRecalOutputs
- jp_CEU_test_data
- jp_CloudTests
- jp_DFBR_cloud
- jp_DF_BaseRecalibrator
- jp_FewReadsWriter
- jp_ReadSourceStringency
- jp_RecalibrationTablesMerger
- jp_adding_first_test
- jp_apply_skel_rebased
- jp_badtype_repro
- jp_bigger_apiref
- jp_binarysearch
- jp_bqsr_newtest
- jp_bqsr_skel_rerebased
- jp_consistentWhitespace
- jp_enable_working_tests
- jp_fixFatJar
- jp_fix_BaseRecal_test
- jp_fix_refapisource
- jp_fix_secrets
- jp_intervalsskiplist
- jp_perf_apply2
- jp_perf_br
- jp_perf_markdups
- jp_readstest
- jp_sam2gatk
- jp_skel_01
- jp_skel_03
- jp_start_with_mandatory_tests
- jp_start_with_mandatory_tests_rebased
- jp_start_with_mandatory_tests_rebased2
- jp_testReadWrite
- jp_uprev_genomics-dataflow
- jpm_bqsr
- jt_typo
- ks_print_reads_by_read_group
- lb_add_key_for_travis
- lb_add_packing_command
- lb_add_rm_rf_shutdownhook_for_da
- lb_bqsr_scaling_tweaks
- lb_change_cran_mirror
- lb_codeship
- lb_coveralls
- lb_dataflow
- lb_dataflow_dependencies
- lb_delete_commandlineparse_exception
- lb_delete_compare_metrics
- lb_delete_illumina_test_data
- lb_delete_unused_classes_relating_to_MarkDuplicates
- lb_dockerizing_for_execution_service
- lb_enable_circle_ci
- lb_error_message_when_R_doesnt_exist
- lb_exception_hidden_by_onShutdown_exception
- lb_expose_test_classes
- lb_fix_137_truncate_names_with_whitespace
- lb_fix_ambigous_parse_with_optional_args
- lb_fix_bqsr_concurrency_issue
- lb_fix_build_failure_from_no_git
- lb_fix_default_collections
- lb_fix_documentation_error
- lb_fix_last_4_warnings
- lb_fix_monstrous_error_message
- lb_fix_required_collections
- lb_fix_travis_button
- lb_gatktool_argument_collection_enhancement
- lb_hide_secret_key
- lb_htsjdk_to_130
- lb_improve_cli_output_for_collections
- lb_improve_parsing_errors
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- lb_insertSizeMetricDataflow
- lb_java_logger_levels
- lb_killing_warnings_again
- lb_limit_circle_ci_gradle_memory
- lb_lower_git_lfs_usage
- lb_lsystem
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- lb_mavenization
- lb_minor_utils_cleanups
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- lb_move_placement_of_travis_wait
- lb_move_testSortingFile_somewhere_sensible
- lb_move_unreliable_test_to_dataflow_todo
- lb_only_download_gsalib_when_needed
- lb_optimize_GATKRead_getLength
- lb_option_to_run_all_tests
- lb_output_failed_tests
- lb_parallel_tests
- lb_port_gvcfwriter
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- lb_r_output_improvement
- lb_reduce_test_time_for_SplitNCigarReads
- lb_reinstate_transformers_and_filters
- lb_remove_deprecated
- lb_remove_encrypted_key_for_now
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- lb_remove_sudo
- lb_remove_the_vampire_that_haunts_valentine
- lb_remove_unecessary_gradle_download
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- lb_replace_TestPipeline_with_GatkTestPipeline
- lb_replace_file_create_temp_file
- lb_return_values
- lb_scale_back_R
- lb_scaling
- lb_simple_interval_constructor
- lb_sort_dependencies
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- lb_suppress_warnings
- lb_test_speedup
- lb_transfer
- lb_travis_container_build
- lb_travis_lfs
- lb_unix_style_options
- lb_update_ReadSource_for_public_consumption
- lb_update_dependencies
- lb_update_gradle_to_2.7
- lb_update_htsjdk
- lb_update_license_to_bsd
- lb_update_sam_header
- lb_update_to_central_htsjdk
- lb_update_to_snapshot_google_http
- lb_updating_dataflow_sdk_and_others
- lb_upload_test_reports
- lb_version_number
- lbergelson-readme-update
- mds_cleanup_picard_package
- mds_fix_compare_sams
- mds_fix_picard_issues
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- mds_picard_sam_2
- mds_port_all_the_things
- mds_resync_picard_sam
- mds_update_integration_test
- mds_vectorize_coveralls_badge
- tn_mark_duplicates
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- tw_hadoop_references
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- tw_hadoop_use_seq_dict
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- vrr_pcov_erc
- vrr_remove_genomeloc_from_erc
- wb_copyright
travis-ci
achevali22323 of 27566 relevant lines covered (80.98%)
0.98 hits per line
Relevant lines Covered
27566
RELEVANT LINES
22323
COVERED LINES
0.98
HITS PER LINE
Source Files on master
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akiezun
droazen
laserson