broadinstitute / hellbender

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• da_playground2
• 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
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• 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_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
• lb_improved_R_installation
• lb_insertSizeMetricDataflow
• lb_java_logger_levels
• lb_killing_warnings_again
• lb_limit_circle_ci_gradle_memory
• lb_lower_git_lfs_usage
• lb_lsystem
• lb_mail_test_result
• lb_make_working_cloud_tests_mandatory
• lb_mavenization
• lb_minor_utils_cleanups
• lb_misencoded_base_test_update
• 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
• lb_r_installation_refactoring
• lb_r_output_improvement
• lb_reduce_test_time_for_SplitNCigarReads
• lb_reinstate_transformers_and_filters
• lb_remove_deprecated
• lb_remove_encrypted_key_for_now
• lb_remove_min_max_elems_cli
• lb_remove_sudo
• lb_remove_the_vampire_that_haunts_valentine
• lb_remove_unecessary_gradle_download
• lb_remove_unused_genotypeutils
• lb_rename_option
• lb_rename_usage_short
• 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
• lb_stop_creating_test_file_in_basedir
• 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
• master
• mds_cleanup_picard_package
• mds_fix_compare_sams
• mds_fix_picard_issues
• mds_migrate_picard_sam
• mds_picard_sam_2
• mds_port_all_the_things
• mds_resync_picard_sam
• mds_update_integration_test
• mds_vectorize_coveralls_badge
• tn_mark_duplicates
• tw_hadoop_bam_writer
• tw_hadoop_references
• tw_hadoop_unmapped_reads
• tw_hadoop_use_seq_dict
• tw_hadoop_variants
• tw_local_base_recalibrator_test
• tw_parallelism_comment
• tw_r_groups
• tw_shared_spark_context
• tw_spark_fix_adam_deps
• tw_spark_mark_dupes_sharded
• tw_spark_markdupes
• tw_spark_markdupes_optimization
• tw_spark_sam_record_optimization
• tw_spark_shadowjar_fix
• tw_spark_sort_bam
• tw_spark_test_group
• tw_test
• tw_ul_spark_bqsr
• ul_parquet_io
• ul_random_uuid_bdg
• vrr_exome_depth
• vrr_exons_from_file
• vrr_feature_iterators
• vrr_help_generation_on_enum_options_change_toSring_to_name
• vrr_mark_duplicates_erc
• vrr_pcov_erc
• vrr_remove_genomeloc_from_erc
• wb_copyright

Build # 2520

Build Type

push

travis-ci

Committed by davidadamsphd

Commit Message

Finally got it running with reasonable path ordering.

Run Details

21336 of 26762 relevant lines covered (79.72%)

0.95 hits per line