• Home
  • Features
  • Pricing
  • Docs
  • Announcements
  • Sign In

broadinstitute / hellbender
73%
master: 81%

Build:
Build:
LAST BUILD BRANCH: dr_disentangle_spark_and_dataflow
DEFAULT BRANCH: master
Repo Added 06 Jan 2015 07:33PM UTC
Files 539
Badge
Embed ▾
README BADGES
x

If you need to use a raster PNG badge, change the '.svg' to '.png' in the link

Markdown

Textile

RDoc

HTML

Rst

LAST BUILD ON BRANCH dr_add_tests_to_ref_api_source
branch: dr_add_tests_to_ref_api_source
CHANGE BRANCH
x
Reset
  • dr_add_tests_to_ref_api_source
  • 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_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

pending completion
1134

push

travis-ci

droazen
More unit tests for RefAPISource

Note that these tests only run if the TestNG "cloud" group is removed
from the "excludeGroups" list in build.gradle

15758 of 21494 relevant lines covered (73.31%)

0.73 hits per line

Relevant lines Covered
Build:
Build:
21494 RELEVANT LINES 15758 COVERED LINES
0.73 HITS PER LINE
Source Files on dr_add_tests_to_ref_api_source
  • List 0
  • Changed 0
  • Source Changed 0
  • Coverage Changed 0
Coverage ∆ File Lines Relevant Covered Missed Hits/Line

Recent builds

Builds Branch Commit Type Ran Committer Via Coverage
1134 dr_add_tests_to_ref_api_source More unit tests for RefAPISource Note that these tests only run if the TestNG "cloud" group is removed from the "excludeGroups" list in build.gradle push 14 Jul 2015 06:10PM UTC droazen travis-ci pending completion  
See All Builds (2517)
  • Repo on GitHub
STATUS · Troubleshooting · Open an Issue · Sales · Support · CAREERS · ENTERPRISE · START FREE · SCHEDULE DEMO
ANNOUNCEMENTS · TWITTER · TOS & SLA · Supported CI Services · What's a CI service? · Automated Testing

© 2025 Coveralls, Inc