• 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 â–¾
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 AddLogStatements
branch: AddLogStatements
CHANGE BRANCH
x
Reset
  • 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
  • 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
1086

push

travis-ci

jean-philippe-martin
added logging to help with perf debugging

15381 of 21002 relevant lines covered (73.24%)

1.46 hits per line

Relevant lines Covered
Build:
Build:
21002 RELEVANT LINES 15381 COVERED LINES
1.46 HITS PER LINE
Source Files on AddLogStatements
Detailed source file information is not available for this build.

Recent builds

Builds Branch Commit Type Ran Committer Via Coverage
1086 AddLogStatements added logging to help with perf debugging push 10 Jul 2015 06:01PM UTC jean-philippe-martin travis-ci pending completion  
1083 AddLogStatements removing whitespace push 10 Jul 2015 05:17PM UTC jean-philippe-martin travis-ci pending completion  
1081 AddLogStatements m push 09 Jul 2015 08:40PM UTC jean-philippe-martin travis-ci pending completion  
1077 AddLogStatements added a unit test push 09 Jul 2015 07:48PM UTC jean-philippe-martin travis-ci pending completion  
1072 AddLogStatements cleanup push 09 Jul 2015 12:24AM UTC jean-philippe-martin travis-ci pending completion  
1071 AddLogStatements added logging to help with perf debugging. push 09 Jul 2015 12:15AM UTC jean-philippe-martin 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