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

broadinstitute / hellbender
80%
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_remove_protective_copies_from_spark_bqsr
branch: dr_remove_protective_copies_from_spark_bqsr
CHANGE BRANCH
x
Reset
  • dr_remove_protective_copies_from_spark_bqsr
  • 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_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
2680

push

travis-ci

droazen
Remove protective copying operations from the spark BQSR

Turns out these may not be needed in spark (unlike in dataflow).
Let's get expert confirmation that this is the case, however,
before merging.

4 of 4 new or added lines in 2 files covered. (100.0%)

21968 of 27327 relevant lines covered (80.39%)

0.97 hits per line

Relevant lines Covered
Build:
Build:
27327 RELEVANT LINES 21968 COVERED LINES
0.97 HITS PER LINE
Source Files on dr_remove_protective_copies_from_spark_bqsr
  • List 0
  • Changed 1
  • Source Changed 1
  • Coverage Changed 1
Coverage ∆ File Lines Relevant Covered Missed Hits/Line

Recent builds

Builds Branch Commit Type Ran Committer Via Coverage
2680 dr_remove_protective_copies_from_spark_bqsr Remove protective copying operations from the spark BQSR Turns out these may not be needed in spark (unlike in dataflow). Let's get expert confirmation that this is the case, however, before merging. push 25 Sep 2015 03:12PM UTC droazen travis-ci pending completion  
2678 dr_remove_protective_copies_from_spark_bqsr Remove protective copying operations from the spark BQSR Turns out these may not be needed in spark (unlike in dataflow). Let's get expert confirmation that this is the case, however, before merging. push 25 Sep 2015 02:41PM 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