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

broadinstitute / hellbender
72%
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 lb_update_ReadSource_for_public_consumption
branch: lb_update_ReadSource_for_public_consumption
CHANGE BRANCH
x
Reset
  • lb_update_ReadSource_for_public_consumption
  • 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_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
315

push

travis-ci

lbergelson
Updating ReadsSource with documentation and tests
We can only test the local file path stuff for now.
Testing bucket bams needs to wait for travis authentication to be worked out.

13295 of 18573 relevant lines covered (71.58%)

0.72 hits per line

Relevant lines Covered
Build:
Build:
18573 RELEVANT LINES 13295 COVERED LINES
0.72 HITS PER LINE
Source Files on lb_update_ReadSource_for_public_consumption
  • List 0
  • Changed 1
  • Source Changed 1
  • Coverage Changed 0
Coverage ∆ File Lines Relevant Covered Missed Hits/Line

Recent builds

Builds Branch Commit Type Ran Committer Via Coverage
315 lb_update_ReadSource_for_public_consumption Updating ReadsSource with documentation and tests We can only test the local file path stuff for now. Testing bucket bams needs to wait for travis authentication to be worked out. push 01 May 2015 06:31PM UTC lbergelson travis-ci pending completion  
284 lb_update_ReadSource_for_public_consumption update push 30 Apr 2015 10:05PM UTC lbergelson 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