https://github.com/broadinstitute/picard
- HEAD
- refs/heads/as_DSDEGP-2191_find_all_broken_bcls_before_dying
- refs/heads/as_fix_liftover_docs
- refs/heads/bcmaster
- refs/heads/bt_make_SamFileTester_accessible
- refs/heads/bw2-no-change-in-clp-output-tester
- refs/heads/ck_CompareSAMs_sophisticated_dup_marking
- refs/heads/ck_ExtractIlluminaBarcodes_WithCache
- refs/heads/ck_Gff3_RnaSeqMetrics
- refs/heads/ck_Test_MBA_ReverseStrandMappedReadInUnmappedBam
- refs/heads/ck_identify_contaminant
- refs/heads/ck_mba_single_overlap_test_example
- refs/heads/cn_display_common
- refs/heads/cn_fix_fastq2sam
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- refs/heads/dc_update_CrosscheckFingerprints_summary_200915
- refs/heads/dm-extract-illumina-barcodes-timeout
- refs/heads/eb_make_even_intervals
- refs/heads/gg_AddOptionalParameterToGtcToVcf
- refs/heads/gg_GL-14_GtcToVcf
- refs/heads/gg_GL-53_ContaminationQcMetric
- refs/heads/gg_GL-853_HaveVcfToAdpcHandleMultiSampleVcfs
- refs/heads/gg_UpdateTo_htsjdk_2.23.0
- refs/heads/ggjw_PO-40902_FixEIB
- refs/heads/gh-pages
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- refs/heads/he_nowhere
- refs/heads/js_lift_over_gvcf
- refs/heads/jts_collectsamerrormetrics_updates
- refs/heads/kt_SamToFastqTest_fix
- refs/heads/lb_better_jre_error_message
- refs/heads/lb_make_it_a_multi
- refs/heads/lb_refactoring_CompareSAMs
- refs/heads/lb_remove_ga4gh_argument
- refs/heads/lb_repro_no_r
- refs/heads/lb_test
- refs/heads/lb_test_htsjdk
- refs/heads/lb_test_htsjdk_release_candidate
- refs/heads/lb_test_htsjdk_update
- refs/heads/ldg_MTvariantMetrics
- refs/heads/ldg_intervalToolsTypo
- refs/heads/lh_ROI_on_MD_set_size_hist
- refs/heads/lh_dup_set_size
- refs/heads/lh_duplicate_set_count
- refs/heads/lh_duplicate_set_index_tag
- refs/heads/lh_fingerprint
- refs/heads/lh_representative_read_tag_rebase_TEST
- refs/heads/lh_representative_read_tags2
- refs/heads/lh_roi_duplicate
- refs/heads/master
- refs/heads/mf_theoretical_sensitivity_improvements
- refs/heads/mg_collectrnaseqmetrics_make_ignore_sequence_optional
- refs/heads/mg_htsjdk_bump
- refs/heads/mg_longread_error_reporting
- refs/heads/mg_longread_error_reporting_dev
- refs/heads/mg_longread_error_reporting_dev_query
- refs/heads/mg_longread_error_reporting_iteration_indel_stratifiers
- refs/heads/mg_longread_error_reporting_iteration_indel_stratifiers_multiple_vcfs
- refs/heads/mg_longread_error_reporting_with_read_output
- refs/heads/ms_HaplotypeMap_bug_fix
- refs/heads/ms_collectsamerrormetrics_bugfix
- refs/heads/ms_flowcell_position
- refs/heads/ms_readnames
- refs/heads/nh_alt_contig_pattern
- refs/heads/nh_c_r_s_p_test
- refs/heads/nh_collect_sam_error_metrics_extension
- refs/heads/nh_collect_sam_error_metrics_no_vcf
- refs/heads/nh_eib_barcode_mismatch
- refs/heads/nh_make_vcf_optional
- refs/heads/nh_mark_duplicates_with_low_q_end
- refs/heads/phs_po-17291_indescriminate_periods
- refs/heads/sc_gl-1338_GTF_files_in_CollectRnaSeqMetrics
- refs/heads/sh_expose_bq_checkFP
- refs/heads/sl_crosscheckfingerprints_docs
- refs/heads/tl_respect_user_output_choice
- refs/heads/tl_sortvcf_dict_validation_stringency
- refs/heads/trivy-action
- refs/heads/ts_annotated
- refs/heads/ts_disjoint_intervals
- refs/heads/ts_dup_rate
- refs/heads/ts_het_sensitivity
- refs/heads/ts_make_trimming_optional
- refs/heads/ts_md_rna_test
- refs/heads/ts_md_umi
- refs/heads/ts_no_mate_number
- refs/heads/ts_ribosome
- refs/heads/ts_rna_bam
- refs/heads/ts_skip_dict_check
- refs/heads/ts_stratify
- refs/heads/ts_update_rna
- refs/heads/ultima.flow.mods.squash
- refs/heads/vd_GTC_to_VCF
- refs/heads/vdauwera-docpatch-CollectSamErrorMetrics
- refs/heads/yf_add_ReconstructTriosCLPs
- refs/heads/yf_add_contig_not_found_error_to_reorderSam
- refs/heads/yf_add_mba_PG_record
- refs/heads/yf_allow_liftover_intervals_to_break_them
- refs/heads/yf_allow_multiple_dictionaries_in_crosscheck
- refs/heads/yf_consider_MQ0_reads_unmapped_for_MD
- refs/heads/yf_contaminator_from_array_vcf
- refs/heads/yf_detect_cancer
- refs/heads/yf_enable_requester_pays_project
- refs/heads/yf_estimate_coverage_dependence_on_flow
- refs/heads/yf_explore_picard_bug_1523
- refs/heads/yf_fix_MBA_string
- refs/heads/yf_fix_bug_in_MV
- refs/heads/yf_fix_collectwgsmetrics_test
- refs/heads/yf_fix_create_dictionary
- refs/heads/yf_fix_intermittent__STDOUT_failures
- refs/heads/yf_fix_short_overflow_in_MD
- refs/heads/yf_fix_variantcallingMEtrics_vis_a_vis_upstreamdeletions
- refs/heads/yf_harden_clean_sam
- refs/heads/yf_liftover_still_has_issues_with_END_attribute
- refs/heads/yf_ls_CollectRrbsMetricsToSinglePassSamProgram
- refs/heads/yf_make_CollectSamErrorMetrics_work_with_unindexed_vcf
- refs/heads/yf_make_fingerprinting_parallel
- refs/heads/yf_make_subtract_not_merge
- refs/heads/yf_optimize_memory_usage_during_crosscheck
- refs/heads/yf_pickBarbodes
- refs/heads/yf_remove_deprecated_usages
- refs/heads/yf_speed_up_nocall
- refs/tags/1.113
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- refs/tags/2.0.1
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- refs/tags/2.3.0
- refs/tags/2.3.0_buildhotfix
- refs/tags/2.4.0
- refs/tags/2.4.1
- refs/tags/2.5.0
- refs/tags/2.5.0-gradle
- bc_4.13
- BCM
- 2.9.5
- 2.9.4
- 2.9.3
- 2.9.2
- 2.9.1
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- 2.8.3
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Tip revision: 801dbf150036233ffa5d004a6b96250dba3613e7 authored by Michael Gatzen on 07 August 2019, 15:07:03 UTC
Merged bugfix
Merged bugfix
Tip revision: 801dbf1
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| testdata | ||
| .dockerignore | -rw-r--r-- | 179 bytes |
| .gitignore | -rw-r--r-- | 190 bytes |
| .pullapprove.yml | -rw-r--r-- | 284 bytes |
| .travis.yml | -rw-r--r-- | 601 bytes |
| Dockerfile | -rw-r--r-- | 848 bytes |
| LICENSE.txt | -rw-r--r-- | 1.0 KB |
| README.md | -rw-r--r-- | 5.5 KB |
| build.gradle | -rw-r--r-- | 14.2 KB |
| build.xml | -rw-r--r-- | 1.1 KB |
| build_push_docker.sh | -rwxr-xr-x | 849 bytes |
| gradlew | -rwxr-xr-x | 4.9 KB |
| settings.gradle | -rw-r--r-- | 28 bytes |
