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as_DSDEGP-2191_find_all_broken_bcls_before_dying
as_fix_liftover_docs
bcmaster
bt_make_SamFileTester_accessible
bw2-no-change-in-clp-output-tester
can_bed2intervallist_stdin_check
ck_CompareSAMs_sophisticated_dup_marking
ck_ExtractIlluminaBarcodes_WithCache
ck_Gff3_RnaSeqMetrics
ck_Test_MBA_ReverseStrandMappedReadInUnmappedBam
ck_identify_contaminant
ck_mba_single_overlap_test_example
cn_build_bam_index
cn_fix_fastq2sam
cn_google_clou_nio
cn_java_17_doclets
cn_legacy_args
cn_nio_reference_files_cn
cn_nio_reference_files_takuto
cn_nio_reference_rebase
cn_vcf_refactor_temp
db_pad_hopping
dm-extract-illumina-barcodes-timeout
eb_make_even_intervals
gg_AddOptionalParameterToGtcToVcf
gg_GL-14_GtcToVcf
gg_GL-53_ContaminationQcMetric
gg_GL-853_HaveVcfToAdpcHandleMultiSampleVcfs
gg_UpdateTo_htsjdk_2.23.0
ggjw_PO-40902_FixEIB
gh-pages
he_CheckScram
he_YossiSort
he_nowhere
js_lift_over_gvcf
jts_collectsamerrormetrics_updates
ks_pom_compile
kt_SamToFastqTest_fix
lb_better_jre_error_message
lb_make_it_a_multi
lb_refactoring_CompareSAMs
lb_remove_ga4gh_argument
lb_repro_no_r
lb_requester_pays
lb_test
lb_test_htsjdk
lb_test_htsjdk_release_candidate
lb_test_htsjdk_update
lb_update_to_21
ldg_MTvariantMetrics
ldg_intervalToolsTypo
lh_ROI_on_MD_set_size_hist
lh_dup_set_size
lh_duplicate_set_count
lh_duplicate_set_index_tag
lh_fingerprint
lh_representative_read_tag_rebase_TEST
lh_representative_read_tags2
lh_roi_duplicate
master
mf_theoretical_sensitivity_improvements
mg_collectrnaseqmetrics_make_ignore_sequence_optional
mg_htsjdk_bump
mg_longread_error_reporting
mg_longread_error_reporting_dev
mg_longread_error_reporting_dev_query
mg_longread_error_reporting_iteration_indel_stratifiers
mg_longread_error_reporting_iteration_indel_stratifiers_multiple_vcfs
mg_longread_error_reporting_with_read_output
ms_HaplotypeMap_bug_fix
ms_collectsamerrormetrics_bugfix
ms_flowcell_position
ms_readnames
nh_alt_contig_pattern
nh_c_r_s_p_test
nh_eib_barcode_mismatch
nh_make_vcf_optional
nh_mark_duplicates_with_low_q_end
phs_po-17291_indescriminate_periods
sc_gl-1338_GTF_files_in_CollectRnaSeqMetrics
sh_expose_bq_checkFP
sl_crosscheckfingerprints_docs
tl_sortvcf_dict_validation_stringency
trivy-action
ts_annotated
ts_cloud_part2
ts_disjoint_intervals
ts_dup_rate
ts_het_sensitivity
ts_make_trimming_optional
ts_md_rna_test
ts_md_umi
ts_no_mate_number
ts_revertsam_lee
ts_ribosome
ts_rna_bam
ts_skip_dict_check
ts_stratify
ts_update_rna
ultima.flow.mods.squash
1.03
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1.100
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1.14
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1.15
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1.21
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