dnanexus-rnd / GLnexus

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• 1.1.12-1_add_max_allele_dv
• HEAD
• allow-N-ref
• bcf_bucket_cache
• bcf_bucket_cache_mt
• better-BCF-range-checks
• cli_command_iter_comp
• compare-2-impl-sampleset-range
• create_residuals_file
• delineation-unification-placeholders-v2
• enable_applet_residuals
• genomic_range_buckets
• gln-docker
• import_gvcf_thread_safety
• main
• master
• measure-loss
• measure-loss-debug
• measure_read_amp
• medium-tests
• mlin-AlleleDepthHelper-refactor
• mlin-BCFBucketCache
• mlin-BCFBucketCache-polishing
• mlin-BCFData-optimize-discover-alleles
• mlin-BCFKeyValueData-duplicate-danglers
• mlin-KeyValue-Iterator
• mlin-KeyValue-iterator-nocopy
• mlin-RocksKeyValue-prefix
• mlin-allele-info
• mlin-allele-target-range
• mlin-allele-unifier-v1
• mlin-backout-cache
• mlin-bcfreader-refactor
• mlin-bulk-insert-buffer
• mlin-call-two-overlapping-variants
• mlin-capnp-sites
• mlin-capnproto-0.7.0
• mlin-censor-nocall-format-fields
• mlin-config-yml
• mlin-deepvariant
• mlin-deepvariant-20181109
• mlin-depr-capnp
• mlin-detect-misaligned-indels
• mlin-disable-PL-validation
• mlin-discover-soft-copy-number
• mlin-discovered-alleles-yaml
• mlin-discovery-bias00
• mlin-discovery-unification-quality
• mlin-docker-pr-build
• mlin-dv-noncalled
• mlin-dv-partial-data
• mlin-dv-pl
• mlin-etl-folders
• mlin-fine-grain-RNC
• mlin-fix-unification-model
• mlin-format-fields
• mlin-format-from-info
• mlin-genotype-revision
• mlin-genotype-revision-ARCHIVED
• mlin-genotype-revision-simplified
• mlin-genotyper-beta2
• mlin-genotyper-log-stalls
• mlin-genotyper-rnc
• mlin-gvcf-manifest
• mlin-gvcf-symbolic-assumption
• mlin-inconsistent-trim
• mlin-issue168
• mlin-jemalloc-tuning
• mlin-measure-loss
• mlin-mem-thread-budgets
• mlin-memoize-all-samples-sampleset
• mlin-metadata-cache
• mlin-milestone1-cli
• mlin-min-dp
• mlin-minAQ2
• mlin-multistage-dockerfile
• mlin-multithread-query-test
• mlin-multithread-scalability
• mlin-multithread-scalability2
• mlin-overlap-compactions-discovery
• mlin-placeholder-gvcf-genotyper
• mlin-pseudo-ref-records
• mlin-range-bcf-end
• mlin-readme
• mlin-reduce-residuals
• mlin-ref-PL
• mlin-refactor-datacache-again
• mlin-refactor-ingestion-exceptions
• mlin-relax-unifier
• mlin-remove-loss-tracking
• mlin-reorder-format
• mlin-residual-containing-range
• mlin-revise-allele-pruning
• mlin-revise-homalt
• mlin-revise11
• mlin-rocksdb-upgrade
• mlin-rockskeyvalue
• mlin-rockskeyvalue-config
• mlin-sample-count
• mlin-sampleset-consistency
• mlin-sampleset-range
• mlin-service-abort-operations
• mlin-shorten-keys
• mlin-simplify-range_of_bcf
• mlin-skip-index
• mlin-spdlog
• mlin-squeeze
• mlin-star-allele
• mlin-strelka2
• mlin-travis-docker
• mlin-travis-modernization
• mlin-travis-release
• mlin-travis-valgrind
• mlin-trim-uncalled-alleles
• mlin-tweak-build
• mlin-unification-alt-dna
• mlin-unification-tests-1109
• mlin-unified-site-yaml-parser
• mlin-unifier-allele-frequencies
• mlin-unifier-max-alleles
• mlin-unifier-memory-usage
• mlin-unifier-prefer-small-alleles
• mlin-universal-compaction
• mlin-unrepresentable-symbolic-allele
• mlin-update-getting-started
• mlin-update-spdlog
• mlin-upgrade-capnp
• mlin-variant-qual
• mlin-weCall-calibration
• mlin-wecall
• mlin-wip
• mlin-workaround-neg-PL
• mlin-xAtlas-calibration
• mlin-xAtlas-wip
• mlin-xatlas
• mlin-zstd
• mlin/GxS
• mlin/dv-prior-calibration
• mlin/ghci
• mlin/test-gvcf-norm
• mlin/top2-half-calls
• mlin20160319
• mlin_minGQ
• one_pass
• orodeh-long-confidence-intervals
• orodeh-profiling
• orodeh-vcf-shard-merge
• orodeh-vcf-shard-merge-bgzip
• orodeh-vcf-shard-merge-mt-bgzip
• orodeh_allele_discovery_in_first_phase
• orodeh_capnp
• orodeh_capnp_debug
• orodeh_capnp_debug_II
• orodeh_capnp_debug_III
• orodeh_cleanup_unify_and_discover
• orodeh_config_param_for_new_subcommands
• orodeh_config_yaml_serialization
• orodeh_discovered_alleles_parallel_load
• orodeh_dynamic_jemalloc
• orodeh_ensure_jemelloc
• orodeh_experiments
• orodeh_expose_bucket_size_arg
• orodeh_gvcf_ingest_validation
• orodeh_lambda_predicate_for_queries
• orodeh_malloc_perf
• orodeh_malloc_static
• orodeh_mt_bgzip
• orodeh_one_db_pass_genotyper
• orodeh_perf_lxc
• orodeh_profiling
• orodeh_report_bad_yaml_file
• orodeh_separate_discover_phase
• orodeh_simple_public_cli
• orodeh_stream_yaml
• orodeh_unify_sites_as_stage
• orodeh_vcf_compare
• orodeh_yaml_stream_unify_sites
• perf_32_cpu
• perf_prof_with_bcf_cache
• performance_profiling
• profiling_WIP
• revert-111-orodeh_capnp_debug_III
• revert-122-mlin-skip-index
• split_ch2
• split_chrom
• split_gvcf_into_chromosomes
• tedyun-fixaq2zero
• test_travis_release
• translate-genotype-REF-check
• travis-master-pr-builds
• ubcf
• ubcf_cleanup
• unify_alleles_on_vector_inputs
• update_bgzip
• v0.1.0
• v0.2.0
• v0.3.0
• v0.3.1
• v0.3.2
• v0.3.3
• v0.5.0
• v0.5.x
• v0.6.1
• v1.0.0
• v1.0.1
• v1.0.2
• v1.1.0
• v1.1.1
• v1.1.10
• v1.1.11
• v1.1.12
• v1.1.12-1
• v1.1.2
• v1.1.3
• v1.1.4
• v1.1.5
• v1.1.6
• v1.1.7
• v1.1.8
• v1.1.9
• v1.1.x
• v1.2.0
• v1.2.0-pre.0
• v1.2.1
• v1.2.2
• v1.2.3
• v1.2.4
• v1.2.5
• v1.2.6
• v1.2.7
• vectorize_applet
• ymen-format-field-defaults
• ymen-format-field-ignore-ref
• ymen-format-fields
• ymen-format-fields-clear-on-rnc
• ymen-genotyper-v0.1
• ymen-genotyper-v1
• ymen-prep-for-genotype-v1
• ymen-trim-alts
• ymen-yaml-test-case
• ymen_genotyper_add_yml_tests
• zero_copy_bucket_scan

add GxS config + minor tolerance tweaks