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Uses log10 sum functions accurate to only 1E-4 */\n-        ORIGINAL(() -> {\n+        ORIGINAL(args -> {\n             final Log10PairHMM hmm = new Log10PairHMM(false);\n             logger.info(\"Using the non-hardware-accelerated Java ORIGINAL PairHMM implementation\");\n             return hmm;\n         }),\n         /* Optimized version of the PairHMM which caches per-read computations and operations in real space to avoid costly sums of log10'ed likelihoods */\n-        LOGLESS_CACHING(() -> {\n+        LOGLESS_CACHING(arg -> {\n             final LoglessPairHMM hmm = new LoglessPairHMM();\n             logger.info(\"Using the non-hardware-accelerated Java LOGLESS_CACHING PairHMM implementation\");\n             return hmm;\n         }),\n         /* Optimized AVX implementation of LOGLESS_CACHING called through JNI. Throws if AVX is not available */\n-        AVX_LOGLESS_CACHING(() -> {\n+        AVX_LOGLESS_CACHING(args -> {\n             // Constructor will throw a UserException if AVX is not available\n-            // TODO: connect PairHMMNativeArguments\n-            final VectorLoglessPairHMM hmm = new VectorLoglessPairHMM(null);\n+            final VectorLoglessPairHMM hmm = new VectorLoglessPairHMM(VectorLoglessPairHMM.Implementation.AVX, args);\n             logger.info(\"Using the AVX-accelerated native PairHMM implementation\");\n             return hmm;\n         }),\n-        /* Uses the fastest available PairHMM implementation (AVX if AVX is available, otherwise LOGLESS_CACHING */\n-        FASTEST_AVAILABLE(() -> {\n+        /* OpenMP Multi-threaded AVX implementation of LOGLESS_CACHING called through JNI. Throws if OpenMP AVX is not available */\n+        AVX_LOGLESS_CACHING_OMP(args -> {\n+            // Constructor will throw a UserException if OpenMP AVX is not available\n+            final VectorLoglessPairHMM hmm = new VectorLoglessPairHMM(VectorLoglessPairHMM.Implementation.OMP, args);\n+            logger.info(\"Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation\");","path":"src/main/java/org/broadinstitute/hellbender/utils/pairhmm/PairHMM.java","position":57,"original_position":57,"commit_id":"69a580c8d0624c1a2871665be94068c4d65c874f","original_commit_id":"69a580c8d0624c1a2871665be94068c4d65c874f","user":{"login":"gspowley","id":10476709,"avatar_url":"https://avatars.githubusercontent.com/u/10476709?v=3","gravatar_id":"","url":"https://api.github.com/users/gspowley","html_url":"https://github.com/gspowley","followers_url":"https://api.github.com/users/gspowley/followers","following_url":"https://api.github.com/users/gspowley/following{/other_user}","gists_url":"https://api.github.com/users/gspowley/gists{/gist_id}","starred_url":"https://api.github.com/users/gspowley/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/gspowley/subscriptions","organizations_url":"https://api.github.com/users/gspowley/orgs","repos_url":"https://api.github.com/users/gspowley/repos","events_url":"https://api.github.com/users/gspowley/events{/privacy}","received_events_url":"https://api.github.com/users/gspowley/received_events","type":"User","site_admin":false},"body":"done","created_at":"2016-11-28T22:44:51Z","updated_at":"2016-11-28T22:44:51Z","html_url":"https://github.com/broadinstitute/gatk/pull/2259#discussion_r89903105","pull_request_url":"https://api.github.com/repos/broadinstitute/gatk/pulls/2259","_links":{"self":{"href":"https://api.github.com/repos/broadinstitute/gatk/pulls/comments/89903105"},"html":{"href":"https://github.com/broadinstitute/gatk/pull/2259#discussion_r89903105"},"pull_request":{"href":"https://api.github.com/repos/broadinstitute/gatk/pulls/2259"}}},"pull_request":{"url":"https://api.github.com/repos/broadinstitute/gatk/pulls/2259","id":93230175,"html_url":"https://github.com/broadinstitute/gatk/pull/2259","diff_url":"https://github.com/broadinstitute/gatk/pull/2259.diff","patch_url":"https://github.com/broadinstitute/gatk/pull/2259.patch","issue_url":"https://api.github.com/repos/broadinstitute/gatk/issues/2259","number":2259,"state":"open","locked":false,"title":"Update to GKL 0.3.1","user":{"login":"gspowley","id":10476709,"avatar_url":"https://avatars.githubusercontent.com/u/10476709?v=3","gravatar_id":"","url":"https://api.github.com/users/gspowley","html_url":"https://github.com/gspowley","followers_url":"https://api.github.com/users/gspowley/followers","following_url":"https://api.github.com/users/gspowley/following{/other_user}","gists_url":"https://api.github.com/users/gspowley/gists{/gist_id}","starred_url":"https://api.github.com/users/gspowley/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/gspowley/subscriptions","organizations_url":"https://api.github.com/users/gspowley/orgs","repos_url":"https://api.github.com/users/gspowley/repos","events_url":"https://api.github.com/users/gspowley/events{/privacy}","received_events_url":"https://api.github.com/users/gspowley/received_events","type":"User","site_admin":false},"body":"Update to GKL 0.3.1 which provides the following features compared to GKL 0.1.2 currently used by GATK:\r\n\r\n1. 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