{"action":"created","comment":{"url":"https://api.github.com/repos/broadinstitute/gatk/pulls/comments/44035455","id":44035455,"diff_hunk":"@@ -91,26 +91,26 @@ private String getCloudInputs() {\n     public Object[][] createBQSRTestDataBucket() {\n         final String GRCh37Ref = ReferenceAPISource.URL_PREFIX + ReferenceAPISource.GRCH37_REF_ID;\n         final String localResources =  getResourceDir();\n-        final String HiSeqBamCloud = getCloudInputs() + \"CEUTrio.HiSeq.WGS.b37.ch20.1m-1m1k.NA12878.bam\";\n-        final String dbSNPb37 =  getResourceDir() + \"dbsnp_132.b37.excluding_sites_after_129.chr17_69k_70k.vcf\";\n+        final String HiSeqBamCloud_chr20 = getCloudInputs() + \"CEUTrio.HiSeq.WGS.b37.ch20.1m-1m1k.NA12878.bam\";\n+        final String dbSNPb37_chr2010 = largeFileTestDir + \"dbsnp_138.b37.20.21.vcf\";\n \n         return new Object[][]{\n                 // input in cloud, computation local.\n-                {new BQSRTest(GRCh37Ref, HiSeqBamCloud, dbSNPb37, \"\", localResources + \"expected.CEUTrio.HiSeq.WGS.b37.ch20.1m-1m1k.NA12878.recal.txt\")},\n+                {new BQSRTest(GRCh37Ref, HiSeqBamCloud_chr20, dbSNPb37_chr2010, \"\", localResources + \"expected.CEUTrio.HiSeq.WGS.b37.ch20.1m-1m1k.NA12878.recal.txt\")},\n         };\n     }\n \n     @DataProvider(name = \"BQSRLocalRefTest\")\n     public Object[][] createBQSRLocalRefTestData() {\n-        final String GRCh37Ref = b37_reference_20_21;\n-        final String GRCh37Ref2bit = b37_2bit_reference_20_21;\n-        final String hiSeqBam = getResourceDir() + \"CEUTrio.HiSeq.WGS.b37.ch20.1m-1m1k.NA12878.bam\";\n-        final String dbSNPb37 =  getResourceDir() + \"dbsnp_132.b37.excluding_sites_after_129.chr17_69k_70k.vcf\";\n+        final String GRCh37Ref_chr2021 = b37_reference_20_21;\n+        final String GRCh37Ref2bit_chr2021 = b37_2bit_reference_20_21;\n+        final String hiSeqBam_chr20 = getResourceDir() + \"CEUTrio.HiSeq.WGS.b37.ch20.1m-1m1k.NA12878.bam\";\n+        final String dbSNPb37_chr2021 = largeFileTestDir + \"dbsnp_138.b37.20.21.vcf\";\n \n         return new Object[][]{\n                 // input local, computation local.\n-                {new BQSRTest(GRCh37Ref2bit, hiSeqBam, dbSNPb37, \"--joinStrategy BROADCAST\", getResourceDir() + \"expected.CEUTrio.HiSeq.WGS.b37.ch20.1m-1m1k.NA12878.recal.txt\")},\n-                {new BQSRTest(GRCh37Ref, hiSeqBam, dbSNPb37, \"--joinStrategy SHUFFLE\", getResourceDir() + \"expected.CEUTrio.HiSeq.WGS.b37.ch20.1m-1m1k.NA12878.recal.txt\")},\n+                {new BQSRTest(GRCh37Ref2bit_chr2021, hiSeqBam_chr20, dbSNPb37_chr2021, \"--joinStrategy BROADCAST\", getResourceDir() + \"expected.CEUTrio.HiSeq.WGS.b37.ch20.1m-1m1k.NA12878.recal.txt\")},\n+                {new BQSRTest(GRCh37Ref_chr2021, hiSeqBam_chr20, dbSNPb37_chr2021, \"--joinStrategy SHUFFLE\", getResourceDir() + \"expected.CEUTrio.HiSeq.WGS.b37.ch20.1m-1m1k.NA12878.recal.txt\")},","path":"src/test/java/org/broadinstitute/hellbender/tools/spark/BaseRecalibratorSparkIntegrationTest.java","position":74,"original_position":74,"commit_id":"4eb735b68f51e582bde48ae388d2b310454d66b8","original_commit_id":"4eb735b68f51e582bde48ae388d2b310454d66b8","user":{"login":"akiezun","id":1993519,"avatar_url":"https://avatars.githubusercontent.com/u/1993519?v=3","gravatar_id":"","url":"https://api.github.com/users/akiezun","html_url":"https://github.com/akiezun","followers_url":"https://api.github.com/users/akiezun/followers","following_url":"https://api.github.com/users/akiezun/following{/other_user}","gists_url":"https://api.github.com/users/akiezun/gists{/gist_id}","starred_url":"https://api.github.com/users/akiezun/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/akiezun/subscriptions","organizations_url":"https://api.github.com/users/akiezun/orgs","repos_url":"https://api.github.com/users/akiezun/repos","events_url":"https://api.github.com/users/akiezun/events{/privacy}","received_events_url":"https://api.github.com/users/akiezun/received_events","type":"User","site_admin":false},"body":"ha, so the reason is that the BAM file and the dbSNP files don't overlap! ","created_at":"2015-11-05T16:48:24Z","updated_at":"2015-11-05T16:48:24Z","html_url":"https://github.com/broadinstitute/gatk/pull/1031#discussion_r44035455","pull_request_url":"https://api.github.com/repos/broadinstitute/gatk/pulls/1031","_links":{"self":{"href":"https://api.github.com/repos/broadinstitute/gatk/pulls/comments/44035455"},"html":{"href":"https://github.com/broadinstitute/gatk/pull/1031#discussion_r44035455"},"pull_request":{"href":"https://api.github.com/repos/broadinstitute/gatk/pulls/1031"}}},"pull_request":{"url":"https://api.github.com/repos/broadinstitute/gatk/pulls/1031","id":48376465,"html_url":"https://github.com/broadinstitute/gatk/pull/1031","diff_url":"https://github.com/broadinstitute/gatk/pull/1031.diff","patch_url":"https://github.com/broadinstitute/gatk/pull/1031.patch","issue_url":"https://api.github.com/repos/broadinstitute/gatk/issues/1031","number":1031,"state":"open","locked":false,"title":"BQSR pipeline without saving + fixed tests for BQSR on spark","user":{"login":"akiezun","id":1993519,"avatar_url":"https://avatars.githubusercontent.com/u/1993519?v=3","gravatar_id":"","url":"https://api.github.com/users/akiezun","html_url":"https://github.com/akiezun","followers_url":"https://api.github.com/users/akiezun/followers","following_url":"https://api.github.com/users/akiezun/following{/other_user}","gists_url":"https://api.github.com/users/akiezun/gists{/gist_id}","starred_url":"https://api.github.com/users/akiezun/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/akiezun/subscriptions","organizations_url":"https://api.github.com/users/akiezun/orgs","repos_url":"https://api.github.com/users/akiezun/repos","events_url":"https://api.github.com/users/akiezun/events{/privacy}","received_events_url":"https://api.github.com/users/akiezun/received_events","type":"User","site_admin":false},"body":"fixes #799 \r\nfixes #1017 \r\nAdds BQSRSpark program that runs 2 steps of BQSR without writing the tables to a 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