add BROADCAST tests and use 2bit reference from bucket #1806
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| @@ -59,6 +59,10 @@ public void setTestVerbosity(){ | |||
| public static final String publicTestDir = new File(gatkDirectory, publicTestDirRelative).getAbsolutePath() + "/"; | |||
| public static final String publicTestDirRoot = publicTestDir.replace(publicTestDirRelative, ""); | |||
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| public static final String GCS_b37_REFERENCE_2BIT = "gs://hellbender/test/resources/benchmark/human_g1k_v37.2bit"; | |||
| public static final String GCS_b37_CHR20_21_REFERENCE_2BIT = "gs://hellbender/test/resources/human_g1k_v37.20.21.2bit"; | |||
| public static final String GCS_b37_CHR17_1M_REFERENCE_2BIT = "gs://hellbender/test/resources/human_g1k_v37.chr17_1Mb.2bit"; | |||
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Is there a declaration in BaseTest for our standard GCS bucket for testing (if not, can you please create one)? Also, I thought at some point we had switched to gs://gatk or something similar -- can you check what other GCS-based tests are using, and make sure they're all consistent?
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Review complete, back to @akiezun for changes |
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back to @droazen - i addressed some comments. Reading from GSC fails for me and so the tests are disabled still. |
| @@ -59,6 +59,11 @@ public void setTestVerbosity(){ | |||
| public static final String publicTestDir = new File(gatkDirectory, publicTestDirRelative).getAbsolutePath() + "/"; | |||
| public static final String publicTestDirRoot = publicTestDir.replace(publicTestDirRelative, ""); | |||
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| public static final String GSC_GATK_TEST_RESOURCES = "gs://hellbender/test/resources/"; | |||
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Back to @akiezun, merge after addressing comments and resolving conflicts with master. |
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extracted the parts of #1756 that are additions
@droazen please review