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Regenerated test files for GermlineCNVCaller numerical accuracy integ…
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…ration tests
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@asmirnov239
asmirnov239 committed Aug 1, 2022
1 parent 649505f commit e4100fe
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Showing 260 changed files with 26,388 additions and 2 deletions.
4 changes: 2 additions & 2 deletions ...java/org/broadinstitute/hellbender/tools/copynumber/GermlineCNVCallerIntegrationTest.java
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Expand Up @@ -35,7 +35,7 @@ public final class GermlineCNVCallerIntegrationTest extends CommandLineProgramTe
private static final File SIM_INTERVAL_LIST_SUBSET_FILE = new File(GCNV_SIM_DATA_DIR + "sim_intervals_subset.interval_list");
private static final File OUTPUT_DIR = createTempDir("test-germline-cnv");
private static final String SAMPLE_DIR_EXT = "SAMPLE_0";
private static final String GCNV_TEST_OUTPUT_DIR = toolsTestDir + "copynumber/gcnv-postprocess/";
private static final String GCNV_TEST_OUTPUT_DIR = toolsTestDir + "copynumber/gcnv-numerical-accuracy/";
private static final String TEST_SHARD = "shard_0";
private static final File MODEL_EXACT_MATCH_EXPECTED_SUB_DIR = new File(GCNV_TEST_OUTPUT_DIR + TEST_SHARD + "-model/");
private static final File CALLS_EXACT_MATCH_EXPECTED_SUB_DIR = new File(GCNV_TEST_OUTPUT_DIR + TEST_SHARD + "-calls/" + SAMPLE_DIR_EXT);
Expand All @@ -48,7 +48,7 @@ public final class GermlineCNVCallerIntegrationTest extends CommandLineProgramTe
final List<String> CALLS_FILES_TO_COMPARE = Arrays.asList("baseline_copy_number_t.tsv", "log_c_emission_tc.tsv",
"log_q_c_tc.tsv", "mu_psi_s_log__.tsv", "mu_read_depth_s_log__.tsv",
"mu_z_su.tsv", "sample_name.txt", "std_psi_s_log__.tsv",
"std_read_depth_s_log__.tsv", "std_z_su.tsv");
"std_read_depth_s_log__.tsv", "std_z_su.tsv", "mu_denoised_copy_ratio_t.tsv", "std_denoised_copy_ratio_t.tsv");

/**
* Make sure that someone didn't leave the {@value UPDATE_EXACT_MATCH_EXPECTED_OUTPUTS} toggle turned on
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174 changes: 174 additions & 0 deletions ...ools/copynumber/gcnv-numerical-accuracy/shard_0-calls/SAMPLE_0/baseline_copy_number_t.tsv
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@CO shape:(170,)
@CO dtype:uint16
@RG ID:GATKCopyNumber SM:SAMPLE_000
BASELINE_COPY_NUMBER
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172 changes: 172 additions & 0 deletions ...der/tools/copynumber/gcnv-numerical-accuracy/shard_0-calls/SAMPLE_0/log_c_emission_tc.tsv
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172 changes: 172 additions & 0 deletions ...hellbender/tools/copynumber/gcnv-numerical-accuracy/shard_0-calls/SAMPLE_0/log_q_c_tc.tsv
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174 changes: 174 additions & 0 deletions ...ls/copynumber/gcnv-numerical-accuracy/shard_0-calls/SAMPLE_0/mu_denoised_copy_ratio_t.tsv
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@CO shape:(170,)
@CO dtype:float64
@RG ID:GATKCopyNumber SM:SAMPLE_000
VALUE_0
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5 changes: 5 additions & 0 deletions ...bender/tools/copynumber/gcnv-numerical-accuracy/shard_0-calls/SAMPLE_0/mu_psi_s_log__.tsv
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@CO shape:(1,)
@CO dtype:float64
@RG ID:GATKCopyNumber SM:SAMPLE_000
VALUE_0
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5 changes: 5 additions & 0 deletions ...tools/copynumber/gcnv-numerical-accuracy/shard_0-calls/SAMPLE_0/mu_read_depth_s_log__.tsv
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@CO shape:(1,)
@CO dtype:float64
@RG ID:GATKCopyNumber SM:SAMPLE_000
VALUE_0
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9 changes: 9 additions & 0 deletions ...te/hellbender/tools/copynumber/gcnv-numerical-accuracy/shard_0-calls/SAMPLE_0/mu_z_su.tsv
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@CO shape:(5,)
@CO dtype:float64
@RG ID:GATKCopyNumber SM:SAMPLE_000
VALUE_0
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1 change: 1 addition & 0 deletions ...ellbender/tools/copynumber/gcnv-numerical-accuracy/shard_0-calls/SAMPLE_0/sample_name.txt
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SAMPLE_000
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