From fee7b9447ed61f67ae4faf817eadfeb1c83aa5c1 Mon Sep 17 00:00:00 2001 From: Andrey Smirnov Date: Mon, 12 Sep 2022 11:09:02 -0400 Subject: [PATCH] Added gCNV integration test to detect numerical differences in the outputs. (#7889) * Added gCNV integration test to detect numerical differences in the output of gCNV in the COHORT mode. Also added two minor tests covering different use cases. * Added an option to update expected outputs for GermlineCNVCallerIntegrationTest and regenerated test files for GermlineCNVCaller numerical accuracy integration tests. --- .../GermlineCNVCallerIntegrationTest.java | 118 +++++++- .../SAMPLE_0/baseline_copy_number_t.tsv | 174 ++++++++++++ .../SAMPLE_0/log_c_emission_tc.tsv | 172 ++++++++++++ .../shard_0-calls/SAMPLE_0/log_q_c_tc.tsv | 172 ++++++++++++ .../SAMPLE_0/mu_denoised_copy_ratio_t.tsv | 174 ++++++++++++ .../shard_0-calls/SAMPLE_0/mu_psi_s_log__.tsv | 5 + .../SAMPLE_0/mu_read_depth_s_log__.tsv | 5 + .../shard_0-calls/SAMPLE_0/mu_z_su.tsv | 9 + .../shard_0-calls/SAMPLE_0/sample_name.txt | 1 + .../SAMPLE_0/std_denoised_copy_ratio_t.tsv | 174 ++++++++++++ .../SAMPLE_0/std_psi_s_log__.tsv | 5 + .../SAMPLE_0/std_read_depth_s_log__.tsv | 5 + .../shard_0-calls/SAMPLE_0/std_z_su.tsv | 9 + .../shard_0-calls/calling_config.json | 10 + .../shard_0-calls/denoising_config.json | 17 ++ .../shard_0-calls/gcnvkernel_version.json | 3 + .../shard_0-calls/interval_list.tsv | 177 ++++++++++++ .../shard_0-model/calling_config.json | 10 + .../shard_0-model/denoising_config.json | 17 ++ .../shard_0-model/gcnvkernel_version.json | 3 + .../shard_0-model/interval_list.tsv | 177 ++++++++++++ .../shard_0-model/log_q_tau_tk.tsv | 173 ++++++++++++ .../shard_0-model/mu_W_tu.tsv | 173 ++++++++++++ .../shard_0-model/mu_ard_u_log__.tsv | 8 + .../shard_0-model/mu_log_mean_bias_t.tsv | 173 ++++++++++++ .../shard_0-model/mu_psi_t_log__.tsv | 173 ++++++++++++ .../shard_0-model/std_W_tu.tsv | 173 ++++++++++++ .../shard_0-model/std_ard_u_log__.tsv | 8 + .../shard_0-model/std_log_mean_bias_t.tsv | 173 ++++++++++++ .../shard_0-model/std_psi_t_log__.tsv | 173 ++++++++++++ .../sim_intervals_shard_0.annotated.tsv | 257 ++++++++++++++++++ .../sim_intervals_shard_0.interval_list | 176 ++++++++++++ .../testutils/CopyNumberTestUtils.java | 8 +- 33 files changed, 3100 insertions(+), 5 deletions(-) create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-numerical-accuracy/shard_0-calls/SAMPLE_0/baseline_copy_number_t.tsv create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-numerical-accuracy/shard_0-calls/SAMPLE_0/log_c_emission_tc.tsv create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-numerical-accuracy/shard_0-calls/SAMPLE_0/log_q_c_tc.tsv create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-numerical-accuracy/shard_0-calls/SAMPLE_0/mu_denoised_copy_ratio_t.tsv create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-numerical-accuracy/shard_0-calls/SAMPLE_0/mu_psi_s_log__.tsv create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-numerical-accuracy/shard_0-calls/SAMPLE_0/mu_read_depth_s_log__.tsv create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-numerical-accuracy/shard_0-calls/SAMPLE_0/mu_z_su.tsv create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-numerical-accuracy/shard_0-calls/SAMPLE_0/sample_name.txt create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-numerical-accuracy/shard_0-calls/SAMPLE_0/std_denoised_copy_ratio_t.tsv create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-numerical-accuracy/shard_0-calls/SAMPLE_0/std_psi_s_log__.tsv create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-numerical-accuracy/shard_0-calls/SAMPLE_0/std_read_depth_s_log__.tsv create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-numerical-accuracy/shard_0-calls/SAMPLE_0/std_z_su.tsv create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-numerical-accuracy/shard_0-calls/calling_config.json create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-numerical-accuracy/shard_0-calls/denoising_config.json create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-numerical-accuracy/shard_0-calls/gcnvkernel_version.json create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-numerical-accuracy/shard_0-calls/interval_list.tsv create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-numerical-accuracy/shard_0-model/calling_config.json create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-numerical-accuracy/shard_0-model/denoising_config.json create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-numerical-accuracy/shard_0-model/gcnvkernel_version.json create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-numerical-accuracy/shard_0-model/interval_list.tsv create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-numerical-accuracy/shard_0-model/log_q_tau_tk.tsv create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-numerical-accuracy/shard_0-model/mu_W_tu.tsv create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-numerical-accuracy/shard_0-model/mu_ard_u_log__.tsv create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-numerical-accuracy/shard_0-model/mu_log_mean_bias_t.tsv create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-numerical-accuracy/shard_0-model/mu_psi_t_log__.tsv create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-numerical-accuracy/shard_0-model/std_W_tu.tsv create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-numerical-accuracy/shard_0-model/std_ard_u_log__.tsv create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-numerical-accuracy/shard_0-model/std_log_mean_bias_t.tsv create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-numerical-accuracy/shard_0-model/std_psi_t_log__.tsv create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-sim-data/sim_intervals_shard_0.annotated.tsv create mode 100644 src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-sim-data/sim_intervals_shard_0.interval_list diff --git a/src/test/java/org/broadinstitute/hellbender/tools/copynumber/GermlineCNVCallerIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/copynumber/GermlineCNVCallerIntegrationTest.java index e24d145d4c1..018e8180491 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/copynumber/GermlineCNVCallerIntegrationTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/copynumber/GermlineCNVCallerIntegrationTest.java @@ -1,22 +1,35 @@ package org.broadinstitute.hellbender.tools.copynumber; +import org.apache.commons.io.FileUtils; import org.broadinstitute.hellbender.CommandLineProgramTest; import org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions; import org.broadinstitute.hellbender.cmdline.argumentcollections.IntervalArgumentCollection; +import org.broadinstitute.hellbender.exceptions.GATKException; import org.broadinstitute.hellbender.testutils.ArgumentsBuilder; +import org.broadinstitute.hellbender.testutils.CopyNumberTestUtils; import org.broadinstitute.hellbender.tools.copynumber.arguments.CopyNumberStandardArgument; import org.broadinstitute.hellbender.tools.copynumber.arguments.GermlineDenoisingModelArgumentCollection; import org.broadinstitute.hellbender.utils.IntervalMergingRule; +import org.testng.Assert; import org.testng.annotations.Test; import java.io.File; +import java.io.IOException; +import java.nio.file.Paths; import java.util.Arrays; +import java.util.List; import java.util.stream.IntStream; + /** * Integration tests for {@link GermlineCNVCaller}. */ public final class GermlineCNVCallerIntegrationTest extends CommandLineProgramTest { + + // If true, update the expected outputs in tests that assert an exact or approximate match vs. prior output, + // instead of actually running the tests. + public static final boolean UPDATE_EXACT_MATCH_EXPECTED_OUTPUTS = false; + private static final String GCNV_SIM_DATA_DIR = toolsTestDir + "copynumber/gcnv-sim-data/"; private static final File[] TEST_COUNT_FILES = IntStream.range(0, 20) .mapToObj(n -> new File(GCNV_SIM_DATA_DIR + String.format("SAMPLE_%03d_counts.tsv", n))) @@ -24,6 +37,29 @@ public final class GermlineCNVCallerIntegrationTest extends CommandLineProgramTe private static final File CONTIG_PLOIDY_CALLS_OUTPUT_DIR = new File(GCNV_SIM_DATA_DIR + "contig-ploidy-calls/"); 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-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); + private static final File SIM_INTERVAL_LIST_SHARD_0 = new File(GCNV_SIM_DATA_DIR + "sim_intervals_shard_0.interval_list"); + private static final File SIM_INTERVAL_LIST_SHARD_0_ANNOTATED_FILE = new File(GCNV_SIM_DATA_DIR + "sim_intervals_shard_0.annotated.tsv"); + private static final double ALLOWED_DELTA_FOR_DOUBLE_VALUES = 1E-6; + + final List MODEL_FILES_TO_COMPARE = Arrays.asList("log_q_tau_tk.tsv", "mu_ard_u_log__.tsv", "mu_psi_t_log__.tsv", + "std_ard_u_log__.tsv", "std_psi_t_log__.tsv", "mu_W_tu.tsv", "mu_log_mean_bias_t.tsv", "std_W_tu.tsv", "std_log_mean_bias_t.tsv"); + final List 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", "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 + */ + @Test + public void assertThatExpectedOutputUpdateToggleIsDisabled() { + Assert.assertFalse(UPDATE_EXACT_MATCH_EXPECTED_OUTPUTS, "The toggle to update expected outputs should not be left enabled"); + } /** * Run the tool in the COHORT mode for all 20 samples on a small subset of intervals @@ -88,11 +124,89 @@ public void testCaseWithHiddenArguments() { runCommandLine(argsBuilder); } - @Test(groups = {"python"}, enabled = false) + /** + * Test that {@link GermlineCNVCaller} outputs fall within a numerical accuracy bound defined. This test is meant + * to detect things like major Python library updates that affect gCNV results, and detect unintentional + * consequences of minor model changes. + */ + @Test(groups = {"python"}) + public void testNumericalAccuracy() { + final ArgumentsBuilder argsBuilder = new ArgumentsBuilder(); + final String outputPrefix = TEST_SHARD; + Arrays.stream(TEST_COUNT_FILES).forEach(argsBuilder::addInput); + final String outputDir = UPDATE_EXACT_MATCH_EXPECTED_OUTPUTS ? GCNV_TEST_OUTPUT_DIR : OUTPUT_DIR.getAbsolutePath(); + + argsBuilder.add(GermlineCNVCaller.RUN_MODE_LONG_NAME, GermlineCNVCaller.RunMode.COHORT.name()) + .add(StandardArgumentDefinitions.INTERVALS_SHORT_NAME, SIM_INTERVAL_LIST_SHARD_0) + .add(IntervalArgumentCollection.INTERVAL_MERGING_RULE_LONG_NAME, IntervalMergingRule.OVERLAPPING_ONLY.toString()) + .add(GermlineCNVCaller.CONTIG_PLOIDY_CALLS_DIRECTORY_LONG_NAME, + CONTIG_PLOIDY_CALLS_OUTPUT_DIR.getAbsolutePath()) + .add(StandardArgumentDefinitions.OUTPUT_LONG_NAME, outputDir) + .add(CopyNumberStandardArgument.OUTPUT_PREFIX_LONG_NAME, outputPrefix); + runCommandLine(argsBuilder); + + // Test that values of outputs are approximately numerically equivalent + if (!UPDATE_EXACT_MATCH_EXPECTED_OUTPUTS) { + MODEL_FILES_TO_COMPARE.forEach(f -> CopyNumberTestUtils.assertFilesEqualUpToAllowedDeltaForDoubleValues( + new File(Paths.get(OUTPUT_DIR.getAbsolutePath(), outputPrefix + "-model").toString(), f), + new File(MODEL_EXACT_MATCH_EXPECTED_SUB_DIR, f), + ALLOWED_DELTA_FOR_DOUBLE_VALUES, + logger)); + CALLS_FILES_TO_COMPARE.forEach(f -> CopyNumberTestUtils.assertFilesEqualUpToAllowedDeltaForDoubleValues( + new File(Paths.get(OUTPUT_DIR.getAbsolutePath(), outputPrefix + "-calls", SAMPLE_DIR_EXT).toString(), f), + new File(CALLS_EXACT_MATCH_EXPECTED_SUB_DIR, f), + ALLOWED_DELTA_FOR_DOUBLE_VALUES, + logger)); + } else { + // remove files not used for testing + try { + FileUtils.deleteDirectory(new File(Paths.get(GCNV_TEST_OUTPUT_DIR, outputPrefix + "-tracking").toString())); + } catch (final IOException ex) { + throw new GATKException("Could not remove GermlineCNVCaller tracking files."); + } + IntStream.range(1, 20).forEach( + s -> { + try { + FileUtils.deleteDirectory(new File(Paths.get(GCNV_TEST_OUTPUT_DIR, outputPrefix + "-calls", "SAMPLE_" + s).toString())); + } catch (final IOException ex) { + throw new GATKException(String.format("Could not remove a GermlineCNVCaller call directory for sample %d", s)); + } + }); + } + } + + /** + * Run the tool in the COHORT mode using a provided model for initialization. Note for developers: the model used + * for initialization is created by the {@link #testCohortWithoutIntervalAnnotations()} test. + */ + @Test(groups = {"python"}, dependsOnMethods = "testCohortWithoutIntervalAnnotations") public void testCohortWithInputModel() { + final ArgumentsBuilder argsBuilder = new ArgumentsBuilder(); + Arrays.stream(TEST_COUNT_FILES).forEach(argsBuilder::addInput); + argsBuilder.add(GermlineCNVCaller.RUN_MODE_LONG_NAME, GermlineCNVCaller.RunMode.COHORT.name()) + .add(StandardArgumentDefinitions.INTERVALS_SHORT_NAME, SIM_INTERVAL_LIST_SUBSET_FILE) + .add(CopyNumberStandardArgument.MODEL_LONG_NAME, + new File(OUTPUT_DIR, "test-germline-cnv-cohort-model").getAbsolutePath()) + .add(GermlineCNVCaller.CONTIG_PLOIDY_CALLS_DIRECTORY_LONG_NAME, + CONTIG_PLOIDY_CALLS_OUTPUT_DIR.getAbsolutePath()) + .add(StandardArgumentDefinitions.OUTPUT_LONG_NAME, OUTPUT_DIR.getAbsolutePath()) + .add(CopyNumberStandardArgument.OUTPUT_PREFIX_LONG_NAME, "test-germline-cnv-cohort-with-input-model") + .add(IntervalArgumentCollection.INTERVAL_MERGING_RULE_LONG_NAME, IntervalMergingRule.OVERLAPPING_ONLY.toString()); + runCommandLine(argsBuilder); } - @Test(groups = {"python"}, enabled = false) + @Test(groups = {"python"}) public void testCohortWithAnnotatedIntervals() { + final ArgumentsBuilder argsBuilder = new ArgumentsBuilder(); + Arrays.stream(TEST_COUNT_FILES).forEach(argsBuilder::addInput); + argsBuilder.add(GermlineCNVCaller.RUN_MODE_LONG_NAME, GermlineCNVCaller.RunMode.COHORT.name()) + .add(StandardArgumentDefinitions.INTERVALS_SHORT_NAME, SIM_INTERVAL_LIST_SHARD_0) + .add(CopyNumberStandardArgument.ANNOTATED_INTERVALS_FILE_LONG_NAME, SIM_INTERVAL_LIST_SHARD_0_ANNOTATED_FILE) + .add(GermlineCNVCaller.CONTIG_PLOIDY_CALLS_DIRECTORY_LONG_NAME, + CONTIG_PLOIDY_CALLS_OUTPUT_DIR.getAbsolutePath()) + .add(StandardArgumentDefinitions.OUTPUT_LONG_NAME, OUTPUT_DIR.getAbsolutePath()) + .add(CopyNumberStandardArgument.OUTPUT_PREFIX_LONG_NAME, "test-germline-cnv-cohort") + .add(IntervalArgumentCollection.INTERVAL_MERGING_RULE_LONG_NAME, IntervalMergingRule.OVERLAPPING_ONLY.toString()); + runCommandLine(argsBuilder); } } diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-numerical-accuracy/shard_0-calls/SAMPLE_0/baseline_copy_number_t.tsv b/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-numerical-accuracy/shard_0-calls/SAMPLE_0/baseline_copy_number_t.tsv new file mode 100644 index 00000000000..4909bf55e22 --- /dev/null +++ b/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-numerical-accuracy/shard_0-calls/SAMPLE_0/baseline_copy_number_t.tsv @@ -0,0 +1,174 @@ +@CO shape:(170,) +@CO dtype:uint16 +@RG ID:GATKCopyNumber SM:SAMPLE_000 +BASELINE_COPY_NUMBER +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-numerical-accuracy/shard_0-calls/SAMPLE_0/log_c_emission_tc.tsv b/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-numerical-accuracy/shard_0-calls/SAMPLE_0/log_c_emission_tc.tsv new file mode 100644 index 00000000000..f8b2f8edc8f --- /dev/null +++ b/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-numerical-accuracy/shard_0-calls/SAMPLE_0/log_c_emission_tc.tsv @@ -0,0 +1,172 @@ +@RG ID:GATKCopyNumber SM:SAMPLE_000 +COPY_NUMBER_0 COPY_NUMBER_1 COPY_NUMBER_2 COPY_NUMBER_3 COPY_NUMBER_4 COPY_NUMBER_5 +-3718.6283251446744 -88.75162669552559 -5.892405769638854 -28.622827280547387 -71.17816858307162 -116.93585145887775 +-9454.442599242697 -90.06709385868929 -7.118479100485037 -32.595755210303466 -73.87391033784156 -116.15496961410193 +-3398.390150797672 -69.67846350395715 -6.1819311977814575 -31.24990831453078 -71.52801754721553 -113.46157362803358 +-4.454863134361248 -2.243951136248023 -3.5329924499361143 -6.200202171896734 -9.57708329639005 -13.36648258616691 +-2619.368205697241 -83.36144421665982 -5.716369177424653 -30.417536292277127 -76.81506842213334 -127.58861902053708 +-1392.0544015185974 -56.23703472106425 -5.031435824393768 -27.89423322653279 -68.40480740885044 -113.15890558377333 +-719.9688140468317 -41.192572741863415 -4.456998969031516 -19.130066350227054 -47.9771574853105 -81.18651019564095 +-5363.973710716001 -92.88082420543512 -6.435660403911864 -39.90409437686533 -93.43931694045698 -148.98156274170407 +-5978.946758593645 -41.087056378534974 -6.840810258156937 -15.316269287314615 -29.722470128922065 -44.50402612390527 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1271440 + . +2 1312168 1312455 + . +2 1319939 1320244 + . +2 1371017 1371482 + . +2 1417135 1417419 + . +2 1418082 1418371 + . +2 1426719 1426998 + . +2 1437112 1437476 + . +2 1439926 1440253 + . +2 1457368 1457692 + . +2 1459750 1460151 + . +2 1480760 1481473 + . +2 1488270 1488723 + . +2 1491495 1491860 + . +2 1497476 1497908 + . +2 1499663 1500066 + . +2 1500269 1500634 + . +2 1507622 1507948 + . +2 1520557 1520851 + . +2 1544268 1544592 + . +2 1546095 1546596 + . +2 1635561 1638192 + . diff --git a/src/testUtils/java/org/broadinstitute/hellbender/testutils/CopyNumberTestUtils.java b/src/testUtils/java/org/broadinstitute/hellbender/testutils/CopyNumberTestUtils.java index 94fba392585..a2950d426c3 100644 --- a/src/testUtils/java/org/broadinstitute/hellbender/testutils/CopyNumberTestUtils.java +++ b/src/testUtils/java/org/broadinstitute/hellbender/testutils/CopyNumberTestUtils.java @@ -17,8 +17,9 @@ public final class CopyNumberTestUtils { /** * This test utility method asserts if two TSV files (each containing a header followed by a matrix of doubles) * are approximately equivalent, by checking if corresponding double values are equal up to some number of decimal - * points represented by the delta parameter. Note that the headers of both files need to be bitwise identical, - * and the number of columns and rows of each matrix encoded in TSV files must be equal as well. + * points represented by the delta parameter. This assertion will also succeed if both compared files contain NaNs + * in the matching fields. Note that the headers of both files need to be bitwise identical, and the number of + * columns and rows of each matrix encoded in TSV files must be equal as well. * * @param f1 first file to compare * @param f2 second file to compare @@ -48,7 +49,8 @@ public static void assertFilesEqualUpToAllowedDeltaForDoubleValues(final File f1 final List splitLine1 = Arrays.asList(line1.split("\t")); final List splitLine2 = Arrays.asList(line2.split("\t")); Assert.assertEquals(splitLine1.size(), splitLine2.size(), - String.format("Line %d does not have the same number of fields in files %s and %s.", i, f1, f2)); + String.format("Line %d does not have the same number of fields in files %s and %s. " + + "Make sure that both files have equal number of header lines.", i, f1, f2)); for (int j = 0; j < splitLine1.size(); j++) { final String field1 = splitLine1.get(j);