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Remove abandoned filter project and unneeded build dependency (#7950)
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TedBrookings authored Jul 19, 2022

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1 parent ace7821 commit 3749fa7
Showing 10 changed files with 5 additions and 1,264 deletions.
3 changes: 0 additions & 3 deletions build.gradle
Original file line number Diff line number Diff line change
@@ -363,9 +363,6 @@ dependencies {
// Required for COSMIC Funcotator data source:
implementation 'org.xerial:sqlite-jdbc:3.36.0.3'

// Required for SV Discovery machine learning
implementation group: 'biz.k11i', name: 'xgboost-predictor', version: '0.3.0'

// natural sort
implementation('net.grey-panther:natural-comparator:1.1')
implementation('com.fasterxml.jackson.module:jackson-module-scala_' + scalaVersion + ':2.9.8')
Original file line number Diff line number Diff line change
@@ -118,12 +118,7 @@ public static class FindBreakpointEvidenceSparkArgumentCollection implements Ser
fullName = "sv-evidence-filter-threshold-probability")
public double svEvidenceFilterThresholdProbability = 0.92;

@Argument(doc = "Filter method for selecting evidence to group into Assembly Intervals",
fullName = "sv-evidence-filter-type")
public SvEvidenceFilterType svEvidenceFilterType = SvEvidenceFilterType.DENSITY;

// ---------- options -----------

@Argument(doc = "Write GFA representation of assemblies in fastq-dir.", fullName = "write-gfas")
public boolean writeGFAs = false;

@@ -267,8 +262,6 @@ public void validate() {
}
}

public enum SvEvidenceFilterType {DENSITY, XGBOOST}

public static class DiscoverVariantsFromContigAlignmentsArgumentCollection implements Serializable {
private static final long serialVersionUID = 1L;

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Original file line number Diff line number Diff line change
@@ -1115,17 +1115,10 @@ private static Iterator<BreakpointEvidence> getFilter(
final StructuralVariationDiscoveryArgumentCollection.FindBreakpointEvidenceSparkArgumentCollection params,
final PartitionCrossingChecker partitionCrossingChecker
) {
switch(params.svEvidenceFilterType) {
case DENSITY:
return new BreakpointDensityFilter(
evidenceItr, readMetadata, params.minEvidenceWeightPerCoverage,
params.minCoherentEvidenceWeightPerCoverage, partitionCrossingChecker, params.minEvidenceMapQ
);
case XGBOOST:
return new XGBoostEvidenceFilter(evidenceItr, readMetadata, params, partitionCrossingChecker);
default:
throw new IllegalStateException("Unknown svEvidenceFilterType: " + params.svEvidenceFilterType);
}
return new BreakpointDensityFilter(
evidenceItr, readMetadata, params.minEvidenceWeightPerCoverage,
params.minCoherentEvidenceWeightPerCoverage, partitionCrossingChecker, params.minEvidenceMapQ
);
}

private static void writeTargetLinks(final Broadcast<ReadMetadata> broadcastMetadata,

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3 changes: 0 additions & 3 deletions src/main/resources/large/sv_evidence_classifier.bin

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Original file line number Diff line number Diff line change
@@ -31,7 +31,6 @@ private static final class FindBreakpointEvidenceSparkIntegrationTestArgs {
final String alignerRefIndexImgLoc;
final String outputDir;
final float bamCoverage;
final String svEvidenceFilterType;
final String svGenomeGapsFile;
final String svGenomeUmapS100File;

@@ -41,7 +40,6 @@ private static final class FindBreakpointEvidenceSparkIntegrationTestArgs {
final String alignerRefIndexImgLoc,
final String outputDir,
final float bamCoverage,
final String svEvidenceFilterType,
final String svGenomeGapsFile,
final String svGenomeUmapS100File) {
this.expectedAlignedContigsLoc = expectedAlignedContigsLoc;
@@ -50,7 +48,6 @@ private static final class FindBreakpointEvidenceSparkIntegrationTestArgs {
this.alignerRefIndexImgLoc = alignerRefIndexImgLoc;
this.outputDir = outputDir;
this.bamCoverage = bamCoverage;
this.svEvidenceFilterType = svEvidenceFilterType;
this.svGenomeGapsFile = svGenomeGapsFile;
this.svGenomeUmapS100File = svGenomeUmapS100File;
}
@@ -65,7 +62,6 @@ String getCommandLine() {
" --target-link-file " + outputDir + "/targetLinks.bedpe" +
" --min-evidence-coverage-ratio " + 15 / bamCoverage +
" --min-coherent-evidence-coverage-ratio " + 7 / bamCoverage +
" --sv-evidence-filter-type " + svEvidenceFilterType +
(svGenomeGapsFile.isEmpty() ? "" : " --sv-genome-gaps-file " + svGenomeGapsFile) +
(svGenomeUmapS100File.isEmpty() ? "" : " --sv-genome-umap-s100-file " + svGenomeUmapS100File);
}
@@ -78,7 +74,6 @@ public String toString() {
", aligner-ref-index-img-loc='" + alignerRefIndexImgLoc + '\'' +
", output-dir='" + outputDir + '\'' +
", bam-coverage='" + bamCoverage + '\'' +
", sv-evidence-filter-type='" + svEvidenceFilterType + '\'' +
'}';
}
}
@@ -97,23 +92,11 @@ public Object[][] createTestData() throws IOException {
SVIntegrationTestDataProvider.TEST_CONTIG_SAM,
SVIntegrationTestDataProvider.TEST_BAM, SVIntegrationTestDataProvider.KMER_KILL_LIST,
SVIntegrationTestDataProvider.ALIGNER_INDEX_IMG, tempDirNew.getAbsolutePath(),
SVIntegrationTestDataProvider.TEST_BAM_COVERAGE, SVIntegrationTestDataProvider.DENSITY_FILTER,
SVIntegrationTestDataProvider.TEST_BAM_COVERAGE,
"", ""
)
}
);
// Test pipeline using classifier filter
tests.add(
new Object[]{
new FindBreakpointEvidenceSparkIntegrationTestArgs(
SVIntegrationTestDataProvider.TEST_CONTIG_SAM_CLASSIFIER,
SVIntegrationTestDataProvider.TEST_BAM, SVIntegrationTestDataProvider.KMER_KILL_LIST,
SVIntegrationTestDataProvider.ALIGNER_INDEX_IMG, tempDirNew.getAbsolutePath(),
SVIntegrationTestDataProvider.TEST_BAM_COVERAGE, SVIntegrationTestDataProvider.CLASSIFIER_FILTER,
SVIntegrationTestDataProvider.TEST_GENOME_GAPS_FILE, SVIntegrationTestDataProvider.TEST_GENOME_UMAP100_FILE
)
}
);

return tests.toArray(new Object[][]{});
}
Original file line number Diff line number Diff line change
@@ -21,14 +21,10 @@ public class SVIntegrationTestDataProvider extends CommandLineProgramTest {
private static final String LARGE_RESOURCES_FOLDER = publicTestDir + "large/";
public static final String TEST_BAM = LARGE_RESOURCES_FOLDER + "/sv/SVIntegrationTest_hg19.bam";
public static final String TEST_GENOME_GAPS_FILE = LARGE_RESOURCES_FOLDER + "/sv/SVIntegrationTest_hg19_gaps.bed.gz";
public static final String TEST_GENOME_UMAP100_FILE = LARGE_RESOURCES_FOLDER + "/sv/SVIntegrationTest_hg19_umap_s100.bed.gz";
public static final String TEST_CONTIG_SAM = THIS_TEST_FOLDER + "/inputs/hg19_DEL_contigAssemblies.sam";
public static final String EXTERNAL_CNV_CALLS = THIS_TEST_FOLDER + "/inputs/hg19_DEL_cnv_calls.vcf";
public static final String KMER_KILL_LIST = THIS_TEST_FOLDER + "/inputs/dummy.kill.kmers";
public static final float TEST_BAM_COVERAGE = 10;
public static final String DENSITY_FILTER = "DENSITY";
public static final String CLASSIFIER_FILTER = "XGBOOST";
public static final String TEST_CONTIG_SAM_CLASSIFIER = THIS_TEST_FOLDER + "/inputs/hg19_DEL_contigAssemblies_" + CLASSIFIER_FILTER + ".sam";


// expected outputs

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