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ah - use new GT encoding #6822
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ah - use new GT encoding #6822
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38 changes: 30 additions & 8 deletions
38
src/main/java/org/broadinstitute/hellbender/tools/variantdb/CommonCode.java
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74 changes: 0 additions & 74 deletions
74
...in/java/org/broadinstitute/hellbender/tools/variantdb/arrays/ArrayMetadataTsvCreator.java
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100 changes: 100 additions & 0 deletions
100
src/main/java/org/broadinstitute/hellbender/tools/variantdb/arrays/ArraySampleFieldEnum.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,100 @@ | ||
| package org.broadinstitute.hellbender.tools.variantdb.arrays; | ||
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| import htsjdk.variant.variantcontext.VariantContext; | ||
| import org.broadinstitute.hellbender.tools.variantdb.CommonCode; | ||
| import org.broadinstitute.hellbender.tools.variantdb.arrays.tables.ProbeInfo; | ||
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| import java.util.*; | ||
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| public enum ArraySampleFieldEnum { | ||
| sample_id, | ||
| sample_name, | ||
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| // This where the validation step (required vs not) lives -- fail if there is missing data for a required field | ||
| // and just leave it empty if not required | ||
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| NUM_ASSAYS { | ||
| public String getColumnValue(final Map<String, String> metricsMap) { | ||
| return metricsMap.get(this.name()); | ||
| } | ||
| }, | ||
| NUM_NON_FILTERED_ASSAYS{ | ||
| public String getColumnValue(final Map<String, String> metricsMap) { | ||
| return metricsMap.get(this.name()); | ||
| } | ||
| }, | ||
| NUM_FILTERED_ASSAYS{ | ||
| public String getColumnValue(final Map<String, String> metricsMap) { | ||
| return metricsMap.get(this.name()); | ||
| } | ||
| }, | ||
| NUM_ZEROED_OUT_ASSAYS{ | ||
| public String getColumnValue(final Map<String, String> metricsMap) { | ||
| return metricsMap.get(this.name()); | ||
| } | ||
| }, | ||
| NUM_SNPS{ | ||
| public String getColumnValue(final Map<String, String> metricsMap) { | ||
| return metricsMap.get(this.name()); | ||
| } | ||
| }, | ||
| NUM_INDELS{ | ||
| public String getColumnValue(final Map<String, String> metricsMap) { | ||
| return metricsMap.get(this.name()); | ||
| } | ||
| }, | ||
| NUM_CALLS{ | ||
| public String getColumnValue(final Map<String, String> metricsMap) { | ||
| return metricsMap.get(this.name()); | ||
| } | ||
| }, | ||
| NUM_AUTOCALL_CALLS{ | ||
| public String getColumnValue(final Map<String, String> metricsMap) { | ||
| return metricsMap.get(this.name()); | ||
| } | ||
| }, | ||
| NUM_NO_CALLS{ | ||
| public String getColumnValue(final Map<String, String> metricsMap) { | ||
| return metricsMap.get(this.name()); | ||
| } | ||
| }, | ||
| NUM_IN_DB_SNP{ | ||
| public String getColumnValue(final Map<String, String> metricsMap) { | ||
| return metricsMap.get(this.name()); | ||
| } | ||
| }, | ||
| NOVEL_SNPS{ | ||
| public String getColumnValue(final Map<String, String> metricsMap) { | ||
| return metricsMap.get(this.name()); | ||
| } | ||
| }, | ||
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| PCT_DBSNP{ | ||
| public String getColumnValue(final Map<String, String> metricsMap) { | ||
| return metricsMap.get(this.name()); | ||
| } | ||
| }, | ||
| CALL_RATE{ | ||
| public String getColumnValue(final Map<String, String> metricsMap) { | ||
| return metricsMap.get(this.name()); | ||
| } | ||
| }, | ||
| AUTOCALL_CALL_RATE{ | ||
| public String getColumnValue(final Map<String, String> metricsMap) { | ||
| return metricsMap.get(this.name()); | ||
| } | ||
| }, | ||
| NUM_SINGLETONS{ | ||
| public String getColumnValue(final Map<String, String> metricsMap) { | ||
| return metricsMap.get(this.name()); | ||
| } | ||
| }; | ||
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| public String getColumnValue(final Map<String, String> metricsMap) { | ||
| throw new IllegalArgumentException("Not implemented"); | ||
| } | ||
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| } |
110 changes: 110 additions & 0 deletions
110
...main/java/org/broadinstitute/hellbender/tools/variantdb/arrays/ArraySampleTsvCreator.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,110 @@ | ||
| package org.broadinstitute.hellbender.tools.variantdb.arrays; | ||
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| import org.apache.logging.log4j.LogManager; | ||
| import org.apache.logging.log4j.Logger; | ||
| import org.broadinstitute.hellbender.exceptions.UserException; | ||
| import org.broadinstitute.hellbender.tools.variantdb.IngestConstants; | ||
| import org.broadinstitute.hellbender.utils.tsv.SimpleXSVWriter; | ||
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| import java.io.*; | ||
| import java.util.ArrayList; | ||
| import java.util.Arrays; | ||
| import java.util.List; | ||
| import java.util.Map; | ||
| import java.util.stream.Collectors; | ||
| import java.util.stream.IntStream; | ||
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| public class ArraySampleTsvCreator { | ||
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| private static final Logger logger = LogManager.getLogger(ArraySampleTsvCreator.class); | ||
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| private SimpleXSVWriter sampleMetadataWriter = null; | ||
| private Map<String, String> metricsMap; | ||
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| public ArraySampleTsvCreator(String metricsFilepath) { | ||
| if (metricsFilepath != null && !metricsFilepath.isEmpty()) { | ||
| BufferedReader reader = null; | ||
| try { | ||
| String columns = null; | ||
| String values = null; | ||
| reader = new BufferedReader(new FileReader(metricsFilepath)); | ||
| String line = reader.readLine(); | ||
| while (line != null) { | ||
| if (!line.startsWith("#") && !line.trim().isEmpty()) { | ||
| if (columns == null) { | ||
| columns = line; | ||
| } else if (values == null) { | ||
| values = line; | ||
| } else { | ||
| // there are more lines than expected - output a warning | ||
| logger.warn("more lines than expected in metrics file: " + line); | ||
| } | ||
| } | ||
| line = reader.readLine(); | ||
| } | ||
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| List<String> colList = Arrays.asList(columns.split("\t")); | ||
| List<String> valList = Arrays.asList(values.split("\t")); | ||
| metricsMap = IntStream.range(0, colList.size()).boxed().collect(Collectors.toMap(colList::get, valList::get)); | ||
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| } catch (IOException e) { | ||
| throw new RuntimeException("could not read metrics file", e); | ||
| } | ||
| } | ||
| } | ||
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| public static List<String> getHeaders() { | ||
| return Arrays.stream(ArraySampleFieldEnum.values()).map(String::valueOf).collect(Collectors.toList()); | ||
| } | ||
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| public void createRow(String sampleName, String sampleId, String tableNumberPrefix, File outputDirectory) { | ||
| // if the metadata tsvs don't exist yet -- create them | ||
| try { | ||
| // Create a metadata file to go into the metadata dir for _this_ sample | ||
| // TODO--this should just be one file per sample set? | ||
| final File sampleMetadataFileName = new File (outputDirectory, IngestConstants.sampleMetadataFilePrefix + tableNumberPrefix + sampleName + IngestConstants.FILETYPE); | ||
| // write header to it | ||
| List<String> sampleListHeader = ArraySampleTsvCreator.getHeaders(); | ||
| sampleMetadataWriter = new SimpleXSVWriter(sampleMetadataFileName.toPath(), IngestConstants.SEPARATOR); | ||
| sampleMetadataWriter.setHeaderLine(sampleListHeader); | ||
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| final List<String> TSVLineToCreateSampleMetadata = createSampleListRow( | ||
| sampleName, | ||
| sampleId); | ||
| sampleMetadataWriter.getNewLineBuilder().setRow(TSVLineToCreateSampleMetadata).write(); | ||
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| } catch (final IOException e) { | ||
| throw new UserException("Could not create sample outputs", e); | ||
| } | ||
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| } | ||
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| private List<String> createSampleListRow(String sampleName, String sampleId) { | ||
| List<String> row = new ArrayList<>(); | ||
| row.add(sampleName); | ||
| row.add(sampleId); | ||
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| for (final ArraySampleFieldEnum fieldEnum : ArraySampleFieldEnum.values()) { | ||
| if (fieldEnum != ArraySampleFieldEnum.sample_id && fieldEnum != ArraySampleFieldEnum.sample_name) { | ||
| if (metricsMap == null) { | ||
| row.add("null"); | ||
| } else { | ||
| row.add(fieldEnum.getColumnValue(metricsMap)); | ||
| } | ||
| } | ||
| } | ||
| return row; | ||
| } | ||
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| public void closeTool() { | ||
| if (sampleMetadataWriter != null) { | ||
| try { | ||
| sampleMetadataWriter.close(); | ||
| } catch (final Exception e) { | ||
| throw new IllegalArgumentException("Couldn't close array sample writer", e); | ||
| } | ||
| } | ||
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| } | ||
| } |
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I'm so surprised this code doesn't exist anywhere? the VCFWriter must be doing (largely) the same thing?
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yes, but it is very embedded in the actual writing of the output and in htsjdk which for some reason i think it's more difficult for us to modify to make it modular.