-
Notifications
You must be signed in to change notification settings - Fork 596
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
add in feature extract code. resulting vcf still has bugs (#6947)
* add in feature extract code. resulting vcf still has bugs
- Loading branch information
Showing
19 changed files
with
806 additions
and
274 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
121 changes: 121 additions & 0 deletions
121
src/main/java/org/broadinstitute/hellbender/tools/variantdb/SampleList.java
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,121 @@ | ||
| package org.broadinstitute.hellbender.tools.variantdb; | ||
|
|
||
| import com.google.cloud.bigquery.FieldValueList; | ||
| import com.google.cloud.bigquery.TableResult; | ||
| import java.io.File; | ||
| import java.io.IOException; | ||
| import java.nio.charset.StandardCharsets; | ||
| import java.nio.file.Files; | ||
| import java.util.*; | ||
| import java.util.stream.Collectors; | ||
| import org.apache.commons.lang.StringUtils; | ||
| import org.apache.logging.log4j.LogManager; | ||
| import org.apache.logging.log4j.Logger; | ||
| import org.broadinstitute.hellbender.utils.bigquery.BigQueryUtils; | ||
| import org.broadinstitute.hellbender.utils.bigquery.TableReference; | ||
|
|
||
| public class SampleList { | ||
| static final Logger logger = LogManager.getLogger(SampleList.class); | ||
|
|
||
| private Map<Long, String> sampleIdMap; | ||
| private Map<String, Long> sampleNameMap; | ||
|
|
||
| public SampleList(String sampleTableName, File sampleFile, boolean printDebugInformation) { | ||
| if (sampleTableName != null) { | ||
| initializeMaps(new TableReference(sampleTableName, SchemaUtils.SAMPLE_FIELDS), printDebugInformation); | ||
| } else if (sampleFile != null) { | ||
| initializeMaps(sampleFile); | ||
| } else { | ||
| throw new IllegalArgumentException("--cohort-sample-names or --cohort-sample-table must be provided."); | ||
| } | ||
| } | ||
|
|
||
| public int size() { | ||
| return sampleIdMap.size(); | ||
| } | ||
|
|
||
| public Collection<String> getSampleNames() { | ||
| return sampleIdMap.values(); | ||
| } | ||
|
|
||
| public String getSampleName(long id) { | ||
| return sampleIdMap.get(id); | ||
| } | ||
|
|
||
| public long getSampleId(String name) { | ||
| return sampleNameMap.get(name); | ||
| } | ||
|
|
||
| public Map<Long, String> getMap() { | ||
| return sampleIdMap; | ||
| } | ||
|
|
||
| // protected Map<String, Integer> getSampleNameMap(TableReference sampleTable, List<String> samples, boolean printDebugInformation) { | ||
| // Map<String, Integer> results = new HashMap<>(); | ||
| // // create optional where clause | ||
| // String whereClause = ""; | ||
| // if (samples != null && samples.size() > 0) { | ||
| // whereClause = " WHERE " + SchemaUtils.SAMPLE_NAME_FIELD_NAME + " in (\'" + StringUtils.join(samples, "\',\'") + "\') "; | ||
| // } | ||
| // | ||
| // TableResult queryResults = querySampleTable(sampleTable.getFQTableName(), whereClause, printDebugInformation); | ||
| // | ||
| // // Add our samples to our map: | ||
| // for (final FieldValueList row : queryResults.iterateAll()) { | ||
| // results.put(row.get(1).getStringValue(), (int) row.get(0).getLongValue()); | ||
| // } | ||
| // return results; | ||
| // } | ||
|
|
||
|
|
||
| protected void initializeMaps(TableReference sampleTable, boolean printDebugInformation) { | ||
|
|
||
| sampleIdMap = new HashMap<>(); | ||
| sampleNameMap = new HashMap<>(); | ||
| TableResult queryResults = querySampleTable(sampleTable.getFQTableName(), "", printDebugInformation); | ||
|
|
||
| // Add our samples to our map: | ||
| for (final FieldValueList row : queryResults.iterateAll()) { | ||
| long id = row.get(0).getLongValue(); | ||
| String name = row.get(1).getStringValue(); | ||
| sampleIdMap.put(id, name); | ||
| sampleNameMap.put(name, id); | ||
| } | ||
| } | ||
|
|
||
| protected void initializeMaps(File cohortSampleFile) { | ||
| try { | ||
| Files.readAllLines(cohortSampleFile.toPath(), StandardCharsets.US_ASCII).stream() | ||
| .map(s -> s.split(",")) | ||
| .forEach(tokens -> { | ||
| long id = Long.parseLong(tokens[0]); | ||
| String name = tokens[1]; | ||
| sampleIdMap.put(id, name); | ||
| sampleNameMap.put(name, id); | ||
| }); | ||
| } catch (IOException e) { | ||
| throw new IllegalArgumentException("Could not parse --cohort-sample-file", e); | ||
| } | ||
| } | ||
|
|
||
| private TableResult querySampleTable(String fqSampleTableName, String whereClause, boolean printDebugInformation) { | ||
| // Get the query string: | ||
| final String sampleListQueryString = | ||
| "SELECT " + SchemaUtils.SAMPLE_ID_FIELD_NAME + ", " + SchemaUtils.SAMPLE_NAME_FIELD_NAME + | ||
| " FROM `" + fqSampleTableName + "`" + whereClause; | ||
|
|
||
|
|
||
| // Execute the query: | ||
| final TableResult result = BigQueryUtils.executeQuery(sampleListQueryString); | ||
|
|
||
| // Show our pretty results: | ||
| if (printDebugInformation) { | ||
| logger.info("Sample names returned:"); | ||
| final String prettyQueryResults = BigQueryUtils.getResultDataPrettyString(result); | ||
| logger.info("\n" + prettyQueryResults); | ||
| } | ||
|
|
||
| return result; | ||
| } | ||
|
|
||
| } |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Oops, something went wrong.