Skip to content

Commit

Permalink
Merge branch 'broadinstitute:master' into master
Browse files Browse the repository at this point in the history
  • Loading branch information
@Schaudge
Schaudge authored Nov 15, 2023
2 parents 9d29091 + 1dc7ee4 commit 0d563d3
Show file tree
Hide file tree
Showing 33 changed files with 2,360 additions and 1,991 deletions.
2 changes: 1 addition & 1 deletion build.gradle
View file
Original file line number Diff line number Diff line change
Expand Up @@ -56,7 +56,7 @@ repositories {
mavenLocal()
}

final htsjdkVersion = System.getProperty('htsjdk.version','3.0.5')
final htsjdkVersion = System.getProperty('htsjdk.version','4.0.2')
final picardVersion = System.getProperty('picard.version','3.1.0')
final barclayVersion = System.getProperty('barclay.version','5.0.0')
final sparkVersion = System.getProperty('spark.version', '3.3.1')
Expand Down
4 changes: 2 additions & 2 deletions scripts/funcotator/data_sources/cosmic/createCosmicFusionGeneTsv.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -90,7 +90,7 @@ def renderFusionGeneDictEntry(geneKey, fusionGeneDict):
tsvReader = GenericTsvReader(inputFilename)
headers = tsvReader.getFieldNames()
print('Found headers (input): ' + str(headers))
if "Translocation Name" not in headers:
if "TRANSLOCATION_NAME" not in headers:
raise NotImplementedError("Could not find Translocation Name column in the input file.")

outputHeaders = ['gene', 'fusion_genes', 'fusion_id']
Expand All @@ -99,7 +99,7 @@ def renderFusionGeneDictEntry(geneKey, fusionGeneDict):
fusionGeneDict = OrderedDict()
last_i = 0
for i, line in enumerate(tsvReader):
fusion_gene_description = line['Translocation Name']
fusion_gene_description = line['TRANSLOCATION_NAME']

if len(fusion_gene_description.strip()) == 0:
# blank
Expand Down
6 changes: 6 additions & 0 deletions scripts/funcotator/data_sources/cosmic/createSqliteCosmicDb.sh
View file
Original file line number Diff line number Diff line change
Expand Up @@ -18,6 +18,7 @@ set -e

COSMIC_FILE=CosmicCompleteTargetedScreensMutantExport.tsv
OUT_DB_FILE="Cosmic.db"
OUT_TMP_FOLDER="~/tmp"

################################################################################

Expand All @@ -29,6 +30,10 @@ if [[ $# -gt 1 ]] ; then
OUT_DB_FILE=$2
fi

if [[ $# -gt 2 ]] ; then
OUT_TMP_FOLDER=$3
fi

if [ ! -f ${COSMIC_FILE} ] ; then
echo "ERROR: Given COSMIC file does not exist: ${COSMIC_FILE}" 1>&2
exit 1
Expand All @@ -42,6 +47,7 @@ sqlite3 ${OUT_DB_FILE} <<EOF
.echo on
.mode tabs
.import ${COSMIC_FILE} RawCosmic
pragma temp_store_directory = ${OUT_TMP_FOLDER};
CREATE TABLE Cosmic AS SELECT * FROM RawCosmic WHERE ("Mutation AA" != "" OR "Mutation genome position" != "");
DROP TABLE RawCosmic;
UPDATE Cosmic SET "Mutation genome position" = "chr"||"Mutation genome position" WHERE "Mutation genome position" != "";
Expand Down
15 changes: 6 additions & 9 deletions scripts/funcotator/data_sources/cosmic/getCosmicDataSources.sh
View file
Original file line number Diff line number Diff line change
Expand Up @@ -11,7 +11,7 @@ SCRIPTNAME=$( echo $0 | sed 's#.*/##g' )

################################################################################

version="v84"
version="v98"

EMAIL=""
PASSWORD=""
Expand Down Expand Up @@ -135,15 +135,12 @@ mkdir -vp cosmic/hg19 cosmic/hg38 cosmic_fusion/hg19 cosmic_fusion/hg38 cosmic_t
# Get the data files:

echo "Getting files ... "
lftp --norc -u "${EMAIL}","${PASSWORD}" sftp://sftp-cancer.sanger.ac.uk <<EOF
AUTH_TOKEN=$(echo -n "$EMAIL:$PASSWORD" | base64)

get cosmic/grch37/cosmic/${version}/CosmicCompleteTargetedScreensMutantExport.tsv.gz -o cosmic/hg19/CosmicCompleteTargetedScreensMutantExport.tsv.gz
get cosmic/grch37/cosmic/${version}/CosmicFusionExport.tsv.gz -o cosmic_fusion/hg19/CosmicFusionExport.tsv.gz
get cosmic/grch38/cosmic/${version}/CosmicCompleteTargetedScreensMutantExport.tsv.gz -o cosmic/hg38/CosmicCompleteTargetedScreensMutantExport.tsv.gz
get cosmic/grch38/cosmic/${version}/CosmicFusionExport.tsv.gz -o cosmic_fusion/hg38/CosmicFusionExport.tsv.gz
bye
EOF
curl -sS "$(curl -H "Authorization: Basic $AUTH_TOKEN" https://cancer.sanger.ac.uk/cosmic/file_download/GRCh37/cosmic/${version}/CosmicCompleteTargetedScreensMutantExport.tsv.gz | jq -r '.url')" -o cosmic/hg19/CosmicCompleteTargetedScreensMutantExport.tsv.gz
curl -sS "$(curl -H "Authorization: Basic $AUTH_TOKEN" https://cancer.sanger.ac.uk/cosmic/file_download/GRCh37/cosmic/${version}/CosmicFusionExport.tsv.gz | jq -r '.url')" -o cosmic_fusion/hg19/CosmicFusionExport.tsv.gz
curl -sS "$(curl -H "Authorization: Basic $AUTH_TOKEN" https://cancer.sanger.ac.uk/cosmic/file_download/GRCh38/cosmic/${version}/CosmicCompleteTargetedScreensMutantExport.tsv.gz | jq -r '.url')" -o cosmic/hg38/CosmicCompleteTargetedScreensMutantExport.tsv.gz
curl -sS "$(curl -H "Authorization: Basic $AUTH_TOKEN" https://cancer.sanger.ac.uk/cosmic/file_download/GRCh38/cosmic/${version}/CosmicFusionExport.tsv.gz | jq -r '.url')" -o cosmic_fusion/hg38/CosmicFusionExport.tsv.gz

echo "Retrieved COSMIC version ${version} on $(date) from sftp-cancer.sanger.ac.uk by: ${SCRIPTNAME}:" > cosmic/metadata.txt
echo "User: ${EMAIL}" >> cosmic/metadata.txt
Expand Down
2 changes: 1 addition & 1 deletion scripts/funcotator/data_sources/downloadHgncDataSource.sh
View file
Original file line number Diff line number Diff line change
Expand Up @@ -2,5 +2,5 @@

# Downloads the HGNC data source from the HGNC website.

curl 'https://www.genenames.org/cgi-bin/download?col=gd_hgnc_id&col=gd_app_sym&col=gd_app_name&col=gd_status&col=gd_locus_type&col=gd_locus_group&col=gd_prev_sym&col=gd_prev_name&col=gd_aliases&col=gd_name_aliases&col=gd_pub_chrom_map&col=gd_date_mod&col=gd_date_sym_change&col=gd_date_name_change&col=gd_pub_acc_ids&col=gd_enz_ids&col=gd_pub_eg_id&col=gd_pub_ensembl_id&col=gd_pubmed_ids&col=gd_pub_refseq_ids&col=family.id&col=family.name&col=gd_ccds_ids&col=gd_vega_ids&col=md_eg_id&col=md_mim_id&col=md_refseq_id&col=md_prot_id&col=md_ensembl_id&col=md_ucsc_id&status=Approved&status_opt=2&where=&order_by=gd_app_sym_sort&format=text&limit=&hgnc_dbtag=on&submit=submit' > hgnc_download_$(date +%b%d%Y).tsv
curl 'https://www.genenames.org/cgi-bin/download/custom?col=gd_hgnc_id&amp;col=gd_app_sym&amp;col=gd_app_name&amp;col=gd_status&amp;col=gd_locus_type&amp;col=gd_locus_group&amp;col=gd_prev_sym&amp;col=gd_prev_name&amp;col=gd_aliases&amp;col=gd_name_aliases&amp;col=gd_pub_chrom_map&amp;col=gd_date_mod&amp;col=gd_date_sym_change&amp;col=gd_date_name_change&amp;col=gd_pub_acc_ids&amp;col=gd_enz_ids&amp;col=gd_pub_eg_id&amp;col=gd_pub_ensembl_id&amp;col=gd_pubmed_ids&amp;col=gd_pub_refseq_ids&amp;col=family.id&amp;col=family.name&amp;col=gd_ccds_ids&amp;col=gd_vega_ids&amp;col=md_eg_id&amp;col=md_mim_id&amp;col=md_refseq_id&amp;col=md_prot_id&amp;col=md_ensembl_id&amp;col=md_ucsc_id&amp;status=Approved&amp;status_opt=2&amp;where=&amp;order_by=gd_app_sym_sort&amp;format=text&amp;limit=&amp;hgnc_dbtag=on&amp;submit=submi' > hgnc_download_$(date +%b%d%Y).tsv

28 changes: 28 additions & 0 deletions scripts/funcotator/data_sources/finalizeFuncotatorReleaseDirectory.sh
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,28 @@
#!/usr/bin/env bash

#NOTE: This script has been checked in to aid in the release process for future Funcotator datasource bundles.

echo "Making Tarballs of each Datasource Directory..."

tar -zcvf funcotator_dataSources.v1.8.hg38.20230908s.tar.gz funcotator_dataSources.v1.8.hg38.20230908s
tar -zcvf funcotator_dataSources.v1.8.hg38.20230908g.tar.gz funcotator_dataSources.v1.8.hg38.20230908g
tar -zcvf funcotator_dataSources.v1.8.hg19.20230908s.tar.gz funcotator_dataSources.v1.8.hg19.20230908s
tar -zcvf funcotator_dataSources.v1.8.hg19.20230908g.tar.gz funcotator_dataSources.v1.8.hg19.20230908g

echo "Making the various hashfiles for release"

find funcotator_dataSources.v1.8.hg38.20230908s -type f | xargs md5sum > funcotator_dataSources.v1.8.hg38.20230908s.dir.long.md5sum
md5sum funcotator_dataSources.v1.8.hg38.20230908s.tar.gz | awk '{print $1}' > funcotator_dataSources.v1.8.hg38.20230908s.dir.md5sum
sha256sum funcotator_dataSources.v1.8.hg38.20230908s.tar.gz > funcotator_dataSources.v1.8.hg38.20230908s.sha256

find funcotator_dataSources.v1.8.hg38.20230908g -type f | xargs md5sum > funcotator_dataSources.v1.8.hg38.20230908g.dir.long.md5sum
md5sum funcotator_dataSources.v1.8.hg38.20230908g.tar.gz | awk '{print $1}' > funcotator_dataSources.v1.8.hg38.20230908g.dir.md5sum
sha256sum funcotator_dataSources.v1.8.hg38.20230908g.tar.gz > funcotator_dataSources.v1.8.hg38.20230908g.sha256

find funcotator_dataSources.v1.8.hg19.20230908s -type f | xargs md5sum > funcotator_dataSources.v1.8.hg19.20230908s.dir.long.md5sum
md5sum funcotator_dataSources.v1.8.hg19.20230908s.tar.gz | awk '{print $1}' > funcotator_dataSources.v1.8.hg19.20230908s.dir.md5sum
sha256sum funcotator_dataSources.v1.8.hg19.20230908s.tar.gz > funcotator_dataSources.v1.8.hg19.20230908s.sha256

find funcotator_dataSources.v1.8.hg19.20230908g -type f | xargs md5sum > funcotator_dataSources.v1.8.hg19.20230908g.dir.long.md5sum
md5sum funcotator_dataSources.v1.8.hg19.20230908g.tar.gz | awk '{print $1}' > funcotator_dataSources.v1.8.hg19.20230908g.dir.md5sum
sha256sum funcotator_dataSources.v1.8.hg19.20230908g.tar.gz > funcotator_dataSources.v1.8.hg19.20230908g.sha256
2 changes: 1 addition & 1 deletion scripts/funcotator/data_sources/getGencode.sh
View file
Original file line number Diff line number Diff line change
Expand Up @@ -15,7 +15,7 @@ MAXARGS=0

# Latest release numbers for our references.
# Update these numbers when a new Gencode is released.
LATEST_RELEASE=34
LATEST_RELEASE=43

DATA_SOURCE_NAME="Gencode"
OUT_DIR_NAME='gencode'
Expand Down
4 changes: 2 additions & 2 deletions scripts/funcotator/data_sources/getGencodeXHGNC.sh
View file
Original file line number Diff line number Diff line change
Expand Up @@ -8,10 +8,10 @@ outFileBaseName="gencode_xhgnc"
outExt=".tsv"

hg19db="homo_sapiens_core_75_37"
hg38db="homo_sapiens_core_90_38"
hg38db="homo_sapiens_core_110_38"

hg19FileName=${outFileBaseName}_v75_37.hg19${outExt}
hg38FileName=${outFileBaseName}_v90_38.hg38${outExt}
hg38FileName=${outFileBaseName}_v110_38.hg38${outExt}

################################################################################

Expand Down
4 changes: 2 additions & 2 deletions scripts/funcotator/data_sources/getGencodeXRefseq.sh
View file
Original file line number Diff line number Diff line change
Expand Up @@ -8,10 +8,10 @@ outFileBaseName="gencode_xrefseq"
outExt=".tsv"

hg19db="homo_sapiens_core_75_37"
hg38db="homo_sapiens_core_90_38"
hg38db="homo_sapiens_core_110_38"

hg19FileName=${outFileBaseName}_v75_37.hg19${outExt}
hg38FileName=${outFileBaseName}_v90_38.hg38${outExt}
hg38FileName=${outFileBaseName}_v110_38.hg38${outExt}

################################################################################

Expand Down
7 changes: 5 additions & 2 deletions src/main/java/org/broadinstitute/hellbender/tools/funcotator/Funcotator.java
View file
Original file line number Diff line number Diff line change
Expand Up @@ -874,7 +874,6 @@ public void apply(final VariantContext variant, final ReadsContext readsContext,
// Get the correct reference for B37/HG19 compliance:
// This is necessary because of the variant transformation that gets applied in VariantWalkerBase::apply.
final ReferenceContext correctReferenceContext = funcotatorEngine.getCorrectReferenceContext(variant, referenceContext);

// Place the variant on our queue to be funcotated:
enqueueAndHandleVariant(variant, correctReferenceContext, featureContext);
}
Expand Down Expand Up @@ -924,7 +923,11 @@ protected void enqueueAndHandleVariant(final VariantContext variant, final Refer

final FuncotationMap funcotationMap = funcotatorEngine.createFuncotationMapForVariant(variant, referenceContext, featureContext);

// This is necessary because we want to revert the variant contig name change if it was applied in the FuncotatorEngine::getCorrectVariantContextForReference method before outputting the vcf.
// NOTE: this will only revert the variantContext if it was originally changed (only for B37 VCFs)
final VariantContext variantContextForOutput = funcotatorEngine.getCorrectVariantContextForOutput(variant);

// At this point there is only one transcript ID in the funcotation map if canonical or best effect are selected
outputRenderer.write(variant, funcotationMap);
outputRenderer.write(variantContextForOutput, funcotationMap);
}
}
77 changes: 61 additions & 16 deletions ...n/java/org/broadinstitute/hellbender/tools/funcotator/FuncotatorDataSourceDownloader.java
View file
Original file line number Diff line number Diff line change
Expand Up @@ -32,8 +32,8 @@
* <p>
* To download and extract the data sources, you can invoke {@link FuncotatorDataSourceDownloader} in the following ways:
* <ul>
* <li>For <strong>somatic</strong> data sources:<br /><pre>{@code ./gatk FuncotatorDataSourceDownloader --somatic --validate-integrity --extract-after-download}</pre></li>
* <li>For <strong>germline</strong> data sources:<br /><pre>{@code ./gatk FuncotatorDataSourceDownloader --germline --validate-integrity --extract-after-download}</pre></li>
* <li>For <strong>somatic</strong> data sources:<br /><pre>{@code ./gatk FuncotatorDataSourceDownloader --somatic --validate-integrity --hg38 --extract-after-download}</pre></li>
* <li>For <strong>germline</strong> data sources:<br /><pre>{@code ./gatk FuncotatorDataSourceDownloader --germline --validate-integrity --hg19 --extract-after-download}</pre></li>
* </ul>
* </p>
*
Expand Down Expand Up @@ -63,6 +63,8 @@ public class FuncotatorDataSourceDownloader extends CommandLineProgram {
public static final String GERMLINE_ARG_LONG_NAME = "germline";
public static final String OVERWRITE_ARG_LONG_NAME = "overwrite-output-file";
public static final String EXTRACT_AFTER_DOWNLOAD = "extract-after-download";
public static final String HG38_ARG_LONG_NAME = "hg38";
public static final String HG19_ARG_LONG_NAME = "hg19";

//==================================================================================================================
// Private Static Members:
Expand All @@ -73,18 +75,27 @@ public class FuncotatorDataSourceDownloader extends CommandLineProgram {
// Private Static Members:

// Set to always get the latest version of the data sources:
private static final String BASE_URL = DataSourceUtils.DATA_SOURCES_BUCKET_PATH +
DataSourceUtils.DATA_SOURCES_NAME_PREFIX + "." + DataSourceUtils.getDataSourceMaxVersionString();
private static final String HG38_BASE_URL = DataSourceUtils.DATA_SOURCES_BUCKET_PATH +
DataSourceUtils.DATA_SOURCES_NAME_PREFIX + "." + DataSourceUtils.getDataSourceMaxVersionString(38);
private static final String HG19_BASE_URL = DataSourceUtils.DATA_SOURCES_BUCKET_PATH +
DataSourceUtils.DATA_SOURCES_NAME_PREFIX + "." + DataSourceUtils.getDataSourceMaxVersionString(19);

private static final String HG38_GERMLINE_GCLOUD_DATASOURCES_BASEURL = HG38_BASE_URL + DataSourceUtils.DS_GERMLINE_NAME_MODIFIER;
private static final String HG19_GERMLINE_GCLOUD_DATASOURCES_BASEURL = HG19_BASE_URL + DataSourceUtils.DS_GERMLINE_NAME_MODIFIER;

private static final String GERMLINE_GCLOUD_DATASOURCES_BASEURL = BASE_URL + DataSourceUtils.DS_GERMLINE_NAME_MODIFIER;
@VisibleForTesting
static final Path GERMLINE_GCLOUD_DATASOURCES_PATH = IOUtils.getPath(GERMLINE_GCLOUD_DATASOURCES_BASEURL + DataSourceUtils.DS_EXTENSION);
private static final Path GERMLINE_GCLOUD_DATASOURCES_SHA256_PATH = IOUtils.getPath(GERMLINE_GCLOUD_DATASOURCES_BASEURL + DataSourceUtils.DS_CHECKSUM_EXTENSION);
static final Path HG38_GERMLINE_GCLOUD_DATASOURCES_PATH = IOUtils.getPath(HG38_GERMLINE_GCLOUD_DATASOURCES_BASEURL + DataSourceUtils.DS_EXTENSION);
static final Path HG19_GERMLINE_GCLOUD_DATASOURCES_PATH = IOUtils.getPath(HG19_GERMLINE_GCLOUD_DATASOURCES_BASEURL + DataSourceUtils.DS_EXTENSION);
private static final Path HG38_GERMLINE_GCLOUD_DATASOURCES_SHA256_PATH = IOUtils.getPath(HG38_GERMLINE_GCLOUD_DATASOURCES_BASEURL + DataSourceUtils.DS_CHECKSUM_EXTENSION);
private static final Path HG19_GERMLINE_GCLOUD_DATASOURCES_SHA256_PATH = IOUtils.getPath(HG19_GERMLINE_GCLOUD_DATASOURCES_BASEURL + DataSourceUtils.DS_CHECKSUM_EXTENSION);

public static final String SOMATIC_GCLOUD_DATASOURCES_BASEURL = BASE_URL + DataSourceUtils.DS_SOMATIC_NAME_MODIFIER;;
public static final String HG38_SOMATIC_GCLOUD_DATASOURCES_BASEURL = HG38_BASE_URL + DataSourceUtils.DS_SOMATIC_NAME_MODIFIER;;
public static final String HG19_SOMATIC_GCLOUD_DATASOURCES_BASEURL = HG19_BASE_URL + DataSourceUtils.DS_SOMATIC_NAME_MODIFIER;;

public static final Path SOMATIC_GCLOUD_DATASOURCES_PATH = IOUtils.getPath(SOMATIC_GCLOUD_DATASOURCES_BASEURL + DataSourceUtils.DS_EXTENSION);
private static final Path SOMATIC_GCLOUD_DATASOURCES_SHA256_PATH = IOUtils.getPath(SOMATIC_GCLOUD_DATASOURCES_BASEURL + DataSourceUtils.DS_CHECKSUM_EXTENSION);
public static final Path HG38_SOMATIC_GCLOUD_DATASOURCES_PATH = IOUtils.getPath(HG38_SOMATIC_GCLOUD_DATASOURCES_BASEURL + DataSourceUtils.DS_EXTENSION);
public static final Path HG19_SOMATIC_GCLOUD_DATASOURCES_PATH = IOUtils.getPath(HG19_SOMATIC_GCLOUD_DATASOURCES_BASEURL + DataSourceUtils.DS_EXTENSION);
private static final Path HG38_SOMATIC_GCLOUD_DATASOURCES_SHA256_PATH = IOUtils.getPath(HG38_SOMATIC_GCLOUD_DATASOURCES_BASEURL + DataSourceUtils.DS_CHECKSUM_EXTENSION);
private static final Path HG19_SOMATIC_GCLOUD_DATASOURCES_SHA256_PATH = IOUtils.getPath(HG19_SOMATIC_GCLOUD_DATASOURCES_BASEURL + DataSourceUtils.DS_CHECKSUM_EXTENSION);

//==================================================================================================================
// Private Members:
Expand Down Expand Up @@ -129,6 +140,23 @@ public class FuncotatorDataSourceDownloader extends CommandLineProgram {
optional = true)
protected boolean extractDataSourcesAfterDownload = false;

@Argument(
shortName = HG38_ARG_LONG_NAME,
fullName = HG38_ARG_LONG_NAME,
mutex = {HG19_ARG_LONG_NAME, TESTING_OVERRIDE_PATH_FOR_DATA_SOURCES_SHA256_ARG},
doc = "If set, will extract data from the HG38 data sources bucket.",
optional = true)
protected boolean getHg38Datasources = false;

@Argument(
//TODO should these be MUTEX or should one be allowed to download either?
shortName = HG19_ARG_LONG_NAME,
fullName = HG19_ARG_LONG_NAME,
mutex = {HG38_ARG_LONG_NAME, TESTING_OVERRIDE_PATH_FOR_DATA_SOURCES_SHA256_ARG},
doc = "If set, will extract data from the HG19 data sources bucket.",
optional = true)
protected boolean getHg19Datasources = false;

// Testing arguments:
@Hidden
@Advanced
Expand Down Expand Up @@ -164,6 +192,11 @@ protected void onStartup() {
throw new UserException("Must select either somatic or germline datasources.");
}

// Make sure the user specified at least one reference source to download:
if ((!getHg38Datasources) && (!getHg19Datasources) && (testingOverrideDataSourcesPath == null)) {
throw new UserException("Must select either HG19 or HG38 datasources.");
}

// Make sure the testing inputs are correct:
if ( ((testingOverrideDataSourcesPath == null) && (testingOverrideDataSourcesSha256Path != null)) ||
((testingOverrideDataSourcesSha256Path == null) && (testingOverrideDataSourcesPath != null)) ) {
Expand All @@ -184,14 +217,26 @@ protected Object doWork() {

// Get the correct data source:
if ( getSomaticDataSources ) {
dataSourceDescription = "Somatic";
dataSourcesPath = SOMATIC_GCLOUD_DATASOURCES_PATH;
dataSourcesSha256Path = SOMATIC_GCLOUD_DATASOURCES_SHA256_PATH;
if (getHg38Datasources) {
dataSourceDescription = "HG38_Somatic";
dataSourcesPath = HG38_SOMATIC_GCLOUD_DATASOURCES_PATH;
dataSourcesSha256Path = HG38_SOMATIC_GCLOUD_DATASOURCES_SHA256_PATH;
} else { // Okay because HG38 and HG19 datasources are currently MUTEX and at least one is required
dataSourceDescription = "HG19_Somatic";
dataSourcesPath = HG19_SOMATIC_GCLOUD_DATASOURCES_PATH;
dataSourcesSha256Path = HG19_SOMATIC_GCLOUD_DATASOURCES_SHA256_PATH;
}
}
else if ( getGermlineDataSources ) {
dataSourceDescription = "Germline";
dataSourcesPath = GERMLINE_GCLOUD_DATASOURCES_PATH;
dataSourcesSha256Path = GERMLINE_GCLOUD_DATASOURCES_SHA256_PATH;
if (getHg38Datasources) {
dataSourceDescription = "HG38_Germline";
dataSourcesPath = HG38_GERMLINE_GCLOUD_DATASOURCES_PATH;
dataSourcesSha256Path = HG38_GERMLINE_GCLOUD_DATASOURCES_SHA256_PATH;
} else {
dataSourceDescription = "HG19_Germline";
dataSourcesPath = HG19_GERMLINE_GCLOUD_DATASOURCES_PATH;
dataSourcesSha256Path = HG19_GERMLINE_GCLOUD_DATASOURCES_SHA256_PATH;
}
}
else {
// Test case:
Expand Down
Loading

0 comments on commit 0d563d3

Please sign in to comment.