Merge pull request #365 from overture-stack/rc/5.9.0

rc/5.9.0
overture-stack · May 8, 2023 · baa9ccf · baa9ccf
2 parents 69df945 + 1de26c2
commit baa9ccf
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Showing 10 changed files with 15 additions and 9 deletions.
diff --git a/pom.xml b/pom.xml
@@ -20,7 +20,7 @@ ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF S
 
   <groupId>bio.overture</groupId>
   <artifactId>score</artifactId>
-  <version>5.8.4</version>
+  <version>5.9.0</version>
   <packaging>pom</packaging>
   <name>${project.artifactId}</name>
   <description>${project.name}</description>

diff --git a/score-client/pom.xml b/score-client/pom.xml
@@ -21,7 +21,7 @@ ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF S
   <parent>
     <groupId>bio.overture</groupId>
     <artifactId>score</artifactId>
-    <version>5.8.4</version>
+    <version>5.9.0</version>
     <relativePath>../pom.xml</relativePath>
   </parent>
 
@@ -252,7 +252,7 @@ ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF S
 
     <!-- Versions - Genomics -->
     <!--  <htsjdk.version>1.138</htsjdk.version> -->
-    <htsjdk.version>2.1.0</htsjdk.version>
+    <htsjdk.version>2.16.0</htsjdk.version>
 
     <!-- Versions - FUSE -->
     <javafs.version>0.1.0</javafs.version>

diff --git a/score-client/src/main/bin/score-client b/score-client/src/main/bin/score-client
@@ -51,7 +51,6 @@ CLIENT_DIR="$(cd ${BASE_DIR} && pwd -P)"
 exec java -Xmx3G \
 	--add-opens=java.base/jdk.internal.ref=ALL-UNNAMED \
 	--add-opens=java.base/java.nio=ALL-UNNAMED \
-	--illegal-access=deny \
 	-Dlogging.path=${BASE_DIR}/logs \
 	-Dspring.config.additional-location=${CLIENT_DIR}/conf/ \
 	-Dlogging.config=${CLIENT_DIR}/conf/logback.xml \

diff --git a/score-client/src/main/java/bio/overture/score/client/ClientMain.java b/score-client/src/main/java/bio/overture/score/client/ClientMain.java
@@ -23,6 +23,7 @@
 import bio.overture.score.client.exception.BadManifestException;
 import bio.overture.score.client.metadata.EntityNotFoundException;
 import com.beust.jcommander.*;
+import htsjdk.samtools.util.Log;
 import lombok.Getter;
 import lombok.extern.slf4j.Slf4j;
 import lombok.val;
@@ -89,6 +90,8 @@ public class ClientMain implements CommandLineRunner {
 
   public static void main(String[] args) {
     try {
+      Log.setGlobalLogLevel(Log.LogLevel.ERROR);
+
       // Bootstrap
       val profiles = bootstrap(args);
 

diff --git a/score-client/src/main/java/bio/overture/score/client/command/ViewCommand.java b/score-client/src/main/java/bio/overture/score/client/command/ViewCommand.java
@@ -307,7 +307,8 @@ private void validateParms() {
     }
 
     checkParameter(objectId != null || sequenceFile != null || manifestResource != null,
-      "One of --object-id, --input-file or --manifest must be specified");
+      "One of --object-id, --input-file or --manifest must be specified. " +
+              "For CRAM files, please additionally include --reference-file.");
 
     if (objectId == null && sequenceFile == null) {
       checkParameter(manifestResource != null && outputDir != null,

diff --git a/score-client/src/main/java/bio/overture/score/client/view/Viewer.java b/score-client/src/main/java/bio/overture/score/client/view/Viewer.java
@@ -73,6 +73,9 @@ public SamFileBuilder getBuilder(@NonNull SeekableStream inputStream, SeekableSt
       // Since CRAM is a compressed form of BAM file that saves space by only recording
       // the differences between an individual BAM file and a standard reference file.
       // we need to have the reference file in order to decode the CRAM file.
+      if(referenceFile == null){
+        throw new RuntimeException("CRAM file type detected, an indexed (fai) reference file (fa, fasta) must be provided. Please specify via --reference-file.");
+      }
       val reference = new ReferenceSource(referenceFile);
       val primitiveReader = new CRAMFileReader(inputStream, indexStream,reference, ValidationStringency.DEFAULT_STRINGENCY);
       val reader = new SamReader.PrimitiveSamReaderToSamReaderAdapter(

diff --git a/score-core/pom.xml b/score-core/pom.xml
@@ -21,7 +21,7 @@ ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF S
   <parent>
     <groupId>bio.overture</groupId>
     <artifactId>score</artifactId>
-    <version>5.8.4</version>
+    <version>5.9.0</version>
     <relativePath>../pom.xml</relativePath>
   </parent>
 

diff --git a/score-fs/pom.xml b/score-fs/pom.xml
@@ -21,7 +21,7 @@ ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF S
   <parent>
     <groupId>bio.overture</groupId>
     <artifactId>score</artifactId>
-    <version>5.8.4</version>
+    <version>5.9.0</version>
     <relativePath>../pom.xml</relativePath>
   </parent>
 

diff --git a/score-server/pom.xml b/score-server/pom.xml
@@ -21,7 +21,7 @@ ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF S
   <parent>
     <groupId>bio.overture</groupId>
     <artifactId>score</artifactId>
-    <version>5.8.4</version>
+    <version>5.9.0</version>
     <relativePath>../pom.xml</relativePath>
   </parent>
 

diff --git a/score-test/pom.xml b/score-test/pom.xml
@@ -21,7 +21,7 @@ ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF S
   <parent>
     <groupId>bio.overture</groupId>
     <artifactId>score</artifactId>
-    <version>5.8.4</version>
+    <version>5.9.0</version>
     <relativePath>../pom.xml</relativePath>
   </parent>