Changeset 5723

Timestamp:

Nov 13, 2019, 9:07:07 AM (3 years ago)

Author:

Nicklas Nordborg

Message:

References #1199: Implement Variant calling pipeline

Auto-confirmation need to be handled differently if the variant calling is raw-only mode or full mode. The current implementation can be used for the raw-only mode which simply put the alignment back into the variant calling pipeline list.

Location:

extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie

Files:

• autoconfirm/AutoConfirmService.java (modified) (5 diffs)
• autoconfirm/RawOnlyVariantCallAutoConfirmer.java (moved) (moved from extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/autoconfirm/VariantCallAutoConfirmer.java) (4 diffs)
• grid/VariantCallingJobCreator.java (modified) (2 diffs)

extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/autoconfirm/AutoConfirmService.java

@@ -207 +207 @@
       RawDataType cufflinksType = Rawdatatype.CUFFLINKS.getRawDataType();
       RawDataType stringTieType = Rawdatatype.STRINGTIE.getRawDataType();
+      RawDataType variantCallType = Rawdatatype.VARIANT_CALL.getRawDataType();
       
       // Collection AutoConfirm actions
@@ -277 +278 @@
           ac = new StringTieAutoConfirmer(raw);
         }
+        else if (variantCallType.equals(rawType))
+        {
+          //ac = new VariantCallAutoConfirmer(raw);
+        }
       
         manager.checkRulesAndAdd(dc, ac);
@@ -291 +296 @@
       // Check if there are any failed mBAF analysis or variant calling jobs
       numItems += confirmMBafAnalysis(dc, manager, "mbaf_genotype.vcf");
-      numItems += confirmVariantCalling(dc, manager, "variants-raw.vcf.gz");
+      numItems += confirmRawOnlyVariantCalling(dc, manager, "variants-raw.vcf.gz");
       
       // Commit now so that all items are reverted to manual flow just in case
@@ -382 +387 @@
     @since 4.24
   */
-  private int confirmVariantCalling(DbControl dc, AutoConfirmManager manager, String vcfName)
+  private int confirmRawOnlyVariantCalling(DbControl dc, AutoConfirmManager manager, String vcfName)
   {
     ItemQuery<DerivedBioAssay> query = DerivedBioAssay.getQuery();
@@ -399 +404 @@
       numItems++;
       DerivedBioAssay alignment = it.next();
-      AutoConfirmer<?> ac = new VariantCallAutoConfirmer(alignment, vcfName);
+      AutoConfirmer<?> ac = new RawOnlyVariantCallAutoConfirmer(alignment, vcfName);
       manager.checkRulesAndAdd(dc, ac);
     }

extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/autoconfirm/RawOnlyVariantCallAutoConfirmer.java

@@ -10 +10 @@
 
 /**
-  Auto-confirm implementation for alignments after running variant calling.
+  Auto-confirm implementation for alignments after running raw-only variant calling.
   This auto-confirmer is needed to handle the case when the analysis fails.
   In this case the 'variants-raw.vcf.gz' will be linked to the failed JOB instead 
@@ -22 +22 @@
   @since 4.24
 */
-public class VariantCallAutoConfirmer 
+public class RawOnlyVariantCallAutoConfirmer 
   extends AutoConfirmer<DerivedBioAssay> 
 {
@@ -28 +28 @@
   private AnyToAny link;
   
-  public VariantCallAutoConfirmer(DerivedBioAssay alignment, String vcfName)
+  public RawOnlyVariantCallAutoConfirmer(DerivedBioAssay alignment, String vcfName)
   {
     super(alignment, null);
@@ -81 +81 @@
   {
     if (!super.equals(o)) return false;
-    VariantCallAutoConfirmer other = (VariantCallAutoConfirmer)o;
+    RawOnlyVariantCallAutoConfirmer other = (RawOnlyVariantCallAutoConfirmer)o;
     return other.vcfName.equals(vcfName);
   }

extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/grid/VariantCallingJobCreator.java

@@ -287 +287 @@
         if (autoConfirm)
         {
-          // TODO -- what about raw-only mode??
           Annotationtype.AUTO_PROCESSING.setAnnotationValue(dc, raw, "AutoConfirm");
         }
@@ -295 +294 @@
         ScriptUtil.checkValidScriptParameter(raw.getName());
       }
-      
-      // Temporary link to the job so that it is possible to handle failed jobs in the VariantCallingAutoConfirmer
-      if (autoConfirm)
-      {
-        // TODO -- what about filtering mode??
-        AnyToAny link = AnyToAny.getNewOrExisting(dc, aligned, "variants-raw.vcf.gz", vCallJob, false);
-        if (!link.isInDatabase()) dc.saveItem(link);
+      else
+      {
+        // Temporary link to the job so that it is possible to handle failed jobs in the RawOnlyVariantCallingAutoConfirmer
+        if (autoConfirm)
+        {
+          AnyToAny link = AnyToAny.getNewOrExisting(dc, aligned, "variants-raw.vcf.gz", vCallJob, false);
+          if (!link.isInDatabase()) dc.saveItem(link);
+        }
       }