changed IS_GERMLINE to SV_STATUS

core/src/main/java/org/mskcc/cbio/maf/TabDelimitedFileUtil.java

@@ -141,11 +141,19 @@ public static Long getPartLong(int index, String[] parts) {
 		}
 	}
 
+	// This method does not call Integer.parseInt() as one might expect.
+	// Presumably this is to allow the convertion of strings like "6.2" to "6".
+	// The method previously called (int)Float.parseFloat() but floats
+	// reserve 23 bits for the mantissa and ints are 32 bits so precision
+	// was lost parsing "138536968" which was converted to 138536960. 
+	// Now we call (int)Double.parseDouble() because double allocates
+	// 52 bits for the mantissa. Note getPartLong calls Long.parseLong()
+	// when this does not call Integer.parseInt() which seems inconsistent.
 	public static Integer getPartInt(int index, String[] parts)
 	{
 		try {
 			String part = parts[index];
-			return (int)(Float.parseFloat(part));
+			return (int)(Double.parseDouble(part));
 		} catch (ArrayIndexOutOfBoundsException e) {
 			return NA_INT;
 		} catch (NumberFormatException e) {

core/src/main/java/org/mskcc/cbio/portal/dao/DaoMutation.java

@@ -188,8 +188,7 @@ public static void createMutationCountClinicalData(GeneticProfile geneticProfile
              * We do not add the MUTATION_COUNT clinical data for the sample if
              * it's not profiled. If it *is* profiled but there are 0
              * mutations, add a MUTATION_COUNT with 0 value record. Do not
-             * include germline and fusions (msk internal) when counting
-             * mutations.
+             * include germline when counting mutations.
              *
              * Use REPLACE (conditional INSERT/UPDATE) which inserts
              * new counts if they don't exist and overwrites them if they do.
@@ -207,7 +206,6 @@ public static void createMutationCountClinicalData(GeneticProfile geneticProfile
                     "LEFT JOIN mutation ON mutation.`SAMPLE_ID` = sample_profile.`SAMPLE_ID` " +
                     "AND ( mutation.`MUTATION_STATUS` <> 'GERMLINE' OR mutation.`MUTATION_STATUS` IS NULL ) " +
                     "LEFT JOIN mutation_event ON mutation.`MUTATION_EVENT_ID` = mutation_event.`MUTATION_EVENT_ID` " +
-                    "AND ( mutation_event.`MUTATION_TYPE` <> 'Fusion' OR mutation_event.`MUTATION_TYPE` IS NULL ) " +
                     "INNER JOIN genetic_profile ON genetic_profile.`GENETIC_PROFILE_ID` = sample_profile.`GENETIC_PROFILE_ID` " +
                     "WHERE genetic_profile.`GENETIC_ALTERATION_TYPE` = 'MUTATION_EXTENDED' " +
                     "AND genetic_profile.`GENETIC_PROFILE_ID`=? " +

core/src/main/java/org/mskcc/cbio/portal/dao/DaoStructuralVariant.java

@@ -80,7 +80,8 @@ public static void addStructuralVariantToBulkLoader(StructuralVariant structural
                                             "CLASS",
                                             "LENGTH",
                                             "COMMENTS",
-                                            "EXTERNAL_ANNOTATION"
+                                            "EXTERNAL_ANNOTATION",
+                                            "SV_STATUS",
                                             };
         bl.setFieldNames(fieldNames);
 
@@ -89,13 +90,13 @@ public static void addStructuralVariantToBulkLoader(StructuralVariant structural
            Long.toString(structuralVariant.getInternalId()),
            Integer.toString(structuralVariant.getGeneticProfileId()),
            Integer.toString(structuralVariant.getSampleIdInternal()),
-           Long.toString(structuralVariant.getSite1EntrezGeneId()),
+           structuralVariant.getSite1EntrezGeneId() == null ? null : Long.toString(structuralVariant.getSite1EntrezGeneId()),
            structuralVariant.getSite1EnsemblTranscriptId(),
            Integer.toString(structuralVariant.getSite1Exon()),
            structuralVariant.getSite1Chromosome(),
            Integer.toString(structuralVariant.getSite1Position()),
            structuralVariant.getSite1Description(),
-           Long.toString(structuralVariant.getSite2EntrezGeneId()),
+           structuralVariant.getSite2EntrezGeneId() == null ? null : Long.toString(structuralVariant.getSite2EntrezGeneId()),
            structuralVariant.getSite2EnsemblTranscriptId(),
            Integer.toString(structuralVariant.getSite2Exon()),
            structuralVariant.getSite2Chromosome(),
@@ -121,7 +122,8 @@ public static void addStructuralVariantToBulkLoader(StructuralVariant structural
            structuralVariant.getVariantClass(),
            Integer.toString(structuralVariant.getLength()),
            structuralVariant.getComments(),
-           structuralVariant.getExternalAnnotation());
+           structuralVariant.getExternalAnnotation(),
+           structuralVariant.getSvStatus());
 
         if ((structuralVariant.getDriverFilter() != null
             && !structuralVariant.getDriverFilter().isEmpty()
@@ -237,6 +239,7 @@ private static StructuralVariant extractStructuralVariant(ResultSet rs) throws S
         structuralVariant.setDriverFilterAnn(rs.getString("DRIVER_FILTER_ANNOTATION"));
         structuralVariant.setDriverTiersFilter(rs.getString("DRIVER_TIERS_FILTER"));
         structuralVariant.setDriverTiersFilterAnn(rs.getString("DRIVER_TIERS_FILTER_ANNOTATION"));
+        structuralVariant.setSvStatus(rs.getString("SV_STATUS"));
         return structuralVariant;
     }
 }

core/src/main/java/org/mskcc/cbio/portal/model/CancerStudy.java

@@ -1,5 +1,5 @@
 /*
- * Copyright (c) 2015 - 2016 Memorial Sloan-Kettering Cancer Center.
+ * Copyright (c) 2015 - 2022 Memorial Sloan-Kettering Cancer Center.
  *
  * This library is distributed in the hope that it will be useful, but WITHOUT
  * ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF MERCHANTABILITY OR FITNESS
@@ -445,23 +445,6 @@ public boolean hasSurvivalData() throws DaoException {
                     attrs.contains(ClinicalAttribute.DFS_STATUS);
     }
 
-    /**
-     * Check if study has fusion data 
-     * @return true if has fusion data, false when it's not
-     */
-    public boolean hasFusionData() {
-        ArrayList<GeneticProfile> geneticProfiles = DaoGeneticProfile.getAllGeneticProfiles(studyID);
-        boolean hasFusionData = false;
-        for (GeneticProfile geneticProfile : geneticProfiles) {
-            if (geneticProfile.getDatatype().equals("SV")) { // check if genetic profiles contains Structural Variant
-                                                             // data type
-                hasFusionData = true;
-                break;
-            }
-        }
-        return hasFusionData;
-    }
-
     public String getTypeOfCancer() throws DaoException {
         return DaoTypeOfCancer.getTypeOfCancerById(this.typeOfCancerId).getName();
     }