core: implement the alignment length filter for alignment datasets, c…

…loses #70
opencb · Aug 23, 2016 · d066306 · d066306
1 parent 22c1347
commit d066306
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Showing 2 changed files with 20 additions and 1 deletion.
diff --git a/hpg-bigdata-core/src/main/java/org/opencb/hpg/bigdata/core/lib/AlignmentDataset.java b/hpg-bigdata-core/src/main/java/org/opencb/hpg/bigdata/core/lib/AlignmentDataset.java
@@ -38,7 +38,7 @@ protected void updateDataset(Query query) {
         }
     }
 
-    // mapping quuality filter
+    // mapping quality filter
     public AlignmentDataset mappingQualityFilter(String value) {
         query.put("mapq", value);
         return this;
@@ -49,4 +49,10 @@ public AlignmentDataset templateLengthFilter(String value) {
         query.put("tlen", value);
         return this;
     }
+
+    // alignment length filter
+    public AlignmentDataset alignmentLengthFilter(String value) {
+        query.put("alen", value);
+        return this;
+    }
 }
diff --git a/hpg-bigdata-core/src/test/java/org/opencb/hpg/bigdata/core/lib/AlignmentDatasetTest.java b/hpg-bigdata-core/src/test/java/org/opencb/hpg/bigdata/core/lib/AlignmentDatasetTest.java
@@ -93,4 +93,17 @@ public void tlenFilter() {
         System.out.println("--------------------------------------");
     }
 
+    @Test
+    public void alenFilter() {
+        initDataset();
+        System.out.println(">>>> Running alignmentLengthFilter...");
+
+        long count;
+
+        System.out.println("-------------------------------------- using alignmentLengthFilter");
+
+        ad.alignmentLengthFilter(">50;<50").show();
+
+        System.out.println("--------------------------------------");
+    }
 }