core: implement the template length filter for alignment datasets, cl…

…oses #69
opencb · Aug 23, 2016 · 22c1347 · 22c1347
1 parent 563c803
commit 22c1347
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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
@@ -44,4 +44,9 @@ public AlignmentDataset mappingQualityFilter(String value) {
         return this;
     }
 
+    // template length filter
+    public AlignmentDataset templateLengthFilter(String value) {
+        query.put("tlen", 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
@@ -78,4 +78,19 @@ public void mapqFilter() {
 
         System.out.println("--------------------------------------");
     }
+
+    @Test
+    public void tlenFilter() {
+        initDataset();
+        System.out.println(">>>> Running templateLengthFilter...");
+
+        long count;
+
+        System.out.println("-------------------------------------- using templateLengthFilter");
+
+        ad.templateLengthFilter(">398;<400").show();
+
+        System.out.println("--------------------------------------");
+    }
+
 }