Rarely a division by 0 error would occur, for a value we no longer us…

…e (old library complexity estimate). This is now deleted.
aidenlab · Sep 15, 2017 · 8be1a47 · 8be1a47
1 parent 955f9f9
commit 8be1a47
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Showing 10 changed files with 5 additions and 30 deletions.
diff --git a/AWS/scripts/LibraryComplexity.class b/AWS/scripts/LibraryComplexity.class
diff --git a/AWS/scripts/LibraryComplexity.java b/AWS/scripts/LibraryComplexity.java
@@ -109,8 +109,6 @@ public static void main(String[] args) {
     decimalFormat.setMinimumFractionDigits(2);
     decimalFormat.setMaximumFractionDigits(2);
 
-    long result2 = readPairs*readPairs/(2*(readPairs-uniqueReadPairs));
-
     System.out.print("Unique Reads: " + NumberFormat.getInstance().format(uniqueReadPairs) + " ");
     if (totalReadPairs > 0) {
       System.out.println("(" + decimalFormat.format(uniqueReadPairs/(double)totalReadPairs) + ")");
@@ -138,12 +136,9 @@ public static void main(String[] args) {
       result = estimateLibrarySize(readPairs, uniqueReadPairs);
     }
     catch (NullPointerException e) {
-      System.err.println("Library complexity undefined when total = " + readPairs + " and unique = " + uniqueReadPairs);
-      return;
+      result = 0;
     }
     System.out.println("Library Complexity Estimate: " + nf.format(result));
-    //    System.out.println("Library complexity (old): " + nf.format(result2));
-
   }
 
   /**

diff --git a/CPU/common/LibraryComplexity.class b/CPU/common/LibraryComplexity.class
diff --git a/CPU/common/LibraryComplexity.java b/CPU/common/LibraryComplexity.java
@@ -109,8 +109,6 @@ public static void main(String[] args) {
     decimalFormat.setMinimumFractionDigits(2);
     decimalFormat.setMaximumFractionDigits(2);
 
-    long result2 = readPairs*readPairs/(2*(readPairs-uniqueReadPairs));
-
     System.out.print("Unique Reads: " + NumberFormat.getInstance().format(uniqueReadPairs) + " ");
     if (totalReadPairs > 0) {
       System.out.println("(" + decimalFormat.format(uniqueReadPairs/(double)totalReadPairs) + ")");
@@ -138,12 +136,9 @@ public static void main(String[] args) {
       result = estimateLibrarySize(readPairs, uniqueReadPairs);
     }
     catch (NullPointerException e) {
-      System.err.println("Library complexity undefined when total = " + readPairs + " and unique = " + uniqueReadPairs);
-      return;
+      result = 0;
     }
     System.out.println("Library Complexity Estimate: " + nf.format(result));
-    //    System.out.println("Library complexity (old): " + nf.format(result2));
-
   }
 
   /**

diff --git a/LSF/scripts/LibraryComplexity.class b/LSF/scripts/LibraryComplexity.class
diff --git a/LSF/scripts/LibraryComplexity.java b/LSF/scripts/LibraryComplexity.java
@@ -109,8 +109,6 @@ public static void main(String[] args) {
     decimalFormat.setMinimumFractionDigits(2);
     decimalFormat.setMaximumFractionDigits(2);
 
-    long result2 = readPairs*readPairs/(2*(readPairs-uniqueReadPairs));
-
     System.out.print("Unique Reads: " + NumberFormat.getInstance().format(uniqueReadPairs) + " ");
     if (totalReadPairs > 0) {
       System.out.println("(" + decimalFormat.format(uniqueReadPairs/(double)totalReadPairs) + ")");
@@ -138,12 +136,9 @@ public static void main(String[] args) {
       result = estimateLibrarySize(readPairs, uniqueReadPairs);
     }
     catch (NullPointerException e) {
-      System.err.println("Library complexity undefined when total = " + readPairs + " and unique = " + uniqueReadPairs);
-      return;
+      result = 0;
     }
     System.out.println("Library Complexity Estimate: " + nf.format(result));
-    //    System.out.println("Library complexity (old): " + nf.format(result2));
-
   }
 
   /**

diff --git a/SLURM/scripts/LibraryComplexity.class b/SLURM/scripts/LibraryComplexity.class
diff --git a/SLURM/scripts/LibraryComplexity.java b/SLURM/scripts/LibraryComplexity.java
@@ -109,8 +109,6 @@ public static void main(String[] args) {
     decimalFormat.setMinimumFractionDigits(2);
     decimalFormat.setMaximumFractionDigits(2);
 
-    long result2 = readPairs*readPairs/(2*(readPairs-uniqueReadPairs));
-
     System.out.print("Unique Reads: " + NumberFormat.getInstance().format(uniqueReadPairs) + " ");
     if (totalReadPairs > 0) {
       System.out.println("(" + decimalFormat.format(uniqueReadPairs/(double)totalReadPairs) + ")");
@@ -138,12 +136,9 @@ public static void main(String[] args) {
       result = estimateLibrarySize(readPairs, uniqueReadPairs);
     }
     catch (NullPointerException e) {
-      System.err.println("Library complexity undefined when total = " + readPairs + " and unique = " + uniqueReadPairs);
-      return;
+      result = 0;
     }
     System.out.println("Library Complexity Estimate: " + nf.format(result));
-    //    System.out.println("Library complexity (old): " + nf.format(result2));
-
   }
 
   /**

diff --git a/UGER/scripts/LibraryComplexity.class b/UGER/scripts/LibraryComplexity.class
diff --git a/UGER/scripts/LibraryComplexity.java b/UGER/scripts/LibraryComplexity.java
@@ -109,8 +109,6 @@ public static void main(String[] args) {
     decimalFormat.setMinimumFractionDigits(2);
     decimalFormat.setMaximumFractionDigits(2);
 
-    long result2 = readPairs*readPairs/(2*(readPairs-uniqueReadPairs));
-
     System.out.print("Unique Reads: " + NumberFormat.getInstance().format(uniqueReadPairs) + " ");
     if (totalReadPairs > 0) {
       System.out.println("(" + decimalFormat.format(uniqueReadPairs/(double)totalReadPairs) + ")");
@@ -138,12 +136,9 @@ public static void main(String[] args) {
       result = estimateLibrarySize(readPairs, uniqueReadPairs);
     }
     catch (NullPointerException e) {
-      System.err.println("Library complexity undefined when total = " + readPairs + " and unique = " + uniqueReadPairs);
-      return;
+      result = 0;
     }
     System.out.println("Library Complexity Estimate: " + nf.format(result));
-    //    System.out.println("Library complexity (old): " + nf.format(result2));
-
   }
 
   /**