release version 1.2.0-beta10

Author: mathjeff

README.md

@@ -1,6 +1,6 @@
 # X-Mapper: a fast, accurate aligner for genomic sequences
 
-Download the latest release version here: https://github.com/mathjeff/Mapper/releases/download/1.2.0-beta09/x-mapper-1.2.0-beta09.jar
+Download the latest release version here: https://github.com/mathjeff/Mapper/releases/download/1.2.0-beta10/x-mapper-1.2.0-beta10.jar
 
 Read about the algorithm, plus benchmarking and application in the publication here: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-024-03473-7
 

src/main/java/mapper/Serializer.java

@@ -10,7 +10,9 @@
 // It doesn't worry about making sure the written data can still be read by a future version of the code, because we don't need that
 public class Serializer {
   public Serializer(File file) throws IOException {
-    this.outputStream = new BufferedOutputStream(new GZIPOutputStream(new FileOutputStream(file)));
+    this.outputFile = file;
+    this.tempOutputFile = new File(file.toString() + ".tmp");
+    this.outputStream = new BufferedOutputStream(new GZIPOutputStream(new FileOutputStream(tempOutputFile)));
   }
 
   public void writeBytesAndLength(byte[] data) throws IOException {
@@ -40,7 +42,10 @@ public void writeProperty(String key, String value) throws IOException {
 
   public void close() throws IOException {
     this.outputStream.close();
+    this.tempOutputFile.renameTo(this.outputFile);
   }
 
   private BufferedOutputStream outputStream;
+  private File outputFile;
+  private File tempOutputFile;
 }