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revert change to tempdir in SortingCollection introduced in #910 #1030 (
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#1031)

* #910 changed the location of temporary files created by SortingCollection, reverting this change since it was causing problems downstream
* fixes #1030
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tbl3rd authored and lbergelson committed Nov 17, 2017
1 parent d1fd8d6 commit e2a03d6
Showing 1 changed file with 2 additions and 1 deletion.
3 changes: 2 additions & 1 deletion src/main/java/htsjdk/samtools/util/SortingCollection.java
Original file line number Diff line number Diff line change
Expand Up @@ -34,6 +34,7 @@
import java.lang.reflect.Array;
import java.nio.file.Files;
import java.nio.file.Path;
import java.nio.file.Paths;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collection;
Expand Down Expand Up @@ -344,7 +345,7 @@ public static <T> SortingCollection<T> newInstance(final Class<T> componentType,
final Comparator<T> comparator,
final int maxRecordsInRAM) {

final Path tmpDir = IOUtil.getDefaultTmpDirPath();
final Path tmpDir = Paths.get(System.getProperty("java.io.tmpdir"));
return new SortingCollection<T>(componentType, codec, comparator, maxRecordsInRAM, tmpDir);
}

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