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Merge pull request #284 from broadinstitute/dr_fewer_stranded_temp_files 

Reduce number of leftover temp files in GATK runs
This commit is contained in:
Mark DePristo 2013-06-14 13:06:28 -07:00
parent b72880cc94 d167292688
commit 52677429a0
3 changed files with 10 additions and 0 deletions
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1
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToBinaryPed.java
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@ -176,6 +176,7 @@ public class VariantsToBinaryPed extends RodWalker<Integer,Integer> {
// Cut down on memory. // Cut down on memory.
try { try {
File temp = File.createTempFile("VariantsToBPed_"+sample, ".tmp"); File temp = File.createTempFile("VariantsToBPed_"+sample, ".tmp");
temp.deleteOnExit();
printMap.put(sample,new PrintStream(temp)); printMap.put(sample,new PrintStream(temp));
tempFiles.put(sample,temp); tempFiles.put(sample,temp);
} catch (IOException e) { } catch (IOException e) {

5
public/java/src/org/broadinstitute/sting/utils/sam/ArtificialBAMBuilder.java
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@ -182,6 +182,11 @@ public class ArtificialBAMBuilder {
try { try {
final File file = File.createTempFile("tempBAM", ".bam"); final File file = File.createTempFile("tempBAM", ".bam");
file.deleteOnExit(); file.deleteOnExit();
// Register the bam index file for deletion on exit as well:
new File(file.getAbsolutePath().replace(".bam", ".bai")).deleteOnExit();
new File(file.getAbsolutePath() + ".bai").deleteOnExit();
return makeBAMFile(file); return makeBAMFile(file);
} catch ( IOException e ) { } catch ( IOException e ) {
throw new RuntimeException(e); throw new RuntimeException(e);

4
public/java/test/org/broadinstitute/sting/WalkerTest.java
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@ -312,6 +312,10 @@ public class WalkerTest extends BaseTest {
for (int i = 0; i < spec.nOutputFiles; i++) { for (int i = 0; i < spec.nOutputFiles; i++) {
String ext = spec.exts == null ? ".tmp" : "." + spec.exts.get(i); String ext = spec.exts == null ? ".tmp" : "." + spec.exts.get(i);
File fl = createTempFile(String.format("walktest.tmp_param.%d", i), ext); File fl = createTempFile(String.format("walktest.tmp_param.%d", i), ext);
// Mark corresponding *.idx for deletion on exit as well just in case an index is created for the temp file:
new File(fl.getAbsolutePath() + ".idx").deleteOnExit();
tmpFiles.add(fl); tmpFiles.add(fl);
} }