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update htsjdk to 2.19.0 #5812
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update htsjdk to 2.19.0 #5812
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9 changes: 2 additions & 7 deletions
9
...va/org/broadinstitute/hellbender/tools/spark/sv/utils/SingleSequenceReferenceAligner.java
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Original file line number | Diff line number | Diff line change |
---|---|---|
|
@@ -5,6 +5,7 @@ | |
import htsjdk.samtools.BamFileIoUtils; | ||
import htsjdk.samtools.cram.build.CramIO; | ||
import htsjdk.samtools.util.BlockCompressedInputStream; | ||
import htsjdk.samtools.util.IOUtil; | ||
import htsjdk.tribble.Tribble; | ||
import htsjdk.tribble.util.TabixUtils; | ||
import org.apache.commons.compress.archivers.tar.TarArchiveEntry; | ||
|
@@ -702,7 +703,7 @@ public static Path createTempPath(String name, String extension) { | |
final String filename = path.getFileName().toString(); | ||
IOUtils.deleteOnExit(path.resolveSibling(filename + Tribble.STANDARD_INDEX_EXTENSION)); | ||
IOUtils.deleteOnExit(path.resolveSibling(filename + TabixUtils.STANDARD_INDEX_EXTENSION)); | ||
IOUtils.deleteOnExit(path.resolveSibling(filename + BAMIndex.BAMIndexSuffix)); | ||
IOUtils.deleteOnExit(path.resolveSibling(filename + BAMIndex.BAI_INDEX_SUFFIX)); | ||
IOUtils.deleteOnExit(path.resolveSibling(filename.replaceAll(extension + "$", ".bai"))); | ||
IOUtils.deleteOnExit(path.resolveSibling(filename + ".md5")); | ||
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||
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@@ -1021,14 +1022,8 @@ public static void deleteOnExit(final Path fileToDelete){ | |
* Delete rootPath recursively | ||
* @param rootPath is the file/directory to be deleted | ||
*/ | ||
public static void deleteRecursively(final Path rootPath) throws IOException { | ||
final List<Path> pathsToDelete = Files.walk(rootPath) | ||
.sorted(Comparator.reverseOrder()) | ||
.collect(Collectors.toList()); | ||
|
||
for (Path path : pathsToDelete) { | ||
Files.deleteIfExists(path); | ||
} | ||
public static void deleteRecursively(final Path rootPath) { | ||
IOUtil.recursiveDelete(rootPath); | ||
There was a problem hiding this comment. Choose a reason for hiding this commentThe reason will be displayed to describe this comment to others. Learn more. New implementation in htsjdk. We might want to just remove this one actually. |
||
} | ||
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/** | ||
|
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Is the behavior previously controlled by the two
true
booleans here being preserved in the newFastaReferenceWriterBuilder
call?There was a problem hiding this comment.
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Looks like these were
makeFai
andmakeDict
, both of which aretrue
by default in the new builder.