ExtractIlluminaBarcodes throws a NullPointerException in the case of an empty lane directory #948

nh13 · 2017-10-04T17:32:03Z

@jacarey want to take a look?

Exception:

Exception in thread "main" java.lang.NullPointerException
	at java.util.Objects.requireNonNull(Objects.java:203)
	at java.util.Arrays$ArrayList.<init>(Arrays.java:3813)
	at java.util.Arrays.asList(Arrays.java:3800)
	at picard.illumina.parser.IlluminaFileUtil.hasCbcls(IlluminaFileUtil.java:270)
	at picard.illumina.ExtractIlluminaBarcodes.customCommandLineValidation(ExtractIlluminaBarcodes.java:447)
	at picard.cmdline.CommandLineProgram.parseArgs(CommandLineProgram.java:323)
	at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:196)
	at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:98)
	at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:108)

cycle sub-directory does not.

coveralls · 2017-10-04T17:54:41Z

Coverage increased (+0.002%) to 76.871% when pulling f15e39b on nh_haz_cbcls into 17a95b5 on master.

yfarjoun · 2017-10-13T13:35:02Z

src/main/java/picard/illumina/parser/IlluminaFileUtil.java

@@ -265,6 +265,11 @@ public static boolean hasCbcls(final File basecallDir, final int lane) {
        final File laneDir = new File(basecallDir, IlluminaFileUtil.longLaneStr(lane));
        final File[] cycleDirs = IOUtil.getFilesMatchingRegexp(laneDir, IlluminaFileUtil.CYCLE_SUBDIRECTORY_PATTERN);

+        // Either the lane or the cycle directory do not exist!
+        if (cycleDirs == null) {
+            return false;


As this is an error, not an empty directory...should we throw/catch a more detailed error, or at least log something here?

yfarjoun · 2017-10-22T14:20:09Z

@nh13 you are able to merge, right?

nh13 added 2 commits October 4, 2017 10:27

Test showing a NPE

b45c83c

Fix a null pointer exception if the basecalls directory exists but the

f15e39b

cycle sub-directory does not.

nh13 requested a review from jacarey October 4, 2017 17:32

yfarjoun reviewed Oct 13, 2017

View reviewed changes

jacarey approved these changes Oct 16, 2017

View reviewed changes

nh13 merged commit 9275e28 into master Oct 22, 2017

nh13 deleted the nh_haz_cbcls branch October 22, 2017 15:06

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ExtractIlluminaBarcodes throws a NullPointerException in the case of an empty lane directory #948

ExtractIlluminaBarcodes throws a NullPointerException in the case of an empty lane directory #948

nh13 commented Oct 4, 2017

coveralls commented Oct 4, 2017 •

edited

yfarjoun Oct 13, 2017

yfarjoun commented Oct 22, 2017

ExtractIlluminaBarcodes throws a NullPointerException in the case of an empty lane directory #948

ExtractIlluminaBarcodes throws a NullPointerException in the case of an empty lane directory #948

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nh13 commented Oct 4, 2017

coveralls commented Oct 4, 2017 • edited

yfarjoun Oct 13, 2017

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yfarjoun commented Oct 22, 2017

coveralls commented Oct 4, 2017 •

edited