Error when providing path to directory containing allele definitions

Do you want to request a feature or report a bug?

bug

**What is the current behavior?***

I have an eror, when I try to use pharmcat with argument -na (path to definitions dir):

java.lang.NullPointerException
    at sun.nio.fs.UnixPath.normalizeAndCheck(UnixPath.java:77)
    at sun.nio.fs.UnixPath.<init>(UnixPath.java:71)
    at sun.nio.fs.UnixFileSystem.getPath(UnixFileSystem.java:281)
    at java.nio.file.Paths.get(Paths.java:84)
    at org.pharmgkb.common.io.util.CliHelper.getValidDirectory(CliHelper.java:217)
    at org.pharmgkb.pharmcat.PharmCAT.main(PharmCAT.java:71)

If the current behavior is a bug, please provide the steps to reproduce and, if possible, your example input data via a Gist or similar. At first, I tried to use path to the directory with my custom exemptions.json file and default genes json files.

java -jar /home/kvergy/pharmcat/pharmcat-0.7.1-all.jar -na /home/kvergy/CYP/test/2C19 -vcf chip_hg38.vcf -o .

And I have an error:

java.lang.NullPointerException
    at sun.nio.fs.UnixPath.normalizeAndCheck(UnixPath.java:77)
    at sun.nio.fs.UnixPath.<init>(UnixPath.java:71)
    at sun.nio.fs.UnixFileSystem.getPath(UnixFileSystem.java:281)
    at java.nio.file.Paths.get(Paths.java:84)
    at org.pharmgkb.common.io.util.CliHelper.getValidDirectory(CliHelper.java:217)
    at org.pharmgkb.pharmcat.PharmCAT.main(PharmCAT.java:71)

Then I tried to give -na argument using the path to the default directory from the source code (https://github.com/PharmGKB/PharmCAT/releases/tag/v0.7.1):

java -jar pharmcat-0.7.1-all.jar -vcf chip_hg38.vcf -o . -na /home/kvergy/CYP/test/git/PharmCAT-0.7.1/src/main/resources/org/pharmgkb/pharmcat/definition/alleles/

And I have the same error.

What is the expected behavior? Custom exemptions.json are used instead of default files.
What is the motivation / use case for changing the behavior?

I want to use my custom allele definitions.

Please tell us about your environment:
- PharmCAT Version: pharmcat-0.7.1
- JDK Version: openjdk version "1.8.0_275"
- Environment: Linux
Other information (e.g. detailed explanation, stacktraces, related issues, suggestions how to fix, links for us to have context, eg. stackoverflow, gitter, etc)

PharmGKB / PharmCAT

Error when providing path to directory containing allele definitions #44