-phenotyper -po sample.tsv problem

[Ahmadhajeer89]

*** What is the current behavior?**

I am facing this error when I am trying to use outside calls, using the sample file from PharmCAT website, as the following:

java -jar pharmcat-2.15.5-all.jar -phenotyper -po sample.tsv
java.lang.NullPointerException: Cannot invoke "java.nio.file.Path.resolve(String)" because "this.m_baseDir" is null
	at org.pharmgkb.pharmcat.Pipeline.<init>(Pipeline.java:131)
	at org.pharmgkb.pharmcat.PharmCAT.main(PharmCAT.java:197)

Note that using the -VCF works well without problems.

• PharmCAT Version:
  pharmcat-2.15.5-all.jar

• JDK Version: [ JDK8 | OpenJDK | etc ]:
  openjdk 21.0.5 2024-10-15 LTS
  OpenJDK Runtime Environment Temurin-21.0.5+11 (build 21.0.5+11-LTS)
  OpenJDK 64-Bit Server VM Temurin-21.0.5+11 (build 21.0.5+11-LTS, mixed mode)

• Environment: [macOS, Monterery ]

[markwoon]

Apologies for the delay in responding. Can you try providing the full path to the sample.tsv file?

[Ahmadhajeer89]

It works with the following warning:

apple@Apples-MacBook-Pro genehint % java -jar hintapp.jar -phenotyper -po /Users/apple/Downloads/genehint/sample.tsv
WARNING: Undocumented MT-RNR1 named variant in outside call: 1555A>G
Saving phenotyper JSON results to /Users/apple/Downloads/genehint/sample.phenotype.json
Done.

so the sample has an un-documented variant?

[markwoon]

so the sample has an un-documented variant?

Looks like it.

See https://pharmcat.org/methods/NamedAlleleMatcher-201/#undocumented-variations for details