PeptideMapper crashes when peptide input file contains empty lines

[cbielow]

Hi,

invoking PeptideMapper with a peptide file with empty lines causes:

Start mapping using 1 threads
 0%
10% 30% 50% 60%Error: mapping went wrong
Exception in thread "main" java.lang.NullPointerException
        at java.base/java.util.Objects.requireNonNull(Objects.java:209)
        at java.base/sun.nio.fs.UnixFileSystem.getPath(UnixFileSystem.java:263)
        at java.base/java.nio.file.Path.of(Path.java:147)
        at java.base/java.nio.file.Paths.get(Paths.java:69)
        at com.compomics.cli.peptide_mapper.PeptideMapperCLI.handleError(PeptideMapperCLI.java:380)
        at com.compomics.cli.peptide_mapper.PeptideMapperCLI.runMapping(PeptideMapperCLI.java:467)
        at com.compomics.cli.peptide_mapper.PeptideMapperCLI.handleParameters(PeptideMapperCLI.java:364)
        at com.compomics.cli.peptide_mapper.PeptideMapperCLI.main(PeptideMapperCLI.java:81)

One empty line at the end of the file seems ok, though. Adding two at the end, or one in the middle, yields the above error.
It may not be obvious why the crash occurs to new users.
Maybe this can be fixed or yield a better error message?

[mvaudel]

Thank you for reporting this. I have tried to correct the issue with missing lines but the stack trace relates to something else so I am a bit confused. Can you try the latest release and see if the problem is solved?