Paths with whitespaces are broken

milaboratory / mixcr

MiXCR is an ultimate software platform for analysis of Next-Generation Sequencing (NGS) data for immune profiling.

https://mixcr.com

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Paths with whitespaces are broken #71

Closed fabio-t closed 8 years ago

fabio-t commented 8 years ago

$ mixcr align -f --library local -r log_align.txt -l TRA -s mm "../../local/mol_med/tcr_cd3/150909 TC/150909-MID1_S1_L001_R1_001.fastq" mid1.vdjca
Exception in thread "main" java.io.FileNotFoundException: ../../local/mol_med/tcr_cd3/150909 (No such file or directory)

mikessh commented 8 years ago

Unfortunately, it looks like a problem with JCommander (https://github.com/cbeust/jcommander/issues/128). Is it so, @dbolotin ?

dbolotin commented 8 years ago

Yes, it is a problem with JCommander. I just updated it to 1.48 (milaboratory/mitools#7) and this seems to fix the problem. This fix will be included in 1.8 release.

@fabioticconi thanks for reporting!