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immunoengineer / gliph

Grouping of Lymphocyte Interactions by Paratope Hotspots
GNU General Public License v3.0
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HLA option error #4

Open judell-nmdp opened 6 years ago

judell-nmdp commented 6 years ago

Specifying either --hla_table or --hla results in error: "Unknown option". Documentation isn't clear on which is correct, and --help doesn't list it in the options. This is a really exciting feature and I hope it gets fixed!

TracyYXChen commented 6 years ago

--hla works for me

gblock173 commented 4 years ago

Hi, I have the same problem. Entering the --hla option will cause unknown to be returned. It running without a problem?

.... ./gliph-group-discovery.pl --tcr gliph_input.txt --hla hlaTypesAll_gliph.txt ....

Unknown option: hla

loading reference db ../GLIPH/gliph/db/tcrab-naive-refdb-pseudovdjfasta.fa Establishing global convergence significance cutoff

Evaluating depth of input sample in determining distance cutoff

Preparing local convergence motifs (3mers,4mers,xx.x,x.xx)

simulated stochastic resampling of depth 31563 from reference db loading kmers from sample... kmers obtained: 38856 mindepth>=3 kmers obtained: 15570 reference db has already been loaded Subsampling (depth 31563): ##################################################