Minor updates to StxTyper and usage message

Includes new tests for StxTyper and an addition to the usage message to clarify that assembled nucleotide sequence is required. Hopefully to reduce confusion as seen in Git issues 141 and 148.
ncbi · Sep 11, 2024 · a2a00ef · a2a00ef
1 parent f1ae2d7
commit a2a00ef
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Showing 2 changed files with 2 additions and 2 deletions.
diff --git a/amrfinder.cpp b/amrfinder.cpp
@@ -357,7 +357,7 @@ struct ThisApplication : ShellApplication
       addKey ("dir", "Common directory of the --protein, --nucleotide and --gff files", "", '\0', "DIRECTORY");
     #endif
     	addKey ("protein", "Input protein FASTA file (can be gzipped)", "", 'p', "PROT_FASTA");
-    	addKey ("nucleotide", "Input nucleotide FASTA file (can be gzipped)", "", 'n', "NUC_FASTA");
+    	addKey ("nucleotide", "Input assembled nucleotide FASTA file (can be gzipped)", "", 'n', "NUC_FASTA");
     	addKey ("gff", "GFF file for protein locations (can be gzipped). Protein id should be in the attribute 'Name=<id>' (9th field) of the rows with type 'CDS' or 'gene' (3rd field).", "", 'g', "GFF_FILE");
 
       {    	

diff --git a/stxtyper b/stxtyper
+3 −3		Makefile
+0 −30		amrfinder_columns.hpp
+23 −25		stxtyper.cpp
+23 −1		test_stxtyper.sh
+1 −1		version.txt