fix some small bugs that occur when running on some osx computers, an…

…d fix typo in README

README.md

@@ -67,7 +67,7 @@ PreProcessR -i <PATH_TO_GENOME_FILES> [OPTIONS]
 
 The path to a directory containing only the genome files to be quantified. Accepted file formats are .fna and .fasta
 
-**-o or --outidr:**
+**-o or --outdir:**
 
 Path to desired directory for output files to be stored in. Directory does not need to be made before running `PreProcessR`. If the output directory already exists before a run, make sure it is empty. Default is `./StrainR2DB`
 

src/Plot.R

@@ -36,7 +36,7 @@ Norm<-
   select(StrainID, ContigID, Start_Stop, Unique_Kmers=Nunique, Length_Contig=Length, Bases, Coverage, Mapped_Reads=Reads, Mapped_Frags=Frags, Total_Mapped_Reads_In_Sample) %>%
   mutate(FUKM=Mapped_Frags/(Unique_Kmers/1e3)/(Total_Mapped_Reads_In_Sample/1e6)) %>%
   group_by(StrainID)%>%
-  filter(Unique_Kmers>=quantile(Unique_Kmers,opt$subcontigfilter/100))%>%
+  filter(Unique_Kmers>=quantile(Unique_Kmers,opt$subcontigfilter/100, na.rm=T))%>%
   ungroup()
 
 write_tsv(Norm, paste0(opt$abundances, "/", opt$prefix,".abundances"))

src/PreProcessR

@@ -48,7 +48,7 @@ fi
 #preprocessr pipeline
 echo "Creating subcontigs"
 mkdir "$outdir"
-ksize=$(("$readsize" * 2 + 1))
+ksize=$(($readsize * 2 + 1))
 
 if ! [ -z "$subcontigsize" ]; then
   subcontigsize="-s $subcontigsize"