From a328403f5758f93bb60228dac726171e7ad7c9d3 Mon Sep 17 00:00:00 2001
From: kheber <kerim@heber.org>
Date: Wed, 7 Aug 2024 20:22:37 -0400
Subject: [PATCH] fix some small bugs that occur when running on some osx
 computers, and fix typo in README

---
 README.md       | 2 +-
 src/Plot.R      | 2 +-
 src/PreProcessR | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/README.md b/README.md
index 46e2d80..b0f28d4 100644
--- a/README.md
+++ b/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`
 
diff --git a/src/Plot.R b/src/Plot.R
index d1b916a..fd98c8f 100755
--- a/src/Plot.R
+++ b/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"))
diff --git a/src/PreProcessR b/src/PreProcessR
index 5b9f0e3..a53547d 100755
--- a/src/PreProcessR
+++ b/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"