Changes to simulations tooling scripts

pirl-unc · Sep 16, 2024 · 00c9b81 · 00c9b81
1 parent 4dc6630
commit 00c9b81
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diff --git a/art_helper.sh b/art_helper.sh
@@ -5,6 +5,7 @@
 #SBATCH -n 1
 #SBATCH -t 02:00:00
 
+
 OUTDIR=shortreads
 [ ! -d ${OUTDIR} ] && mkdir ${OUTDIR}
 

diff --git a/badread_helper.sh b/badread_helper.sh
@@ -7,6 +7,7 @@
 
 OUTDIR=longreads
 
+
 [ ! -d ${OUTDIR} ] && mkdir ${OUTDIR}
 echo $1
 echo $2

diff --git a/generate_breakpoints.R b/generate_breakpoints.R
@@ -3,6 +3,7 @@ library(Biostrings)
 
 arg <- commandArgs(trailingOnly=TRUE)
 
+
 fa <- readDNAStringSet(arg[2])
 #fa <- Biostrings::readDNAStringSet('longread-fusion-transcript-pipeline/Homo_sapiens.GRCh38.cdna.all.fa')
-Original file line number
+Diff line change
@@ Expand Up / @@ -7,6 +7,7 @@ @@
     OUTDIR=longreads
     [ ! -d ${OUTDIR} ] && mkdir ${OUTDIR}
     echo $1
     echo $2
@@ Expand Down @@
Original file line number	Diff line number	Diff line change
Expand Up		@@ -3,6 +3,7 @@ library(Biostrings)

		arg <- commandArgs(trailingOnly=TRUE)


		fa <- readDNAStringSet(arg[2])
		#fa <- Biostrings::readDNAStringSet('longread-fusion-transcript-pipeline/Homo_sapiens.GRCh38.cdna.all.fa')

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