From ff278c91ae83896fa220ef90287a9eebc7d3f2ad Mon Sep 17 00:00:00 2001
From: skchronicles <kuhnsa3@gmail.com>
Date: Tue, 17 Dec 2024 15:16:39 -0500
Subject: [PATCH] Updating contrasts file parser, short hand for --skip-index
 option

---
 workflow/scripts/do_run_rMATS | 9 +++++++--
 1 file changed, 7 insertions(+), 2 deletions(-)

diff --git a/workflow/scripts/do_run_rMATS b/workflow/scripts/do_run_rMATS
index 081f8d2..8a8c94d 100755
--- a/workflow/scripts/do_run_rMATS
+++ b/workflow/scripts/do_run_rMATS
@@ -227,7 +227,7 @@ function main(){
         key="$1"
         case $key in
           -h  | --help) usage && exit 0;;
-          -b | --skip-index) args["skip_index"]=true; shift;;
+          -s  | --skip-index) args["skip_index"]=true; shift;;
           -*  | --*) err "Error: Failed to parse unsupported argument: '${key}'."; usage && exit 1;;
           *) err "Error: Failed to parse unrecognized argument: '${key}'. Do any of your inputs have spaces?"; usage && exit 1;;
         esac
@@ -249,7 +249,12 @@ function main(){
     read_length_index=$(_get_read_length "Reports/multiqc_matrix.tsv" \
                         | awk -v wd="$PWD" \
                             '{print wd"/rMATS/STAR/2.7.6a/genes-"$1"/"}')
-    while read g1 g2; do 
+
+    # Works even if the last line does
+    # not contain a new line character,
+    # technically tsv/text files should
+    # but this is more robust.
+    while read g1 g2 || { [ -n "$g1" ] && [ -n "$g2" ]; }; do 
         # Run rMATS for each constrast
         # $1 = Group 1
         # $2 = Group 2