From 487c5d26d48de9596651aa039688b7499c0ad35f Mon Sep 17 00:00:00 2001
From: Sai Nirmayi Yasa <92786623+sainirmayi@users.noreply.github.com>
Date: Wed, 7 Feb 2024 11:53:39 +0100
Subject: [PATCH] Fix featurecounts (#20)

* check if junction counts file exists

* add test without junctions
---
 src/featurecounts/script.sh |  4 +++-
 src/featurecounts/test.sh   | 26 +++++++++++++++++++++++++-
 2 files changed, 28 insertions(+), 2 deletions(-)

diff --git a/src/featurecounts/script.sh b/src/featurecounts/script.sh
index b8da615f..7fbafa39 100644
--- a/src/featurecounts/script.sh
+++ b/src/featurecounts/script.sh
@@ -82,4 +82,6 @@ featureCounts \
 
 [[ ! -z "$par_counts" ]] && mv "$tmp_dir/output.txt" "$par_counts"
 [[ ! -z "$par_summary" ]] && mv "$tmp_dir/output.txt.summary" "$par_summary"
-[[ ! -z "$par_junctions" ]] && mv "$tmp_dir/output.txt.jcounts" "$par_junctions"
+if [[ ! -z "$par_junctions" ]] && [[ -e "$tmp_dir/output.txt.jcounts" ]]; then 
+  mv "$tmp_dir/output.txt.jcounts" "$par_junctions"
+fi
diff --git a/src/featurecounts/test.sh b/src/featurecounts/test.sh
index 26494f98..3349d016 100644
--- a/src/featurecounts/test.sh
+++ b/src/featurecounts/test.sh
@@ -4,7 +4,7 @@ set -e
 
 dir_in="$meta_resources_dir/test_data"
 
-echo "> Run featureCounts"
+echo "> Run featureCounts (with junctions)"
 "$meta_executable" \
   --input "$dir_in/a.bam" \
   --annotation "$dir_in/annotation.gtf" \
@@ -32,4 +32,28 @@ echo ">> Check if output is empty"
 [ ! -s "junction_counts.txt" ] && echo "Output file junction_counts.txt is empty" && exit 1
 [ ! -s "detailed_results/a.bam.featureCounts.sam" ] && echo "Output file detailed_results/a.bam.featureCounts.sam is empty" && exit 1
 
+echo "> Run featureCounts (without junctions)"
+"$meta_executable" \
+  --input "$dir_in/a.bam" \
+  --annotation "$dir_in/annotation.gtf" \
+  --counts "features.tsv" \
+  --summary "summary.tsv" \
+  --overlapping \
+  --frac_overlap 0.2 \
+  --paired \
+  --strand 0 \
+  --detailed_results detailed_results \
+  --detailed_results_format SAM
+
+echo ">> Checking output"
+[ ! -f "features.tsv" ] && echo "Output file features.tsv does not exist" && exit 1
+[ ! -f "summary.tsv" ] && echo "Output file summary.tsv does not exist" && exit 1
+[ ! -d "detailed_results" ] && echo "Output directory detailed_results does not exist" && exit 1
+[ ! -f "detailed_results/a.bam.featureCounts.sam" ] && echo "Output file detailed_results/a.bam.featureCounts.sam does not exist" && exit 1
+
+echo ">> Check if output is empty"
+[ ! -s "features.tsv" ] && echo "Output file features.tsv is empty" && exit 1
+[ ! -s "summary.tsv" ] && echo "Output file summary.tsv is empty" && exit 1
+[ ! -s "detailed_results/a.bam.featureCounts.sam" ] && echo "Output file detailed_results/a.bam.featureCounts.sam is empty" && exit 1
+
 echo "> Test successful"
\ No newline at end of file