run_MUSIC script SAM file fix

gersteinlab · Mar 8, 2016 · c5c65c3 · c5c65c3
1 parent c24c039
commit c5c65c3
Showing 1 changed file with 9 additions and 0 deletions.
diff --git a/bin/run_MUSIC.csh b/bin/run_MUSIC.csh
@@ -37,7 +37,16 @@ then
 	elif [[ "$read_file_name" == *.bowtie.gz ]]
 	then
 		gzip -cd $2 | MUSIC -preprocess bowtie stdin $output_dir
+	elif [[ "$read_file_name" == *.sam ]]
+	then
+		cat $2 | MUSIC -preprocess SAM stdin $output_dir
+	elif [[ "$read_file_name" == *.SAM ]]
+	then
+		cat $2 | MUSIC -preprocess SAM stdin $output_dir
 	elif [[ "$read_file_name" == *.bam ]]
+	then
+		samtools view $2 | MUSIC -preprocess SAM stdin $output_dir
+	elif [[ "$read_file_name" == *.BAM ]]
 	then
 		samtools view $2 | MUSIC -preprocess SAM stdin $output_dir
 	fi