fixed bug that caused CIRCexplorer2-segemehl to underestimate circrna…

… read count
egaffo · Mar 14, 2020 · 281abae · 281abae
1 parent 1735b7a
commit 281abae
Showing 1 changed file with 1 addition and 1 deletion.
diff --git a/src/ccp_circexplorer2.scons b/src/ccp_circexplorer2.scons
@@ -99,7 +99,7 @@ if env['ALIGNER'].lower() == 'segemehl':
 
     ## for segemehl >= v0.3.0 modify the input BED file
     fixed_bed_cmd = '''grep ';B\\|C;' ${SOURCES} | cut -f1,2,3,6 | sort | '''\
-                    '''uniq -c | sed -r 's/.*([0-9]+) ([^\\t]+)\\t([^\\t]+)'''\
+                    '''uniq -c | sed -r 's/ *([0-9]+) ([^\\t]+)\\t([^\\t]+)'''\
                     '''\\t([^\\t]+)\\t([^\\t]+).*/echo "\\2\\t$$((\\3+1))\\t\\4\\tsplits:'''\
                     '''\\1:\\1:\\1:C:P\\t0\\t\\5"/e' > $TARGET'''