From 281abae8b5ea304c8795470a77e568f847de2947 Mon Sep 17 00:00:00 2001 From: Enrico Gaffo Date: Sat, 14 Mar 2020 18:00:23 +0000 Subject: [PATCH] fixed bug that caused CIRCexplorer2-segemehl to underestimate circrna read count --- src/ccp_circexplorer2.scons | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/ccp_circexplorer2.scons b/src/ccp_circexplorer2.scons index 52aab47..c745f17 100644 --- 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'''