Merge pull request #3 from ggirelli/dev

v2.0.3 release

CHANGELOG.md

@@ -11,6 +11,15 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 - ...
 
 
+
+## [2.0.3] - 2019-07-01
+### Changed
+- Optimized UMI de-duplication step.
+
+### Fixed
+- Fraction of final output VS input with prefix.
+
+
 ## [2.0.2] - 2018-04-04
 ### Changed
 - Updated submodules.
@@ -125,6 +134,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 
 
 [Unreleased] https://github.com/ggirelli/gpseq-seq-gg
+[2.0.3] https://github.com/ggirelli/gpseq-seq-gg/releases/tag/v2.0.3
 [2.0.2] https://github.com/ggirelli/gpseq-seq-gg/releases/tag/v2.0.2
 [2.0.1] https://github.com/ggirelli/gpseq-seq-gg/releases/tag/v2.0.1
 [2.0.0] https://github.com/ggirelli/gpseq-seq-gg/releases/tag/v2.0.0

main.sh

@@ -16,7 +16,7 @@
 # ENV VAR ======================================================================
 export LC_ALL=C.UTF-8
 export LANG=C.UTF-8
-version="2.0.2"
+version="2.0.3"
 
 # DEPENDENCIES =================================================================
 

modules/main.umi_prep.mod.sh

@@ -54,8 +54,8 @@ function prepare_umi() {
 			# Deduplicating UMIs -----------------------------------------------
 			echo -e "\nDeduplicating UMIs ..."
 			time $scriptdir/umi_dedupl.R $cout/$condition/ $expID $condition \
-				-p $platform -co $pthr -c $threads -cs $cslbool \
-				-em $emax -ep $eperc & pid0=$!
+				-p $platform --co $pthr -c $threads --cs $cslbool \
+				--em $emax --ep $eperc & pid0=$!
 			wait $pid0
 		else
 			if [[ -n "$csList" ]]; then
@@ -101,7 +101,7 @@ function prepare_umi() {
 		# Update summary -------------------------------------------------------
 
 		# Prefix reads
-		npr=`grep -P "^$condition" $out/summary | cut -f 5 | head -n 1`
+		npr=`grep -P "^$condition" $out/summary | cut -f 6 | head -n 1`
 
 		# Input reads
 		ir=`cat $cout/"$condition"/"$condition".umi_prep_notes.txt | \