remove all comments (resolve repeated calls) (170fc43a) · Commits · github_fork / Universc

launch_universc.sh

+7 −7

Original line number	Diff line number	Diff line
		@@ -1538,15 +1538,15 @@ if [[ $lock -eq 0 ]]; then
		if [[ $verbose ]]; then
		echo "restore barcode checks"
		fi
		sed -i "s/#if gem_group == prev_gem_group/if gem_group == prev_gem_group/g" ${cellrangerpath}-cs/${cellrangerversion}/mro/stages/counter/report_molecules/__init__.py
		sed -i "s/#assert barcode_idx >= prev_barcode_idx/assert barcode_idx >= prev_barcode_idx/g" ${cellrangerpath}-cs/${cellrangerversion}/mro/stages/counter/report_molecules/__init__.py
		sed -i "s/#assert np.array_equal(in_mc.get_barcodes(), barcodes)/assert np.array_equal(in_mc.get_barcodes(), barcodes)/g" ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/molecule_counter.py
		sed -i "s/#*#if gem_group == prev_gem_group/if gem_group == prev_gem_group/g" ${cellrangerpath}-cs/${cellrangerversion}/mro/stages/counter/report_molecules/__init__.py
		sed -i "s/#*#assert barcode_idx >= prev_barcode_idx/assert barcode_idx >= prev_barcode_idx/g" ${cellrangerpath}-cs/${cellrangerversion}/mro/stages/counter/report_molecules/__init__.py
		sed -i "s/#*#assert np.array_equal(in_mc.get_barcodes(), barcodes)/assert np.array_equal(in_mc.get_barcodes(), barcodes)/g" ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/molecule_counter.py
		#restore cloupe generation
		if [[ $verbose ]]; then
		echo "restore cloupe"
		fi
		sed -i '/output_for_cloupe/s/^#//g' ${cellrangerpath}-cs/${cellrangerversion}/mro/*mro
		sed -i '/out cloupe cloupe/ {s/^#//g}' ${cellrangerpath}-cs/${cellrangerversion}/mro/*mro
		sed -i '/output_for_cloupe/s/^##//g' ${cellrangerpath}-cs/${cellrangerversion}/mro/mro
		sed -i '/out cloupe cloupe/ {s/^##//g}' ${cellrangerpath}-cs/${cellrangerversion}/mro/mro
		elif [[ $lastcall == "10x" ]] \|\| [[ ! -f $lastcallfile ]]; then
		#disable checking barcodes
		if [[ $verbose ]]; then
		@@ -1559,8 +1559,8 @@ if [[ $lock -eq 0 ]]; then
		if [[ $verbose ]]; then
		echo "diasble cloupe"
		fi
		# sed -i '/output_for_cloupe/s/^#//g' ${cellrangerpath}-cs/${cellrangerversion}/mro/*mro
		# sed -i '/out cloupe cloupe/ {s/^#//g}' ${cellrangerpath}-cs/${cellrangerversion}/mro/*mro
		# sed -i '/output_for_cloupe/s/^##//g' ${cellrangerpath}-cs/${cellrangerversion}/mro/mro
		# sed -i '/out cloupe cloupe/ {s/^##//g}' ${cellrangerpath}-cs/${cellrangerversion}/mro/mro
		sed -i '/output_for_cloupe/s/^/#/g' ${cellrangerpath}-cs/${cellrangerversion}/mro/*mro
		sed -i '/out cloupe cloupe/ {s/^/#/g}' ${cellrangerpath}-cs/${cellrangerversion}/mro/*mro
		fi

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