Merge branch 'dev' of github.com:kbattenb/universc into dev (7a68a288) · Commits · github_fork / Universc

launch_universc.sh

+10 −2

Original line number	Diff line number	Diff line
		@@ -1853,7 +1853,7 @@ if [[ $verbose ]]; then
		fi
		if [[ -f ${barcodefile} ]]; then
		if [[ $verbose ]]; then
		echo " barcodefile file exists"
		echo " barcodefile file exists: ${barcodefile}"
		fi
		if ! [[ "${barcodefile}" == "${whitelistdir}"* ]]; then
		if [[ $verbose ]]; then
		@@ -3635,7 +3635,15 @@ fi
		#####extracting per cell data#####
		if [[ $percelldata == true ]]; then
		echo "generating basic run statistics and per cell data"
		if [[ ${barcodefile} == "default:10x" ]]; then
		barcodefile=${barcodedir}/${v3}.gz
		gunzip ${barcodefile}
		barcodefile=`echo ${barcodefile} \| sed 's/\.[^.]*$//'`
		perl ${PERCELLSTATS} ${barcodefile} ${barcodeadjust} ${id}
		gzip ${barcodefile}
		else
		perl ${PERCELLSTATS} ${barcodefile} ${barcodeadjust} ${id}
		fi
		echo "per cell data generated"
		fi
		##########

+3 −2

Original line number	Diff line number	Diff line
		@@ -28,6 +28,7 @@ my $matrix_file = $indir."/outs/filtered_feature_bc_matrix/matrix.mtx.gz";
		my $summary_file = $indir."/outs/metrics_summary.csv";
		my $bam_file = $indir."/outs/possorted_genome_bam.bam";
		my $out_file = $indir."/outs/basic_stats.txt";
		my $standard_length = 16;

		if (! -e $indir) {
		die "Error: Data directory needs to be specified.\n";
		@@ -50,8 +51,7 @@ while (my $line = <ORIGINAL>) {

		my $adjusted = $original;
		if ($adjust_length >= 0) {
		my $length = $adjust_length;
		$adjusted = substr ($adjusted, 0, $length);
		$adjusted = substr ($adjusted, $adjust_length, $standard_length);
		}
		else {
		my $length = abs ($adjust_length);
		@@ -60,6 +60,7 @@ while (my $line = <ORIGINAL>) {
		}

		$adjusted2original{$adjusted} = $original;
		print "Original($original) -> Adjusted($adjusted) $adjust_length\n";
		}
		close (ORIGINAL);

+1 −1

Original line number	Diff line number	Diff line
		@@ -30,7 +30,7 @@ while (my $line = <ORIGINAL>) {
		my $adjusted = $original;
		if ($adjust_length >= 0) {
		my $length = $adjust_length;
		$adjusted = substr ($length, 0, $adjusted);
		$adjusted = substr ($adjusted, $length);
		}
		else {
		my $length = abs ($adjust_length);