From 1e5fa922d6e36ebd5919f5e7d5e93204002a601f Mon Sep 17 00:00:00 2001
From: mmterpstra <m.m.terpstra.cluster@gmail.com>
Date: Fri, 21 Jul 2017 09:37:59 +0200
Subject: [PATCH] added N extention to UMI if too short with option -l for
 UmiAwareMarkDuplicatesWithMateCigar

---
 ...oups-0.1.10-foss-2016a-Perl-5.20.2-bare.eb | 36 +++++++++++++++++++
 src/NugeneDigitalSplitter.pl                  | 10 ++++--
 2 files changed, 43 insertions(+), 3 deletions(-)
 create mode 100644 eb/DigitalBarcodeReadgroups-0.1.10-foss-2016a-Perl-5.20.2-bare.eb

diff --git a/eb/DigitalBarcodeReadgroups-0.1.10-foss-2016a-Perl-5.20.2-bare.eb b/eb/DigitalBarcodeReadgroups-0.1.10-foss-2016a-Perl-5.20.2-bare.eb
new file mode 100644
index 0000000..94cbbe1
--- /dev/null
+++ b/eb/DigitalBarcodeReadgroups-0.1.10-foss-2016a-Perl-5.20.2-bare.eb
@@ -0,0 +1,36 @@
+easyblock = 'Tarball'
+
+name = 'DigitalBarcodeReadgroups'
+version = '0.1.10'
+
+homepage = 'https://github.com/mmterpstra/%s' % (name)
+description = """Misc tools"""
+
+toolchain = {'name': 'foss', 'version': '2016a'}
+
+source_urls = [('https://github.com/mmterpstra/%s/archive/' % (name) )]
+sources = [ '%s.tar.gz' % version ]
+
+perl = 'Perl'
+perlver = '5.20.2'
+perlversuffix = '-bare'
+versionsuffix = '-%s-%s%s' % (perl, perlver, perlversuffix)
+
+samtools='SAMtools'
+samtoolsver='1.3'
+
+dependencies = [
+    (perl, perlver, perlversuffix),
+    (samtools, samtoolsver),
+]
+
+#
+# Check if all binaries are present.
+#
+
+sanity_check_paths = {
+    'files': [ 'src/NugeneDigitalSplitter.pl', 'src/NugeneMergeFastqFiles.pl' ],
+    'dirs': [ 'src/' ],
+}
+
+moduleclass = 'bio'
diff --git a/src/NugeneDigitalSplitter.pl b/src/NugeneDigitalSplitter.pl
index 4199ee6..41cea16 100644
--- a/src/NugeneDigitalSplitter.pl
+++ b/src/NugeneDigitalSplitter.pl
@@ -125,10 +125,14 @@ sub ApplyPicardTag {
 			@{$sam} = split("\t",$line);
 			#my $rgID = SamGetReadGroupID($sam);
 			my $randombc = SamGetRandombc($sam);
+
+                        $sam = SamRemoveRandombc($sam);
+                       	$line = SamAsString($sam);
+
 			$randombc = substr($randombc,0,$opts -> {'l'}) if(defined($opts -> {'l'}) && $opts -> {'l'} > 0);
-			$sam = SamRemoveRandombc($sam);
-			$line = SamAsString($sam);
-			#a
+			#
+			$randombc = $randombc .'N' x ($opts -> {'l'} - length($randombc)) if(defined($opts -> {'l'}) && $opts -> {'l'} > 0 && length($randombc) < $opts -> {'l'});
+			
 			$line .= "\t$tag:Z:$randombc";
 			#die "$line";
 			print $out $line."\n";