From f235486d1558360efc085d9e9d4f16b660782d94 Mon Sep 17 00:00:00 2001
From: mmterpstra <m.m.terpstra.cluster@gmail.com>
Date: Wed, 19 Jul 2017 12:05:35 +0200
Subject: [PATCH] fixes to NugeneDigitalsplitter.pl

---
 ...roups-0.1.9-foss-2016a-Perl-5.20.2-bare.eb | 36 +++++++++++++++++++
 src/NugeneDigitalSplitter.pl                  | 11 ++++--
 2 files changed, 44 insertions(+), 3 deletions(-)
 create mode 100644 eb/DigitalBarcodeReadgroups-0.1.9-foss-2016a-Perl-5.20.2-bare.eb

diff --git a/eb/DigitalBarcodeReadgroups-0.1.9-foss-2016a-Perl-5.20.2-bare.eb b/eb/DigitalBarcodeReadgroups-0.1.9-foss-2016a-Perl-5.20.2-bare.eb
new file mode 100644
index 0000000..4159eaf
--- /dev/null
+++ b/eb/DigitalBarcodeReadgroups-0.1.9-foss-2016a-Perl-5.20.2-bare.eb
@@ -0,0 +1,36 @@
+easyblock = 'Tarball'
+
+name = 'DigitalBarcodeReadgroups'
+version = '0.1.9'
+
+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 c0ea80a..4199ee6 100644
--- a/src/NugeneDigitalSplitter.pl
+++ b/src/NugeneDigitalSplitter.pl
@@ -96,6 +96,7 @@ sub VERSION_MESSAGE {
 }
 
 sub validateSamTag {
+	my $tag = shift @_;
 	die "## ".localtime(time())." ## ERROR invalid tag does not match /[A-Za-z][A-Za-z0-9]/" if(not($tag =~ m/[A-Za-z][A-Za-z0-9]/));
 }
 
@@ -109,7 +110,7 @@ sub ApplyPicardTag {
 	my $cmdin = "samtools view -h $bam";
 	open(my $in,'-|',$cmdin) or die "## ".localtime(time())." ## ERROR invalid read from command $cmdin";
 	
-	my $cmdout = "samtools view  -S -b - > $bamout";
+	my $cmdout = "samtools view -h -S -b > $bamout";
 	#my $cmdout = "cat - > $bamout";
 	open(my $out,'|-',$cmdout) or die "## ".localtime(time())." ## ERROR invalid write to command $cmdout";
 	
@@ -126,7 +127,7 @@ sub ApplyPicardTag {
 			my $randombc = SamGetRandombc($sam);
 			$randombc = substr($randombc,0,$opts -> {'l'}) if(defined($opts -> {'l'}) && $opts -> {'l'} > 0);
 			$sam = SamRemoveRandombc($sam);
-			
+			$line = SamAsString($sam);
 			#a
 			$line .= "\t$tag:Z:$randombc";
 			#die "$line";
@@ -137,6 +138,10 @@ sub ApplyPicardTag {
 	warn "## ".localtime(time())." ## DONE\n"
 }
 
+sub SamAsString {
+	my $sam = shift @_;
+	return join("\t", @{$sam});
+}
 sub CollectNugeneRgData {
 	my $bam = shift @_;
 	
@@ -265,7 +270,7 @@ sub SamRemoveRandombc {
 	$readname[2] =~ s/[ATCGN]+$//g;
 	#my $randombc=$1;
 	#die "No randombc present in sam record! Dump of sam record:".Dumper($sam) if(not(defined($randombc)));
-	$sam->[0]=join("\t",@readname);
+	$sam->[0]=join(':',@readname);
 	
 	return $sam;
 }