- Made the fastq filter in src/NugeneMergeFastqFiles.pl optional

- Added eb files for new version

eb/DigitalBarcodeReadgroups-0.1.2-foss-2016a-Perl-5.20.2-bare.eb

@@ -0,0 +1,36 @@
+easyblock = 'Tarball'
+
+name = 'DigitalBarcodeReadgroups'
+version = '0.1.2'
+
+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'

eb/DigitalBarcodeReadgroups-0.1.4-foss-2016a-Perl-5.20.2-bare.eb

@@ -0,0 +1,36 @@
+easyblock = 'Tarball'
+
+name = 'DigitalBarcodeReadgroups'
+version = '0.1.4'
+
+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'

eb/DigitalBarcodeReadgroups-0.1.4-goolf-1.7.20-Perl-5.20.2-bare.eb

@@ -0,0 +1,36 @@
+easyblock = 'Tarball'
+
+name = 'DigitalBarcodeReadgroups'
+version = '0.1.4'
+
+homepage = 'https://github.com/mmterpstra/%s' % (name)
+description = """Misc tools"""
+
+toolchain = {'name': 'goolf', 'version': '1.7.20'}
+
+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='1.2'
+
+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'

src/NugeneMergeFastqFiles.pl

@@ -2,33 +2,41 @@
 use warnings;
 use strict;
 use Data::Dumper;
+use Getopt::Std;
+use Scalar::Util qw(looks_like_number);
+
 &main();
 
-our $qualFilter = 10;
 sub main {
 	#use List::Util qw/max/; my $in;
-	my $use="$0 randombarcodes.fq.gz outdir reads_1.fq.gz reads_2.fq.gz.
+
+	my $use="$0 [-q INT] randombarcodes.fq.gz outdir reads_1.fq.gz reads_2.fq.gz.
 
 Note:
-now filters for q<$qualFilter barcode reads and N bases in randombarcodes.fq.gz";
+now filters for illumina 1.8 base quality < -q INT barcode reads and N bases in randombarcodes.fq.gz";
 
 	#open/check some resuired files
 
+	my $opts;
+        getopts('q:', \%{$opts});
+        die "[FATAL] if '-q INT' is specified use integer for INT".$use if(defined($opts -> {'q'}) && not(looks_like_number($opts -> {'q'})));
+
+	die $use."\n" if(scalar(@ARGV) < 2);
+
 	open(my $randomBcHandle,"-|",'gzip -dc '.$ARGV[0]) 
 	or die "Cannot read open randombarcode file ".$ARGV[0]."\n".$use;
 
 	if(! -e $ARGV[1]){
 		die "Outdir does not exist! ".$ARGV[1]."\n".$use;;
 	}
 
-
 	#open handles fastq files
 
 	open(my $fastq1Handle,"-|",'gzip -dc '.$ARGV[2]) 
-	or die "Cannot read open fq1 file ".$ARGV[2];
+	or die "[FATAL] Cannot read open fq1 file ".$ARGV[2];
 
 	open(my $fastq1OutHandle,"|-",'gzip -c > '.GetOutFileName($ARGV[1],$ARGV[2])) 
-	or die "Cannot write fq1 file ".$ARGV[2];
+	or die "[FATAL] Cannot write fq1 file ".$ARGV[2];
 
 	my $fastq2Handle;
 	my $fastq2OutHandle;
@@ -63,7 +71,7 @@ sub main {
 		my $fcid= getFCID($fq1);
 
 		$stats -> {'recordcount'}++;
-		if(TestRandomBarcodeQual($rfq)){
+		if(not(defined($opts -> {'q'})) || TestRandomBarcodeQual($opts -> {'q'},$rfq)){
 			$stats -> {'passcount'}++;
 
 			$fq1 = setFCID($fq1,$fcid."_".$rbc);
@@ -150,6 +158,7 @@ sub GetOutFileName {
 }
 
 sub TestRandomBarcodeQual {
+	my $q = shift @_;
 	my $fq = shift @_;
 	if(not( $fq->[1] =~ /^[ATCGatcg]*$/)){
 		#warn $fq->[1] . $&;
@@ -162,9 +171,9 @@ sub TestRandomBarcodeQual {
 	my @qualsOrd = map{ord()}(@quals);
 	for my $qual (@qualsOrd){
 		#die Dumper($fq,\@quals);
-		if($qual < (33+$qualFilter)){
+		if($qual < (33+$q)){
 			#die Dumper($fq,\@quals,\@qualsOrd);
-			return 0 if($qual < (33+10));
+			return 0 ;#if($qual < (33+$q));
 		}
 	}
 	return 1;