diff --git a/CHANGES.md b/CHANGES.md
index f6bca2e..5f77972 100644
--- a/CHANGES.md
+++ b/CHANGES.md
@@ -1,3 +1,10 @@
+### 1.11.0
+* bam_stats - new rna switch to give more appropriate insert size stats
+* bam_stats - more robust handling of optional RG header entries
+* bam_stats - allows streaming IO (thanks to @jenniferliddle)
+* bwa_mem.pl - Handle `'` in RG header line/IDs
+* Generally improved version handling and updated versions of some tools.
+
 ### 1.9.1
 * Changed final log folder to include sample name and analysis type, prevents clash when lots of data to same output loc.
 
diff --git a/MYMETA.json b/MYMETA.json
deleted file mode 100644
index 5e35ff9..0000000
--- a/MYMETA.json
+++ /dev/null
@@ -1,61 +0,0 @@
-{
-   "abstract" : "unknown",
-   "author" : [
-      "unknown"
-   ],
-   "dynamic_config" : 0,
-   "generated_by" : "ExtUtils::MakeMaker version 6.68, CPAN::Meta::Converter version 2.142690",
-   "license" : [
-      "gpl_2"
-   ],
-   "meta-spec" : {
-      "url" : "http://search.cpan.org/perldoc?CPAN::Meta::Spec",
-      "version" : "2"
-   },
-   "name" : "PCAP",
-   "no_index" : {
-      "directory" : [
-         "t",
-         "inc"
-      ]
-   },
-   "prereqs" : {
-      "build" : {
-         "requires" : {
-            "ExtUtils::MakeMaker" : "0"
-         }
-      },
-      "configure" : {
-         "requires" : {
-            "ExtUtils::MakeMaker" : "0"
-         }
-      },
-      "runtime" : {
-         "requires" : {
-            "Bio::DB::Sam" : "1.39",
-            "Bio::Root::Version" : "1.006923",
-            "Capture::Tiny" : "0.24",
-            "Config::IniFiles" : "2.83",
-            "Const::Fast" : "0.014",
-            "Data::UUID" : "1.219",
-            "Devel::Cover" : "1.09",
-            "File::Which" : "0.05",
-            "GD" : "2.52",
-            "IPC::System::Simple" : "1.25",
-            "List::Util" : "1.38",
-            "Math::Gradient" : "0.04",
-            "Module::Build" : "0.42",
-            "Pod::Coverage" : "0.23",
-            "Proc::PID::File" : "1.27",
-            "Proc::ProcessTable" : "0.5",
-            "Sub::Exporter::Progressive" : "0.001011",
-            "Term::UI" : "0.42",
-            "Test::Fatal" : "0.013",
-            "Try::Tiny" : "0.19",
-            "XML::Simple" : "2.2"
-         }
-      }
-   },
-   "release_status" : "stable",
-   "version" : "v1.10.0"
-}
diff --git a/MYMETA.yml b/MYMETA.yml
deleted file mode 100644
index 3e62035..0000000
--- a/MYMETA.yml
+++ /dev/null
@@ -1,42 +0,0 @@
----
-abstract: unknown
-author:
-  - unknown
-build_requires:
-  ExtUtils::MakeMaker: '0'
-configure_requires:
-  ExtUtils::MakeMaker: '0'
-dynamic_config: 0
-generated_by: 'ExtUtils::MakeMaker version 6.68, CPAN::Meta::Converter version 2.142690'
-license: gpl
-meta-spec:
-  url: http://module-build.sourceforge.net/META-spec-v1.4.html
-  version: '1.4'
-name: PCAP
-no_index:
-  directory:
-    - t
-    - inc
-requires:
-  Bio::DB::Sam: '1.39'
-  Bio::Root::Version: '1.006923'
-  Capture::Tiny: '0.24'
-  Config::IniFiles: '2.83'
-  Const::Fast: '0.014'
-  Data::UUID: '1.219'
-  Devel::Cover: '1.09'
-  File::Which: '0.05'
-  GD: '2.52'
-  IPC::System::Simple: '1.25'
-  List::Util: '1.38'
-  Math::Gradient: '0.04'
-  Module::Build: '0.42'
-  Pod::Coverage: '0.23'
-  Proc::PID::File: '1.27'
-  Proc::ProcessTable: '0.5'
-  Sub::Exporter::Progressive: '0.001011'
-  Term::UI: '0.42'
-  Test::Fatal: '0.013'
-  Try::Tiny: '0.19'
-  XML::Simple: '2.2'
-version: v1.10.0
diff --git a/Makefile.PL b/Makefile.PL
index edf419e..ad346ee 100644
--- a/Makefile.PL
+++ b/Makefile.PL
@@ -61,6 +61,7 @@ WriteMakefile(
                      'Term::UI' => 0.42, # currently in core but scheduled for removal 5.17, no alternative recommended
                      'Sub::Exporter::Progressive' => 0.001011,
                      'XML::Simple' => 2.20,
+                     'version' => 0.9912,
                    }
 );
 
diff --git a/bin/gnos_pull.pl b/bin/gnos_pull.pl
index 82b9d19..693c01a 100755
--- a/bin/gnos_pull.pl
+++ b/bin/gnos_pull.pl
@@ -49,7 +49,7 @@
 const my @ANALYSIS_TYPES => (qw(ALIGNMENTS CALLS));
 const my @AVAILABLE_COMPOSITE_FILTERS => (qw(caller max_dataset_GB multi_tumour sanger_version broad_version dkfz_embl_version jamboree_approved manual_donor_blacklist));
 const my $DEFAULT_URL => 'http://pancancer.info/gnos_metadata/latest';
-const my $GTDL_COMMAND => '%s%s --max-children 3 --rate-limit 200 -v -c %s -d %scghub/data/analysis/download/%s -p %s';
+const my $GTDL_COMMAND => '%s%s --max-children 3 --rate-limit 200 -vv -c %s -d %scghub/data/analysis/download/%s -p %s';
 
 {
   my $options = option_builder();
@@ -139,28 +139,35 @@ sub pull_data {
   make_path($symbase) unless(-e $symbase);
 
   my $code_ref;
+  my $check_ref;
   if($options->{'analysis'} eq 'CALLS') {
     $code_ref = \&pull_calls;
   }
   elsif($options->{'analysis'} eq 'ALIGNMENTS') {
+    $check_ref = \&check_alignments;
     $code_ref = \&pull_alignments;
   }
 
   my $thread_count = $options->{'threads'};
 
-  if($thread_count > 1) {
-    while(@{$to_process} > 0) {
+
+  while(@{$to_process} > 0) {
+    my $donor = shift @{$to_process};
+    my $donor_uniq = $donor->{'donor_unique_id'};
+    # is PROJECT::donor, so convert to folder
+    $donor_uniq =~ s|[:]{2}|/|;
+    my $donor_base = "$symbase/$donor_uniq";
+    my $orig_base = "$outbase/$donor_uniq";
+    make_path($orig_base) unless(-e $orig_base);
+
+    if(defined $check_ref) {
+      next if($check_ref->($options, $donor, $orig_base, $donor_base) == 0);
+    }
+
+    warn "Submitting: $donor->{donor_unique_id}\n";
+    if($thread_count > 1) {
       if(threads->list(threads::all) < $thread_count) {
-        my $donor = shift @{$to_process};
-        my $donor_uniq = $donor->{'donor_unique_id'};
-        # is PROJECT::donor, so convert to folder
-        $donor_uniq =~ s|[:]{2}|/|;
-        my $donor_base = "$symbase/$donor_uniq";
-        my $orig_base = "$outbase/$donor_uniq";
-        make_path($orig_base) unless(-e $orig_base);
-        warn "Submitted: $donor->{donor_unique_id}\n";
         threads->create($code_ref, $options, $donor, $orig_base, $donor_base);
-
         # don't sleep if not full yet
         next if(threads->list(threads::all) < $thread_count);
       }
@@ -170,6 +177,11 @@ sub pull_data {
         if(my $err = $thr->error) { die "Thread error: $err\n"; }
       }
     }
+    else {
+      $code_ref->($options, $donor, $orig_base, $donor_base);
+    }
+  }
+  if($thread_count > 1) {
     # last gasp for any remaining threads
     sleep 1 while(threads->list(threads::running) > 0);
     for my $thr(threads->list(threads::joinable)) {
@@ -177,17 +189,6 @@ sub pull_data {
       if(my $err = $thr->error) { die "Thread error: $err\n"; }
     }
   }
-  else {
-    for my $donor(@{$to_process}) {
-      my $donor_uniq = $donor->{'donor_unique_id'};
-      # is PROJECT::donor, so convert to folder
-      $donor_uniq =~ s|[:]{2}|/|;
-      my $donor_base = "$symbase/$donor_uniq";
-      my $orig_base = "$outbase/$donor_uniq";
-      make_path($orig_base) unless(-e $orig_base);
-      $code_ref->($options, $donor, $orig_base, $donor_base);
-    }
-  }
 }
 
 sub check_or_create_symlink {
@@ -208,6 +209,51 @@ sub check_or_create_symlink {
   return 1;
 }
 
+sub check_alignments {
+  my ($options, $donor, $outbase, $donor_base) = @_;
+  warn "Checking $donor->{donor_unique_id}\n";
+  my $to_do = 0;
+  # for normal:
+  $to_do += check_bam($options, $donor->{'donor_unique_id'}, $donor->{'normal_alignment_status'}, $outbase, $donor_base, 'normal');
+
+  # for tumour
+  for my $tumour_data(@{$donor->{'tumor_alignment_status'}}) {
+    $to_do += check_bam($options, $donor->{'donor_unique_id'}, $tumour_data, $outbase, $donor_base, 'tumour');
+  }
+  return $to_do;
+}
+
+sub check_bam {
+  my ($options, $donor_id, $bam_data, $outbase, $donor_base, $type) = @_;
+  my $repo = select_repo($options, $bam_data->{'aligned_bam'}->{'gnos_repo'});
+  unless(exists $options->{'keys'}->{$repo}) {
+    warn sprintf "Skipping %s BAM for Donor %s - No permission key for repo %s", $type, $donor_id, $repo;
+    return 0;
+  }
+
+  my $gnos_id = $bam_data->{'aligned_bam'}->{'gnos_id'};
+
+  my $f_base = $outbase.'/'.$gnos_id;
+  my $success = $f_base.'/.success.t';
+
+  my $sample_base = "$donor_base/$type";
+
+  make_path($sample_base) unless(-e $sample_base);
+  my $aliq_id = $bam_data->{'aliquot_id'};
+  my $orig_bam = $f_base.'/'.$bam_data->{'aligned_bam'}->{'bam_file_name'};
+  my $sym_bam = $sample_base.'/'.$bam_data->{'aliquot_id'}.'.bam';
+
+  if(-e $success) {
+    check_or_create_symlink($orig_bam, $sym_bam);
+    check_or_create_symlink($orig_bam.'.bai', $sym_bam.'.bai');
+    create_bas($repo, $gnos_id, $sym_bam);
+    return 0;
+  }
+
+  return 0 if($options->{'symlinks'});
+  return 1;
+}
+
 sub pull_alignments {
   my ($options, $donor, $outbase, $donor_base) = @_;
 
@@ -222,7 +268,6 @@ sub pull_alignments {
 
 sub pull_bam {
   my ($options, $donor_id, $bam_data, $outbase, $donor_base, $type) = @_;
-  my $sample_base = "$donor_base/$type";
 
   my $repo = select_repo($options, $bam_data->{'aligned_bam'}->{'gnos_repo'});
   unless(exists $options->{'keys'}->{$repo}) {
@@ -231,15 +276,11 @@ sub pull_bam {
   }
   my $gnos_id = $bam_data->{'aligned_bam'}->{'gnos_id'};
 
-  my $download = sprintf $GTDL_COMMAND, $options->{'gtdownload'},
-                                          $options->{'gt_timeout'},
-                                          $options->{'keys'}->{$repo},
-                                          $repo,
-                                          $gnos_id,
-                                          $outbase;
   my $f_base = $outbase.'/'.$gnos_id;
   my $success = $f_base.'/.success.t';
 
+  my $sample_base = "$donor_base/$type";
+
   make_path($sample_base) unless(-e $sample_base);
   my $aliq_id = $bam_data->{'aliquot_id'};
   my $orig_bam = $f_base.'/'.$bam_data->{'aligned_bam'}->{'bam_file_name'};
@@ -253,6 +294,13 @@ sub pull_bam {
   }
   return if($options->{'symlinks'});
 
+  my $download = sprintf $GTDL_COMMAND, $options->{'gtdownload'},
+                                        $options->{'gt_timeout'},
+                                        $options->{'keys'}->{$repo},
+                                        $repo,
+                                        $gnos_id,
+                                        $outbase;
+
   my $out_file = "$f_base.out.log";
   my $err_file = "$f_base.err.log";
   $download .= " > $f_base.out.log";
@@ -286,7 +334,7 @@ sub create_bas {
   my ($repo, $gnos_id, $sym_bam) = @_;
   my $bas_file = $sym_bam.'.bas';
   unlink $bas_file if(-l $bas_file);
-  return if(-s $bas_file);
+  return 1 if(-s $bas_file);
   # pull the bas file, done here to handle back fill of this data
   my $get_bas = sprintf '%s %s/xml_to_bas.pl -d %scghub/metadata/analysisFull/%s -o %s -b %s',
                       $^X,
@@ -325,6 +373,7 @@ sub pull_calls {
   my @callers = @{$donor->{'flags'}->{'variant_calling_performed'}};
   # this should loop over the data found in 'is_sanger_vcf_in_jamboree' once modified to be array
   for my $caller(@callers) {
+    next if($caller eq 'embl' || $caller eq 'dkfz');
 
     next if(exists  $options->{'COMPOSITE_FILTERS'}->{'caller'} && index(','.$options->{'COMPOSITE_FILTERS'}->{'caller'}.',', ','.$caller.',') == -1);
     next unless($donor->{'flags'}->{'is_'.$caller.'_variant_calling_performed'});
diff --git a/c/Makefile b/c/Makefile
index c029efe..382291e 100644
--- a/c/Makefile
+++ b/c/Makefile
@@ -99,9 +99,10 @@ valgrind:
 .c.o:
 	$(CC) $(CFLAGS) $(INCLUDES) -c $<  -o $@
 
-clean:
+clean: 
 	@echo clean
-	$(RM) ./*.o *~ $(BAM_STATS_TARGET) ./tests/tests_log $(TESTS) ./*.gcda ./*.gcov ./*.gcno *.gcda *.gcov *.gcno ./tests/*.gcda ./tests/*.gcov ./tests/*.gcno
+	$(RM) ./*.o *~ $(BAM_STATS_TARGET) ./tests/tests_log $(TESTS) ./*.gcda ./*.gcov ./*.gcno *.gcda *.gcov *.gcno ./tests/*.gcda ./tests/*.gcov ./tests/*.gcno 
+	-rm -rf $(HTSTMP)
 
 
 depend: $(SRCS)
diff --git a/c/bam_access.c b/c/bam_access.c
index 0232a0f..e29c706 100644
--- a/c/bam_access.c
+++ b/c/bam_access.c
@@ -37,7 +37,7 @@ void parse_rg_line(char *tmp_line, const int idx, rg_info_t **groups,
   while(tag != NULL){
     int chk = sscanf(tag,"ID:%[^\t\n]",id);
     if(chk == 1){
-      groups[idx]->id = malloc(sizeof(char) * 1000);
+      groups[idx]->id = (char *) malloc(sizeof(char) * 1000);
       strcpy(groups[idx]->id,id);
       tag = strtok(NULL,"\t");
       continue;
@@ -111,22 +111,41 @@ rg_info_t **parse_header(bam_hdr_t *head, int *grps_size, stats_rd_t ****grp_sta
         check_mem(groups[idx]);
         char *id = malloc(sizeof(char) * 1000);
         check_mem(id);
-        char *sm =malloc(sizeof(char) * 1000);
+        id[0] = '\0';
+        char *sm = malloc(sizeof(char) * 1000);
         check_mem(sm);
+        sm[0] = '\0';
         char *pl = malloc(sizeof(char) * 1000);
         check_mem(pl);
+        pl[0] = '\0';
         char *pu = malloc(sizeof(char) * 1000);
         check_mem(pu);
+        pu[0] = '\0';
         char *lib = malloc(sizeof(char) * 1000);
         check_mem(lib);
+        lib[0] = '\0';
         char * tmp = malloc(sizeof(char) * (strlen(line)+1));
         strcpy(tmp,line);
         parse_rg_line(tmp,idx,groups,id,sm,pl,pu,lib);
-        check(id != NULL,"Error recognising ID from RG line.");
-        check(sm != NULL,"Error recognising SM from RG line.");
+        check((id != NULL),"Error recognising ID from RG line. NULL found.");
+        check((strcmp(id,"")!=0),"Error recognising ID from RG line. Empty string.");
+        check((id[0]!='\0'),"Error recognising ID from RG line. Empty string.");
+        check((sm != NULL),"Error recognising SM from RG line.");
+        if((sm[0]=='\0')){
+          groups[idx]->sample = ".";
+        }
         check(pl != NULL,"Error recognising PL from RG line.");
+        if((pl[0]=='\0')){
+          groups[idx]->platform = ".";
+        }
         check(lib != NULL,"Error recognising LB from RG line.");
+        if((lib[0]=='\0')){
+          groups[idx]->lib = ".";
+        }
         check(pu != NULL,"Error recognising PU from RG line.");
+        if((pu[0]=='\0')){
+          groups[idx]->platform_unit = ".";
+        }
         free (tmp);
         idx++;
       }//End of iteration through header lines.
@@ -188,7 +207,7 @@ rg_info_t **parse_header(bam_hdr_t *head, int *grps_size, stats_rd_t ****grp_sta
   return NULL;
 }
 
-int process_reads(htsFile *input, bam_hdr_t *head, rg_info_t **grps, int grps_size, stats_rd_t ****grp_stats){
+int process_reads(htsFile *input, bam_hdr_t *head, rg_info_t **grps, int grps_size, stats_rd_t ****grp_stats, int rna){
   assert(input != NULL);
   assert(head != NULL);
   assert(grps != NULL);
@@ -198,7 +217,7 @@ int process_reads(htsFile *input, bam_hdr_t *head, rg_info_t **grps, int grps_si
   b = bam_init1();
   int ret;
   while((ret = sam_read1(input, head, b)) >= 0){
-    if (b->core.flag & BAM_FSECONDARY) continue; //skip secondary hits so no double counts
+    if (b->core.flag & BAM_FSECONDARY && rna == 0) continue; //skip secondary hits so no double counts
     if (b->core.flag & BAM_FQCFAIL) continue; // skip vendor fail as generally aren't considered
     if (b->core.flag & BAM_FSUPPLEMENTARY) continue; // skip supplimentary
 
diff --git a/c/bam_access.h b/c/bam_access.h
index ca2a57b..3dbccc9 100644
--- a/c/bam_access.h
+++ b/c/bam_access.h
@@ -54,7 +54,7 @@ typedef struct{
 
 rg_info_t **parse_header(bam_hdr_t *head, int *grps_size, stats_rd_t ****grp_stats);
 
-int process_reads(htsFile *input, bam_hdr_t *head, rg_info_t **grps, int grps_size, stats_rd_t ****grp_stats);
+int process_reads(htsFile *input, bam_hdr_t *head, rg_info_t **grps, int grps_size, stats_rd_t ****grp_stats, int rna);
 
 uint64_t get_mapped_base_count_from_cigar(bam1_t *b);
 
diff --git a/c/bam_stats.c b/c/bam_stats.c
index 257c7cc..6e96ff9 100644
--- a/c/bam_stats.c
+++ b/c/bam_stats.c
@@ -31,9 +31,10 @@
 
 #include "khash.h"
 
-static char *input_file;
+static char *input_file = NULL;
 static char *output_file;
 static char *ref_file;
+static int rna = 0;
 int grps_size = 0;
 stats_rd_t*** grp_stats;
 static char *bas_header = "bam_filename\tsample\tplatform\tplatform_unit\tlibrary\treadgroup\tread_length_r1\tread_length_r2\t#_mapped_bases\t#_mapped_bases_r1\t#_mapped_bases_r2\t#_divergent_bases\t#_divergent_bases_r1\t#_divergent_bases_r2\t#_total_reads\t#_total_reads_r1\t#_total_reads_r2\t#_mapped_reads\t#_mapped_reads_r1\t#_mapped_reads_r2\t#_mapped_reads_properly_paired\t#_gc_bases_r1\t#_gc_bases_r2\tmean_insert_size\tinsert_size_sd\tmedian_insert_size\t#_duplicate_reads\n";
@@ -62,7 +63,8 @@ void print_usage (int exit_code){
 	printf ("Optional:\n");
 	printf ("-r --ref-file  File path to reference index (.fai) file.\n");
 	printf ("               NB. If cram format is supplied via -b and the reference listed in the cram header can't be found bam_stats may fail to work correctly.\n");
-	printf ("-p --plots     Folder to contain quality score plots.\n\n");
+	printf ("-a --rna       Uses the RNA method of calculating insert size (ignores anything outside ± ('sd'*standard_dev) of the mean in calculating a new mean)\n");
+	
 	printf ("Other:\n");
 	printf ("-h --help      Display this usage information.\n");
 	printf ("-v --version   Prints the version number.\n\n");
@@ -80,7 +82,7 @@ void options(int argc, char *argv[]){
               {"input",required_argument,0,'i'},
               {"ref-file",required_argument,0,'r'},
               {"output",required_argument,0,'o'},
-              {"plots",required_argument,0,'p'},
+              {"rna",no_argument,0, 'a'},
               { NULL, 0, NULL, 0}
 
    }; //End of declaring opts
@@ -89,7 +91,7 @@ void options(int argc, char *argv[]){
    int iarg = 0;
 
    //Iterate through options
-   while((iarg = getopt_long(argc, argv, "i:o:r:pvh", long_opts, &index)) != -1){
+   while((iarg = getopt_long(argc, argv, "i:o:r:vha", long_opts, &index)) != -1){
    	switch(iarg){
    		case 'i':
         input_file = optarg;
@@ -102,12 +104,11 @@ void options(int argc, char *argv[]){
    		case 'r':
    		  ref_file = optarg;
    		  break;
-
-   		case 'p':
-   		  print_usage(1);
-   			//plots = optarg;
-   			break;
-
+   			
+   		case 'a':
+        rna = 1;
+        break;
+        
    		case 'h':
         print_usage(0);
         break;
@@ -128,9 +129,17 @@ void options(int argc, char *argv[]){
    }//End of iteration through options
 
    //Do some checking to ensure required arguments were passed and are accessible files
-   if(check_exist(input_file) != 1){
-   	printf("Input file (-i) %s does not exist.\n",input_file);
-   	print_usage(1);
+   if (input_file==NULL || strcmp(input_file,"/dev/stdin")==0) {
+    input_file = "-";   // htslib recognises this as a special case
+   }
+   if (strcmp(input_file,"-") != 0) {
+     if(check_exist(input_file) != 1){
+   	  printf("Input file (-i) %s does not exist.\n",input_file);
+   	  print_usage(1);
+     }
+   }
+   if (output_file==NULL || strcmp(output_file,"/dev/stdout")==0) {
+    output_file = "-";   // we recognise this as a special case
    }
    if(ref_file){
      if(check_exist(ref_file) != 1){
@@ -154,16 +163,6 @@ int calculate_mean_sd_median_insert_size(khash_t(ins) *inserts,double *mean, dou
           tt_mean += val;
         });
 
-    /*
-    int i = 0;
-    for(i=0;i<200000;i++){
-      if(inserts[i]>0){
-        pp_mean += (i+1) * inserts[i];
-        tt_mean += inserts[i];
-      }
-    }
-    */
-
     if(tt_mean){//Calculate mean , median, sd
       *mean = (double) ((double)pp_mean/(double)tt_mean);
 
@@ -180,18 +179,6 @@ int calculate_mean_sd_median_insert_size(khash_t(ins) *inserts,double *mean, dou
               prev_insert = key;
             });
 
-      /*
-      int j=0;
-
-      for(j=0;j<200000;j++){
-        if(inserts[j]>0){
-          insert = j+1;
-          running_total += inserts[j];
-          if(running_total >= midpoint) break ;
-          prev_insert = j+1;
-        }
-      }*/
-
       if(tt_mean %2 == 0 && ( running_total - midpoint2 >= insert )){
         //warn "Thinks is even AND split between bins ";
         *median = (((double)insert + (double)prev_insert) / (double)2);
@@ -210,16 +197,7 @@ int calculate_mean_sd_median_insert_size(khash_t(ins) *inserts,double *mean, dou
               tt_sd += val;
             });
 
-      /*
-      int k=0;
-      for(k=0;k<200000;k++){
-        if(inserts[k]>0){
-          double diff = (double)(k+1) - (*mean);
-          pp_sd += (diff * diff) * inserts[k];
-          tt_sd += inserts[k];
-        }
-      }*/
-      kh_destroy(ins, inserts);
+      
 
       if(tt_sd){
         double variance = fabs((double)((double)pp_sd / (double)tt_sd));
@@ -227,13 +205,20 @@ int calculate_mean_sd_median_insert_size(khash_t(ins) *inserts,double *mean, dou
       }else{
         *sd = 0;
       }
+      
+      kh_destroy(ins, inserts);
 
     } //End of if we have data to calculate from.
   return 0;
 }
 
 int print_results(rg_info_t **grps){
-  FILE *out = fopen(output_file,"w");
+  FILE *out;
+  if (strcmp(output_file,"-")==0) {
+    out = stdout;
+  } else {
+    out = fopen(output_file,"w");
+  }
   check(out != NULL,"Error trying to open output file %s for writing.",output_file);
 
   int chk = fprintf(out,"%s",bas_header);
@@ -327,11 +312,11 @@ int print_results(rg_info_t **grps){
       fflush(out);
   }
 
-  fclose(out);
+  if (out != stdout) fclose(out);
   return 0;
 
 error:
-  if(out) fclose(out);
+  if(out && out != stdout) fclose(out);
   return -1;
 
 }
@@ -356,7 +341,7 @@ int main(int argc, char *argv[]){
   check(grps != NULL, "Error fetching read groups from header.");
 
   //Process every read in bam file.
-  int check = process_reads(input,head,grps, grps_size, &grp_stats);
+  int check = process_reads(input,head,grps, grps_size, &grp_stats, rna);
   check(check==0,"Error processing reads in bam file.");
 
   int res = print_results(grps);
diff --git a/docs.tar.gz b/docs.tar.gz
index c0f47f4..39837c4 100644
Binary files a/docs.tar.gz and b/docs.tar.gz differ
diff --git a/lib/PCAP.pm b/lib/PCAP.pm
index d451883..4101943 100644
--- a/lib/PCAP.pm
+++ b/lib/PCAP.pm
@@ -24,7 +24,7 @@ use strict;
 use Const::Fast qw(const);
 use base 'Exporter';
 
-our $VERSION = '1.10.0';
+our $VERSION = '1.11.0';
 our @EXPORT = qw($VERSION);
 
 const my $LICENSE =>
@@ -64,14 +64,15 @@ const my %UPGRADE_PATH => ( '0.1.0'  => 'biobambam,bwa,samtools',
                             '1.6.2'  => 'biobambam,bwa',
                             '1.6.3'  => 'biobambam,bwa',
                             '1.7.0'  => 'biobambam,bwa',
-                            '1.7.1'  => 'bwa',
-                            '1.8.0'  => '',
-                            '1.8.1'  => '',
-                            '1.8.2'  => '',
-                            '1.9.0'  => '',
-                            '1.9.1'  => '',
-                            '1.9.4'  => '',
-                            '1.10.0'  => '',
+                            '1.7.1'  => 'biobambam,bwa',
+                            '1.8.0'  => 'biobambam',
+                            '1.8.1'  => 'biobambam',
+                            '1.8.2'  => 'biobambam',
+                            '1.9.0'  => 'biobambam',
+                            '1.9.1'  => 'biobambam',
+                            '1.9.4'  => 'biobambam',
+                            '1.10.0'  => 'biobambam',
+                            '1.11.0'  => 'biobambam',
                           );
 
 sub license {
diff --git a/lib/PCAP/Bam.pm b/lib/PCAP/Bam.pm
index e2218b7..457c0e1 100644
--- a/lib/PCAP/Bam.pm
+++ b/lib/PCAP/Bam.pm
@@ -107,7 +107,7 @@ sub merge_and_mark_dup {
   $helper_threads = 1 if($helper_threads < 1);
   # uncoverable branch true
   # uncoverable branch false
-  my $command = which('bammarkduplicates') || die "Unable to find 'bammarkduplicates' in path";
+  my $command = which('bammarkduplicates2') || die "Unable to find 'bammarkduplicates' in path";
   $command .= sprintf $BAMBAM_DUP,  $marked,
                                     $met,
                                     File::Spec->catfile($tmp, 'biormdup'),
diff --git a/lib/PCAP/Bwa.pm b/lib/PCAP/Bwa.pm
index c160081..2083863 100644
--- a/lib/PCAP/Bwa.pm
+++ b/lib/PCAP/Bwa.pm
@@ -222,7 +222,10 @@ sub bwa_mem {
     else {
       my ($rg) = $split =~ m|/split/[[:digit:]]+/(.+)_i.fq_[[:digit:]]+.gz$|;
       ($rg_line, undef) = PCAP::Bam::rg_line_for_output($input->in, $options->{'sample'}, undef, $rg);
-      unless($rg_line) {
+      if($rg_line) {
+        $rg_line =~ s/('+)/'"$1"'/g;
+      }
+      else {
         $rg_line = sprintf $FALSE_RG, $split_element, $options->{'sample'};
       }
       $rg_line = q{'}.$rg_line.q{'};
@@ -244,12 +247,14 @@ sub bwa_mem {
     # uncoverable branch true
     # uncoverable branch false
     if($input->paired_fq) {
+      $split =~ s/'/\\'/g;
       my $split2 = $split;
       $split2 =~ s/pairedfq1(\.[[:digit:]]+)/pairedfq2$1/;
       $bwa .= ' '.$split;
       $bwa .= ' '.$split2;
     }
     else {
+      $split =~ s/'/\\'/g;
       $bwa .= ' '.$split;
     }
     $command .= $bwa;
@@ -261,6 +266,7 @@ sub bwa_mem {
 
     my $sorted_bam_stub = $split;
     $sorted_bam_stub =~ s|/split/([[:digit:]]+)/(.+)$|/sorted/$1_$2|;
+    $sorted_bam_stub =~ s/\\'/-/g;
 
     my $ref = exists $options->{'decomp_ref'} ? $options->{'decomp_ref'} : $options->{'reference'};
     my $sort = which('bamsort') || die "Unable to find 'bamsort' in path\n";
diff --git a/lib/PCAP/Threaded.pm b/lib/PCAP/Threaded.pm
index 0189954..a7b03e0 100644
--- a/lib/PCAP/Threaded.pm
+++ b/lib/PCAP/Threaded.pm
@@ -30,7 +30,7 @@ use Carp qw( croak );
 use Config; # so we can see if threads are enabled
 use File::Spec;
 use File::Path qw(make_path);
-use Try::Tiny qw(try catch);
+use Try::Tiny qw(try catch finally);
 use Capture::Tiny qw(capture);
 use IO::File;
 
@@ -208,6 +208,18 @@ sub external_process_handler {
       }
     } catch {
       die $_ if($_);
+    }
+    finally {
+      if($out_fh) {
+        $out_fh->flush;
+        $out_fh->close;
+        undef $out_fh;
+      }
+      if($err_fh) {
+        $err_fh->flush;
+        $err_fh->close;
+        undef $err_fh;
+      }
     };
   }
 
diff --git a/prerelease.sh b/prerelease.sh
index f7c1c61..f0b0000 100755
--- a/prerelease.sh
+++ b/prerelease.sh
@@ -1,6 +1,7 @@
 #!/bin/bash
 
 set -eu # exit on first error or undefined value in subtitution
+set -o pipefail
 
 # get current directory
 INIT_DIR=`pwd`
@@ -25,10 +26,6 @@ export HARNESS_PERL_SWITCHES=-MDevel::Cover=-db,reports,-ignore,'t/.*\.t'
 rm -rf docs
 mkdir -p docs/reports_text
 prove --nocolor -I ./lib | sed 's/^/  /' # indent output of prove
-if [[ $? -ne 0 ]] ; then
-  echo "\n\tERROR: TESTS FAILED\n"
-  exit 1
-fi
 
 echo '### Generating test/pod coverage reports ###'
 # removed 'condition' from coverage as '||' 'or' doesn't work properly
diff --git a/setup.sh b/setup.sh
index 7e4a0e6..986dbce 100755
--- a/setup.sh
+++ b/setup.sh
@@ -11,7 +11,7 @@ SOURCE_HTSLIB="https://github.com/samtools/htslib/archive/1.2.1.tar.gz"
 SOURCE_JKENT_BIN="https://github.com/ENCODE-DCC/kentUtils/raw/master/bin/linux.x86_64"
 
 # for biobambam
-SOURCE_BBB_BIN_DIST="https://github.com/gt1/biobambam/releases/download/0.0.191-release-20150401083643/biobambam-0.0.191-release-20150401083643-x86_64-etch-linux-gnu.tar.gz"
+SOURCE_BBB_BIN_DIST="https://github.com/gt1/biobambam2/releases/download/2.0.25-release-20151105154334/biobambam2-2.0.25-release-20151105154334-x86_64-etch-linux-gnu.tar.gz"
 
 done_message () {
     if [ $? -eq 0 ]; then
@@ -210,10 +210,9 @@ if [[ ",$COMPILE," == *,biobambam,* ]] ; then
       cd $SETUP_DIR
       mkdir -p biobambam
       get_distro "biobambam" $SOURCE_BBB_BIN_DIST
-      mkdir -p $INST_PATH/bin $INST_PATH/include $INST_PATH/lib $INST_PATH/share
-      rm -f biobambam/bin/curl* # breaks OS installs
+      mkdir -p $INST_PATH/bin $INST_PATH/etc $INST_PATH/lib $INST_PATH/share
       cp -r biobambam/bin/* $INST_PATH/bin/.
-      cp -r biobambam/include/* $INST_PATH/include/.
+      cp -r biobambam/etc/* $INST_PATH/etc/.
       cp -r biobambam/lib/* $INST_PATH/lib/.
       cp -r biobambam/share/* $INST_PATH/share/.
       touch $SETUP_DIR/biobambam.success
diff --git a/t/3_external_progs.t b/t/3_external_progs.t
index fa57d29..2675453 100644
--- a/t/3_external_progs.t
+++ b/t/3_external_progs.t
@@ -10,29 +10,30 @@ use List::Util qw(first);
 use Const::Fast qw(const);
 use Capture::Tiny qw(capture);
 use Data::Dumper;
+use version 0.77;
 
-const my @REQUIRED_PROGRAMS => qw(bamcollate2 bammarkduplicates bamsort bwa);
-const my $BIOBAMBAM_VERSION => ['0.0.191'];
-const my $BWA_VERSIONS => ['0.7.12'];
+const my @REQUIRED_PROGRAMS => qw(bamcollate2 bammarkduplicates2 bamsort bwa);
+const my $BIOBAMBAM2_VERSION => '2.0.25';
+const my $BWA_VERSION => '0.7.12';
 
 # can't put regex in const
 my %EXPECTED_VERSION = (
                         'bamcollate2'       => {
                               'get'   => q{ -h},
-                              'match' => qr/This is biobambam version ([[:digit:]\.]+)\./,
-                              'version'       => $BIOBAMBAM_VERSION},
-                        'bammarkduplicates' => {
+                              'match' => qr/This is biobambam2 version ([[:digit:]\.]+)\./,
+                              'version'       => version->parse($BIOBAMBAM2_VERSION)},
+                        'bammarkduplicates2' => {
                               'get'   => q{ -h},
-                              'match' => qr/This is biobambam version ([[:digit:]\.]+)\./,
-                              'version'       => $BIOBAMBAM_VERSION},
+                              'match' => qr/This is biobambam2 version ([[:digit:]\.]+)\./,
+                              'version'       => version->parse($BIOBAMBAM2_VERSION)},
                         'bamsort'           => {
                               'get'   => q{ -h},
-                              'match' => qr/This is biobambam version ([[:digit:]\.]+)\./,
-                              'version'       => $BIOBAMBAM_VERSION},
+                              'match' => qr/This is biobambam2 version ([[:digit:]\.]+)\./,
+                              'version'       => version->parse($BIOBAMBAM2_VERSION)},
                         'bwa'           => {
                               'get'   => q{},
                               'match' => qr/Version: ([[:digit:]\.]+[[:alpha:]]?)/, # we don't care about the revision number
-                              'version'       => $BWA_VERSIONS},
+                              'version'       => version->parse($BWA_VERSION)},
                         );
 
 subtest 'External programs exist on PATH' => sub {
@@ -50,8 +51,9 @@ subtest 'External programs have expected version' => sub {
     my ($stdout, $stderr, $exit) = capture{ system($command); };
     my $reg = $details->{'match'};
     my ($version) = $stderr =~ /$reg/m;
-    my $found = first {$version eq $_} @{$details->{'version'}};
-    ok($found, sprintf 'Expect version %s for %s', (join q{|}, @{$details->{'version'}}), $prog);
+    version->parse($version);
+
+    ok(version->parse($version) >= $details->{'version'}, sprintf 'Expect minimum version of %s for %s', $details->{'version'}, $prog);
   }
 };