diff --git a/.travis.yml b/.travis.yml
new file mode 100644
index 0000000..c1e4294
--- /dev/null
+++ b/.travis.yml
@@ -0,0 +1,34 @@
+notifications:
+  slack: wtsi-cgpit:ptUMR1tkNyZJYd9TpGoss8WR
+  email: false
+
+env:
+ - CC=gcc
+
+addons:
+ apt:
+  packages:
+   - build-essential
+   - autoconf
+   - bsdtar
+   - time
+   - curl
+   - libcurl4-openssl-dev
+   - nettle-dev
+   - zlib1g-dev
+   - libncurses5-dev
+   - libpstreams-dev
+   - unzip
+   - libpng12-dev
+   - libexpat1-dev
+
+install: true
+
+language: perl
+
+perl:
+ - "5.22"
+
+script:
+ - ./setup.sh ~/wtsi-opt
+ - ~/wtsi-opt/bin/samtools view # dump usage to show intact
diff --git a/MANIFEST b/MANIFEST
index 03c4145..607ab83 100644
--- a/MANIFEST
+++ b/MANIFEST
@@ -1,3 +1,5 @@
+.travis.yml
+bin/bam2bedgraph
 bin/bam_stats.pl
 bin/bam_to_sra_sub.pl
 bin/bamToBw.pl
@@ -9,6 +11,7 @@ bin/gnos_pull.pl
 bin/monitor.pl
 bin/xam_coverage_bins.pl
 bin/xml_to_bas.pl
+c/bam2bedgraph.c
 c/bam_access.c
 c/bam_access.h
 c/bam_stats.c
@@ -27,6 +30,7 @@ c/dbg.h
 c/khash.h
 c/reheadSQ.c
 CHANGES.md
+dists/patch/Bio-BigFile_build.patch
 dists/snappy-1.1.2.tar.gz
 docs.tar.gz
 examples/gnos_pull.ini
diff --git a/README.md b/README.md
index 6c55ad0..f8e59dc 100644
--- a/README.md
+++ b/README.md
@@ -1,7 +1,11 @@
 ICGC-TCGA-PCAP
 ==============
 
-NGS reference implementations and helper code for the ICGC/TCGA Pan-Cancer Analysis Project
+NGS reference implementations and helper code for the ICGC/TCGA Pan-Cancer Analysis Project.
+
+| Master | Dev |
+|---|---|
+| [![Build Status](https://travis-ci.org/ICGC-TCGA-PanCancer/PCAP-core.svg?branch=master)](https://travis-ci.org/ICGC-TCGA-PanCancer/PCAP-core) |  [![Build Status](https://travis-ci.org/ICGC-TCGA-PanCancer/PCAP-core.svg?branch=dev)](https://travis-ci.org/ICGC-TCGA-PanCancer/PCAP-core) |
 
 This repository contains code to run genomic alignments of paired end data
 and subsequent calling algorithms.
diff --git a/bin/bamToBw.pl b/bin/bamToBw.pl
index 6df35c8..bc86eb1 100755
--- a/bin/bamToBw.pl
+++ b/bin/bamToBw.pl
@@ -82,6 +82,7 @@ sub setup {
               'r|reference=s' => \$opts{'reference'},
               'p|process=s' => \$opts{'process'},
               'i|index=i' => \$opts{'index'},
+              'f|filter=i' => \$opts{'filter'},
               'j|jobs' => \$opts{'jobs'},
   ) or pod2usage(2);
 
@@ -106,6 +107,7 @@ sub setup {
 
   delete $opts{'process'} unless(defined $opts{'process'});
   delete $opts{'index'} unless(defined $opts{'index'});
+  delete $opts{'filter'} unless(defined $opts{'filter'});
 
   # now safe to apply defaults
   $opts{'threads'} = 1 unless(defined $opts{'threads'});
@@ -160,10 +162,13 @@ =head1 SYNOPSIS
   Required parameters:
     -bam       -b   BAM/CRAM file to be processed.
     -outdir    -o   Folder to output result to.
-    -threads   -t   Number of threads to use. [1]
     -reference -r   Path to genome.fa.
                      - Actually using fa.fai but for convention just provide '.fa' file
 
+  Optional parameters:
+    -threads   -t   Number of threads to use. [1]
+    -filter    -f   Ignore reads with the filter flags [int]
+
   Targeted processing:
     -process   -p   Only process this step then exit, optionally set -index
                          bamToBw - Per chromosome BigWigs
diff --git a/bin/bam_stats.pl b/bin/bam_stats.pl
index 0758be8..01b08a1 100755
--- a/bin/bam_stats.pl
+++ b/bin/bam_stats.pl
@@ -32,11 +32,8 @@
 use Config; # so we can see if threads are enabled
 use Data::Dumper;
 
-BEGIN {
-  if($Config{useithreads}) {
-    require threads;
-  }
-};
+our $CAN_USE_THREADS = 0;
+$CAN_USE_THREADS = eval 'use threads; 1';
 
 use PCAP::Bam::Stats;
 
@@ -54,15 +51,20 @@ BEGIN
     $out_location = 'STDOUT';
   }
 
+  if($opts->{'threads'} > 1 && $CAN_USE_THREADS == 0) {
+    warn "Threading is not available perl component will run as a single process";
+    $opts->{'threads'} = 1;
+  }
+
   try{
     my $stats;
-    if($opts->{'threads'} > 1 && $Config{useithreads}) {
+    if($opts->{'threads'} > 1 && $CAN_USE_THREADS) {
       for my $thread(0..($opts->{'threads'}-1)) {
          my ($thr) = threads->create(\&stat_thread, $opts, $thread);
       }
-      sleep 2 while(threads->list(threads::running) > 0);
+      sleep 2 while(threads->list(threads::running()) > 0);
       my @bas_objs;
-      for my $thr(threads->list(threads::joinable)) {
+      for my $thr(threads->list(threads::joinable())) {
         push @bas_objs, $thr->join;
         if(my $err = $thr->error) { die "Thread error: $err\n"; }
       }
diff --git a/bin/bwa_mem.pl b/bin/bwa_mem.pl
index 6dfdb83..a86031a 100755
--- a/bin/bwa_mem.pl
+++ b/bin/bwa_mem.pl
@@ -97,6 +97,8 @@ sub setup {
               'p|process=s' => \$opts{'process'},
               'i|index=i' => \$opts{'index'},
               'b|bwa=s' => \$opts{'bwa'},
+              'c|cram' => \$opts{'cram'},
+              'sc|scramble=s' => \$opts{'scramble'},
   ) or pod2usage(2);
 
   pod2usage(-verbose => 1, -exitval => 0) if(defined $opts{'h'});
@@ -126,6 +128,9 @@ sub setup {
   delete $opts{'process'} unless(defined $opts{'process'});
   delete $opts{'index'} unless(defined $opts{'index'});
   delete $opts{'bwa'} unless(defined $opts{'bwa'});
+  delete $opts{'scramble'} unless(defined $opts{'scramble'});
+
+  PCAP::Cli::opt_requires_opts('scramble', \%opts, ['cram']);
 
   # now safe to apply defaults
   $opts{'threads'} = 1 unless(defined $opts{'threads'});
@@ -189,10 +194,13 @@ =head1 SYNOPSIS
     -threads   -t   Number of threads to use. [1]
 
   Optional parameters:
-    -fragment  -f   Split input into fragements of X million repairs
+    -fragment  -f   Split input into fragements of X million repairs [10]
     -nomarkdup -n   Don't mark duplicates
-    -bwa       -b   Single quoted string of parameters to pass to BWA
-                     - overrides all defaults except '-t,-p,-R'
+    -cram      -c   Output cram, see '-sc'
+    -scramble  -sc  Single quoted string of parameters to pass to Scramble when '-c' used
+                    - '-I,-O' are used internally and should not be provided
+    -bwa       -b   Single quoted string of additional parameters to pass to BWA
+                     - '-t,-p,-R' are used internally and should not be provided
 
   Targeted processing:
     -process   -p   Only process this step then exit, optionally set -index
diff --git a/bin/gnos_pull.pl b/bin/gnos_pull.pl
index 9eae0bc..eab9cf6 100755
--- a/bin/gnos_pull.pl
+++ b/bin/gnos_pull.pl
@@ -43,6 +43,9 @@
 use Proc::PID::File;
 use Data::Dumper;
 
+my $CAN_USE_THREADS = 0;
+$CAN_USE_THREADS = eval 'use threads; 1';
+
 use PCAP;
 use PCAP::Cli;
 
@@ -99,7 +102,7 @@ sub load_config {
   }
   if(exists $options->{'COMPOSITE_FILTERS'}->{'not_sanger_workflow'}) {
     my %bl_workflows = map { $_ => 1 } split /[\n,]/, $options->{'COMPOSITE_FILTERS'}->{'not_sanger_workflow'};
-    $options->{'COMPOSITE_FILTERS'}->{'not_sanger_workflow'} = [keys \%bl_workflows];
+    $options->{'COMPOSITE_FILTERS'}->{'not_sanger_workflow'} = [keys %bl_workflows];
   }
 
   croak sprintf q{'KEY_FILE' Ssection is absent from %s}, $options->{'config'} unless($cfg->SectionExists('KEY_FILES'));
@@ -132,8 +135,6 @@ sub load_config {
   return 1;
 }
 
-use threads;
-
 sub pull_data {
   my ($options, $to_process) = @_;
 
@@ -153,6 +154,10 @@ sub pull_data {
   }
 
   my $thread_count = $options->{'threads'};
+  if($CAN_USE_THREADS == 0) {
+    warn "Threading is not available perl component will run as a single process";
+    $thread_count = 1;
+  }
 
 
   while(@{$to_process} > 0) {
@@ -170,13 +175,13 @@ sub pull_data {
 
     warn "Submitting: $donor->{donor_unique_id}\n";
     if($thread_count > 1) {
-      if(threads->list(threads::all) < $thread_count) {
+      if(threads->list(threads::all()) < $thread_count) {
         threads->create($code_ref, $options, $donor, $orig_base, $donor_base);
         # don't sleep if not full yet
-        next if(threads->list(threads::all) < $thread_count);
+        next if(threads->list(threads::all()) < $thread_count);
       }
-      sleep 1 while(threads->list(threads::joinable) == 0);
-      for my $thr(threads->list(threads::joinable)) {
+      sleep 1 while(threads->list(threads::joinable()) == 0);
+      for my $thr(threads->list(threads::joinable())) {
         $thr->join;
         if(my $err = $thr->error) { die "Thread error: $err\n"; }
       }
@@ -187,8 +192,8 @@ sub pull_data {
   }
   if($thread_count > 1) {
     # last gasp for any remaining threads
-    sleep 1 while(threads->list(threads::running) > 0);
-    for my $thr(threads->list(threads::joinable)) {
+    sleep 1 while(threads->list(threads::running()) > 0);
+    for my $thr(threads->list(threads::joinable())) {
       $thr->join;
       if(my $err = $thr->error) { die "Thread error: $err\n"; }
     }
diff --git a/c/Makefile b/c/Makefile
index 223215f..8d5c8b4 100644
--- a/c/Makefile
+++ b/c/Makefile
@@ -42,7 +42,7 @@ LFLAGS?= -L$(HTSTMP)
 # define any libraries to link into executable:
 #   if I want to link in libraries (libx.so or libx.a) I use the -llibname
 #   option, something like (this will link in libmylib.so and libm.so:
-LIBS =-lhts -lpthread -lz -lm
+LIBS =-lhts -lpthread -lz -lm -ldl
 
 # define the C source files
 SRCS = ./bam_access.c ./bam_stats_output.c ./bam_stats_calcs.c
@@ -66,6 +66,7 @@ MD := mkdir
 BAM_STATS_TARGET=../bin/bam_stats
 CAT_TARGET=../bin/bwcat
 SQ_TARGET=../bin/reheadSQ
+BAM2BG_TARGET=../bin/bam2bedgraph
 
 #
 # The following part of the makefile is generic; it can be used to
@@ -77,7 +78,7 @@ SQ_TARGET=../bin/reheadSQ
 
 .NOTPARALLEL: test
 
-all: clean pre make_htslib_tmp $(BAM_STATS_TARGET) test remove_htslib_tmp $(CAT_TARGET) $(SQ_TARGET)
+all: clean pre make_htslib_tmp $(BAM_STATS_TARGET) $(BAM2BG_TARGET) test remove_htslib_tmp $(CAT_TARGET) $(SQ_TARGET)
 	@echo  bam_stats, reheadSQ and bwcat compiled.
 
 $(BAM_STATS_TARGET): $(OBJS)
@@ -86,6 +87,9 @@ $(BAM_STATS_TARGET): $(OBJS)
 $(CAT_TARGET):
 	$(CC) $(CAT_INCLUDES) $(CFLAGS) ./bwcat.c $(CAT_LFLAGS) -lBigWig -lz -lcurl -lm -lgnutls -ltasn1 -lhogweed -lnettle -lgmp -lp11-kit -o $(CAT_TARGET)
 
+$(BAM2BG_TARGET): $(OBJS)
+	$(CC) $(CFLAGS) $(INCLUDES) -o $(BAM2BG_TARGET) $(OBJS) $(LFLAGS) $(LIBS) ./bam2bedgraph.c
+
 $(SQ_TARGET):
 	$(CC) $(CFLAGS) ./reheadSQ.c -o $(SQ_TARGET)
 
diff --git a/c/bam2bedgraph.c b/c/bam2bedgraph.c
new file mode 100644
index 0000000..a78cc05
--- /dev/null
+++ b/c/bam2bedgraph.c
@@ -0,0 +1,228 @@
+#include <stdio.h>
+#include <getopt.h>
+#include <stdlib.h>
+#include <string.h>
+#include "htslib/sam.h"
+
+static char *input_file = NULL;
+static char *output_file = NULL;
+static char *region = NULL;
+static int filter = 0;
+
+typedef struct {
+  uint32_t ltid;
+  int      lstart,lcoverage,lpos,beg,end;
+  htsFile *in;
+  hts_idx_t *idx;
+	bam_hdr_t *head;
+	FILE *out;
+} tmpstruct_t;
+
+void print_version (int exit_code){
+  printf ("%s\n",VERSION);
+	exit(exit_code);
+}
+
+int check_exist(char *fname){
+	FILE *fp;
+	if((fp = fopen(fname,"r"))){
+		fclose(fp);
+		return 1;
+	}
+	return 0;
+}
+
+void print_usage (int exit_code){
+
+	printf ("Usage: bam2bedgraph -i input.[cr|b]am -o file [-r region] [-h] [-v]\n\n");
+	printf ("Create a BEDGraph file of genomic coverage. BAM file must be sorted.\n");
+  printf ("-i --input     Path to bam/cram input file. [default: stdin]\n");
+  printf ("-o --output    File path for output. [default: stdout]\n\n");
+	printf ("Optional:\n");
+	printf ("-r --region    Region in bam to access.\n");
+	printf ("-f --filter    Ignore reads with the filter flags [int].\n");
+	printf ("Other:\n");
+	printf ("-h --help      Display this usage information.\n");
+	printf ("-v --version   Prints the version number.\n\n");
+  exit(exit_code);
+}
+
+void options(int argc, char *argv[]){
+	const struct option long_opts[] =
+	  {
+             	{"version", no_argument, 0, 'v'},
+             	{"help",no_argument,0,'h'},
+              {"input",required_argument,0,'i'},
+              {"region",required_argument,0,'r'},
+              {"filter",required_argument,0,'f'},
+              {"output",required_argument,0,'o'},
+              {"rna",no_argument,0, 'a'},
+              { NULL, 0, NULL, 0}
+
+   }; //End of declaring opts
+
+   int index = 0;
+   int iarg = 0;
+
+   //Iterate through options
+   while((iarg = getopt_long(argc, argv, "i:o:r:f:vh", long_opts, &index)) != -1){
+   	switch(iarg){
+   		case 'i':
+        input_file = optarg;
+        break;
+
+   		case 'o':
+				output_file = optarg;
+   			break;
+
+   		case 'r':
+   		  region = optarg;
+   		  break;
+
+   		case 'f':
+   		  if(sscanf(optarg, "%i", &filter) != 1){
+      		printf("Error parsing -f argument '%s'. Should be an integer > 0",optarg);
+      		print_usage(1);
+      	}
+      	break;
+   		case 'h':
+        print_usage(0);
+        break;
+
+      case 'v':
+        print_version(0);
+        break;
+
+			case '?':
+        print_usage (1);
+        break;
+
+      default:
+      	print_usage (1);
+
+   	}; // End of args switch statement
+
+   }//End of iteration through options
+
+   //Do some checking to ensure required arguments were passed and are accessible files
+   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
+   }
+
+   return;
+}
+
+// callback for bam_plbuf_init()
+static int pileup_func(uint32_t tid, uint32_t position, int n, const bam_pileup1_t *pl, void *data)
+{
+  tmpstruct_t *tmp = (tmpstruct_t*)data;
+  int pos          = (int)position;
+  int coverage     = n;
+  int i;
+  for (i=0;i<n;i++)
+    if (pl[i].is_del) coverage--;
+
+  if (tmp->ltid != tid || tmp->lcoverage != coverage || pos > tmp->lpos+1) {
+    if (tmp->lpos > 0 && tmp->lcoverage > 0)
+      fprintf(tmp->out,"%s\t%d\t%d\t%d\n", tmp->head->target_name[tmp->ltid], tmp->lstart,tmp->lpos+1, tmp->lcoverage);
+    tmp->ltid       = tid;
+    tmp->lstart     = pos;
+    tmp->lcoverage  = coverage;
+  }
+  tmp->lpos = pos;
+  return 0;
+}
+
+int main(int argc, char *argv[]){
+	options(argc, argv);
+  tmpstruct_t tmp;
+  bam_plp_t buf = NULL;
+	bam1_t *b = NULL;
+  hts_itr_t *iter = NULL;
+  tmp.beg = 0; tmp.end = 0x7fffffff;
+	tmp.lstart    = 0;
+	tmp.lcoverage = 0;
+	tmp.ltid      = 0;
+	tmp.lpos      = 0;
+
+	if (strcmp(output_file,"-")==0) {
+    tmp.out = stdout;
+  } else {
+    tmp.out = fopen(output_file,"w");
+  }
+	if(tmp.out == NULL){
+	  fprintf(stderr,"Failed to open output file for %s writing.",output_file);
+	  return 1;
+	}
+  tmp.in = hts_open(input_file, "r");
+  if (tmp.in == 0) {
+		fprintf(stderr, "Fail to open [CR|B]AM file %s\n", input_file);
+		return 1;
+	}
+  tmp.head = sam_hdr_read(tmp.in);
+  buf = bam_plp_init(0,0);
+  //Iterate through each read in bam file.
+  b = bam_init1();
+	if(region == NULL){
+	  tmp.idx=NULL;
+    int reto;
+    while((reto = sam_read1(tmp.in, tmp.head, b)) >= 0){
+      if((b->core.flag & filter)>0) continue; //Skip if this is a filtered read
+      int ret, n_plp, tid, pos;
+      const bam_pileup1_t *plp;
+      ret = bam_plp_push(buf, b);
+      if (ret < 0) break;
+      while ((plp = bam_plp_next(buf, &tid, &pos, &n_plp)) != 0)
+          pileup_func(tid, pos, n_plp, plp, &tmp);
+    }
+    bam_plp_push(buf,0);
+	}else{
+
+	  tmp.idx = sam_index_load(tmp.in,input_file);
+    if (tmp.idx == 0) {
+		  fprintf(stderr, "Fail to open [CR|B]AM index for file %s\n", input_file);
+		  return 1;
+	  }
+    iter = sam_itr_querys(tmp.idx, tmp.head, region);
+    int result;
+    while ((result = sam_itr_next(tmp.in, iter, b)) >= 0) {
+      if((b->core.flag & filter)>0) continue; //Skip if this is a filtered read
+      int ret, n_plp, tid, pos;
+      const bam_pileup1_t *plp;
+      ret = bam_plp_push(buf, b);
+      if (ret < 0) break;
+      while ((plp = bam_plp_next(buf, &tid, &pos, &n_plp)) != 0){
+          pileup_func(tid, pos, n_plp, plp, &tmp);
+      }
+    }
+    bam_plp_push(buf,0);
+	}
+
+  //Check we've written everything...
+	int ret, n_plp, tid, pos;
+  const bam_pileup1_t *plp;
+  while ((plp = bam_plp_next(buf, &tid, &pos, &n_plp)) != 0){
+    pileup_func(tid, pos, n_plp, plp, &tmp);
+  }
+
+  fprintf(tmp.out,"%s\t%d\t%d\t%d\n", tmp.head->target_name[tmp.ltid], tmp.lstart,tmp.lpos+1, tmp.lcoverage);
+  bam_plp_destroy(buf);
+  bam_destroy1(b);
+  fflush(tmp.out);
+  fclose(tmp.out);
+  if(iter) sam_itr_destroy(iter);
+  if(tmp.idx) hts_idx_destroy(tmp.idx);
+	if(tmp.in) hts_close(tmp.in);
+	if(tmp.head) bam_hdr_destroy(tmp.head);
+	return 0;
+}
+
diff --git a/dists/patch/Bio-BigFile_build.patch b/dists/patch/Bio-BigFile_build.patch
new file mode 100644
index 0000000..2acbfaf
--- /dev/null
+++ b/dists/patch/Bio-BigFile_build.patch
@@ -0,0 +1,11 @@
+--- Build.PL	2016-08-03 16:36:03.408448000 +0100
++++ Build.PL.new	2016-08-03 16:38:09.324215000 +0100
+@@ -16,7 +16,7 @@
+     dist_abstract      => "Manipulate Jim Kent's BigWig and BigBed index files for genomic features.",
+     license            => 'perl',
+     include_dirs       => [$jk_include],
+-    extra_linker_flags => ["$jk_lib/$LibFile",'-lz','-lssl'],
++    extra_linker_flags => ["$jk_lib/$LibFile",'-lz','-lssl','-pthread'],
+
+     extra_compiler_flags=>[
+ 	# turn off warnings originating in Perl's Newx* calls
diff --git a/docs.tar.gz b/docs.tar.gz
index ee1db10..aff935a 100644
Binary files a/docs.tar.gz and b/docs.tar.gz differ
diff --git a/lib/PCAP.pm b/lib/PCAP.pm
index 5c022da..4c51aa7 100644
--- a/lib/PCAP.pm
+++ b/lib/PCAP.pm
@@ -26,7 +26,7 @@ use base 'Exporter';
 use FindBin qw($Bin);
 use File::Which qw(which);
 
-our $VERSION = '3.0.1';
+our $VERSION = '3.1.0';
 our @EXPORT = qw($VERSION _which);
 
 const my $LICENSE =>
@@ -82,6 +82,7 @@ const my %UPGRADE_PATH => ( # all earlier versions need full upgrade
                             '2.4.0' => 'biobambam',
                             '2.5.0' => 'biobambam',
                             '3.0.0' => '',
+                            '3.1.0' => '',
                           );
 
 sub license {
diff --git a/lib/PCAP/Bam.pm b/lib/PCAP/Bam.pm
index 2aa8a8c..d6bfa7d 100644
--- a/lib/PCAP/Bam.pm
+++ b/lib/PCAP/Bam.pm
@@ -36,8 +36,11 @@ use Data::UUID;
 use PCAP::Threaded;
 
 const my $BAMCOLLATE => q{(%s colsbs=268435456 collate=1 reset=1 exclude=SECONDARY,QCFAIL,SUPPLEMENTARY classes=F,F2 T=%s filename=%s level=1 > %s)};
-const my $BAMBAM_DUP => q{ index=1 md5=1 tmpfile=%s O=%s M=%s markthreads=%s };
-const my $BAMBAM_MERGE => q{ tmpfile=%s md5filename=%s.md5 indexfilename=%s.bai index=1 md5=1 > %s};
+const my $BAMBAM_DUP => q{ %s index=1 md5=1 tmpfile=%s O=%s M=%s markthreads=%s };
+const my $BAMBAM_MERGE => q{ %s tmpfile=%s md5filename=%s.md5 indexfilename=%s.bai index=1 md5=1 > %s};
+const my $BAMBAM_DUP_CRAM => q{ %s tmpfile=%s M=%s markthreads=%s level=0| scramble -r %s -I bam -O cram %s | tee %s | samtools index - %s.crai};
+const my $BAMBAM_MERGE_CRAM => q{ %s tmpfile=%s level=0 | scramble -r %s -I bam -O cram %s | tee %s | samtools index - %s.crai};
+const my $CRAM_CHKSUM => q{md5sum %s | perl -ne '/^(\S+)/; print "$1";' > %s.md5};
 const my $BAM_STATS => q{ -i %s -o %s};
 
 sub new {
@@ -96,45 +99,92 @@ sub merge_and_mark_dup {
   my ($options, $source) = @_;
   my $tmp = $options->{'tmp'};
   my $marked = File::Spec->catdir($options->{'outdir'}, $options->{'sample'});
-  $marked .= '.bam';
-  return $marked if PCAP::Threaded::success_exists(File::Spec->catdir($tmp, 'progress'), 0);
-  my $helper_threads = $options->{'threads'}-1;
-  # uncoverable branch true
-  # uncoverable branch false
-  $helper_threads = 1 if($helper_threads < 1);
-  # uncoverable branch true
-  # uncoverable branch false
-  my $command;
-  if(defined $options->{'nomarkdup'} && $options->{'nomarkdup'} == 1) {
-    $command = _which('bammerge') || die "Unable to find 'bammarkduplicates' in path";
-    $command .= sprintf $BAMBAM_MERGE,  File::Spec->catfile($tmp, 'biormdup'),
-                                        $marked,
-                                        $marked,
-                                        $marked;
+
+  my @commands;
+
+  if($options->{'cram'}) {
+    $marked .= '.cram';
   }
   else {
-    my $met = "$marked.met";
-    $command = _which('bammarkduplicates2') || die "Unable to find 'bammarkduplicates' in path";
-    $command .= sprintf $BAMBAM_DUP,  File::Spec->catfile($tmp, 'biormdup'),
-                                      $marked,
-                                      $met,
-                                      $helper_threads;
+    $marked .= '.bam';
   }
 
+  return $marked if PCAP::Threaded::success_exists(File::Spec->catdir($tmp, 'progress'), 0);
+  my $helper_threads = $options->{'threads'}-1;
+
+  $helper_threads = 1 if($helper_threads < 1);
+
+  my $input_str = q{};
   if(defined $source) {
     opendir(my $dh, $source);
     while(my $file = readdir $dh) {
       next unless($file =~ m/_sorted\.bam$/);
-      $command .= ' I='.File::Spec->catfile($source, $file);
+      $input_str .= ' I='.File::Spec->catfile($source, $file);
     }
     closedir $dh;
   }
   else {
     for(@{$options->{'meta_set'}}) {
-      $command .= ' I='.$_->tstub.'_sorted.bam';
+      $input_str .= ' I='.$_->tstub.'_sorted.bam';
     }
   }
-  PCAP::Threaded::external_process_handler(File::Spec->catdir($tmp, 'logs'), $command, 0);
+
+  my $bbb_tmp = File::Spec->catfile($tmp, 'biormdup');
+
+  if(defined $options->{'nomarkdup'} && $options->{'nomarkdup'} == 1) {
+    $commands[0] = _which('bammerge') || die "Unable to find 'bammerge' in path";
+
+    if($options->{'cram'}) {
+      my $add_sc = $options->{'scramble'} || q{};
+      $commands[0] .= sprintf $BAMBAM_MERGE_CRAM,
+                              $input_str,
+                              $bbb_tmp,
+                              $options->{'reference'},
+                              $add_sc,
+                              $marked,
+                              $marked;
+    }
+    else {
+      $commands[0] .= sprintf $BAMBAM_MERGE,
+                              $input_str,
+                              $bbb_tmp,
+                              $marked,
+                              $marked,
+                              $marked;
+    }
+  }
+  else {
+    my $met = "$marked.met";
+    $commands[0] = _which('bammarkduplicates2') || die "Unable to find 'bammarkduplicates' in path";
+    if($options->{'cram'}) {
+      my $add_sc = $options->{'scramble'} || q{};
+      $commands[0] .= sprintf $BAMBAM_DUP_CRAM,
+                              $input_str,
+                              $bbb_tmp,
+                              $met,
+                              $helper_threads,
+                              $options->{'reference'},
+                              $add_sc,
+                              $marked,
+                              $marked;
+    }
+    else {
+      $commands[0] .= sprintf $BAMBAM_DUP,
+                              $input_str,
+                              $bbb_tmp,
+                              $marked,
+                              $met,
+                              $helper_threads;
+    }
+  }
+
+  if($options->{'cram'}) {
+    unshift @commands, 'set -o pipefail';
+    push @commands, sprintf $CRAM_CHKSUM, $marked, $marked;
+    push @commands, 'set +o pipefail';
+  }
+
+  PCAP::Threaded::external_process_handler(File::Spec->catdir($tmp, 'logs'), \@commands, 0);
   PCAP::Threaded::touch_success(File::Spec->catdir($tmp, 'progress'), 0);
   return $marked;
 }
@@ -143,11 +193,13 @@ sub bam_stats {
   # uncoverable subroutine
   my $options = shift;
   my $tmp = $options->{'tmp'};
-  my $bam = File::Spec->catdir($options->{'outdir'}, $options->{'sample'}).'.bam';;
-  my $bas = "$bam.bas";
+  my $ext = '.bam';
+  $ext = '.cram' if($options->{'cram'});
+  my $xam = File::Spec->catdir($options->{'outdir'}, $options->{'sample'}).$ext;
+  my $bas = "$xam.bas";
   return $bas if PCAP::Threaded::success_exists(File::Spec->catdir($tmp, 'progress'), 0);
   my $command = _which('bam_stats') || die "Unable to find 'bam_stats' in path";
-  $command .= sprintf $BAM_STATS, $bam, $bas;
+  $command .= sprintf $BAM_STATS, $xam, $bas;
   PCAP::Threaded::external_process_handler(File::Spec->catdir($tmp, 'logs'), $command, 0);
   PCAP::Threaded::touch_success(File::Spec->catdir($tmp, 'progress'), 0);
   return $bas;
diff --git a/lib/PCAP/BigWig.pm b/lib/PCAP/BigWig.pm
index 9f11f1d..b2ac2d7 100644
--- a/lib/PCAP/BigWig.pm
+++ b/lib/PCAP/BigWig.pm
@@ -38,6 +38,9 @@ sub bamToBw {
   return if(exists $options->{'index'} && $index != $options->{'index'});
   return if PCAP::Threaded::success_exists(File::Spec->catdir($tmp, 'progress'), $index);
 
+  my $filter = 3844; # see https://broadinstitute.github.io/picard/explain-flags.html
+  $filter = $options->{'filter'} if(exists $options->{'filter'});
+
   my @seqs = @{$options->{'sequences'}};
   my $iter = 1;
   for my $seq(@seqs) {
@@ -46,11 +49,10 @@ sub bamToBw {
     my $outfile = q{'}.File::Spec->catfile($options->{'tmp'}, $seq.'.bw').q{'};
 
     my $command = q{bash -c "set pipefail; };
-    $command .= _which('samtools');
-    $command .= q{ view -T }.$options->{'reference'};
-    $command .= q{ -F 3844}; # don't include data that set these flags
-    $command .= q{ -ub }.$options->{'bam'}.q{ '}.$seq.q{'};
-    $command .= ' | '._which('bam2bedgraph').' - ';
+    $command .= _which('bam2bedgraph');
+    $command .= q{ -f }.$filter;
+    $command .= q{ -r }.$seq;
+    $command .= q{ -i }.$options->{'bam'};
     $command .= ' | ';
     $command .= _which('wigToBigWig');
     $command .= ' -fixedSummaries -keepAllChromosomes stdin '.$options->{'reference'}.'.fai '.$outfile;
diff --git a/lib/PCAP/Bwa.pm b/lib/PCAP/Bwa.pm
index 08d62de..27c9d9a 100644
--- a/lib/PCAP/Bwa.pm
+++ b/lib/PCAP/Bwa.pm
@@ -247,12 +247,12 @@ sub bwa_mem {
     # uncoverable branch true
     # uncoverable branch false
     $interleaved_fq = q{ -p}, unless($input->paired_fq);
-    if(exists $options->{'bwa'}) {
-      $bwa .= sprintf $BWA_MEM, $options->{'bwa'}, $interleaved_fq, $rg_line, $threads, $options->{'reference'};
-    }
-    else {
-      $bwa .= sprintf $BWA_MEM, '-T 0', $interleaved_fq, $rg_line, $threads, $options->{'reference'};
-    }
+
+    my $add_options = q{};
+    $add_options = $options->{'bwa'} if(exists $options->{'bwa'});
+
+    $bwa .= sprintf $BWA_MEM, $add_options, $interleaved_fq, $rg_line, $threads, $options->{'reference'};
+
     # uncoverable branch true
     # uncoverable branch false
     if($input->paired_fq) {
diff --git a/lib/PCAP/Threaded.pm b/lib/PCAP/Threaded.pm
index ae60996..6d0470a 100644
--- a/lib/PCAP/Threaded.pm
+++ b/lib/PCAP/Threaded.pm
@@ -27,17 +27,16 @@ use autodie qw(:all);
 use English qw( -no_match_vars );
 use warnings FATAL => 'all';
 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 finally);
 use Capture::Tiny qw(capture);
 use IO::File;
 use Const::Fast qw(const);
+use Scalar::Util qw(looks_like_number);
 
-BEGIN {
-  if($Config{useithreads}) { use threads; }
-};
+our $CAN_USE_THREADS = 0;
+$CAN_USE_THREADS = eval 'use threads; 1';
 
 const my $SCRIPT_OCT_MODE => 0777;
 
@@ -45,15 +44,16 @@ our $OUT_ERR = 1;
 
 sub new {
   my ($class, $max_threads) = @_;
-  unless($Config{useithreads}) {
-    warn "Threading is not available perl component will run as a single process";
-    $max_threads = 1;
-  }
+  croak "Number of threads was NAN: $max_threads" if(defined $max_threads && !looks_like_number($max_threads));
   unless(defined $max_threads) {
     warn "Thread count not defined, defaulting to 1.\n";
     $max_threads = 1;
   }
-  croak "Number of threads was NAN: $max_threads" if($max_threads !~ m/^[[:digit:]]+$/xms);
+  if($max_threads > 1 && $CAN_USE_THREADS == 0) {
+    warn "Threading is not available perl component will run as a single process";
+    $max_threads = 1;
+  }
+
   my $self = {'threads' => $max_threads,
               'join_interval' => 1,};
   bless $self, $class;
@@ -109,24 +109,24 @@ sub run {
   my $thread_count = $self->{'functions'}->{$function_name}->{'threads'};
 
   # uncoverable branch true
-  if($thread_count > 1 && $Config{useithreads}) {
+  if($thread_count > 1 && $CAN_USE_THREADS) {
     # reserve 0 for when people want to use 'success_exists/touch_success' for non-threaded steps
     # makes it easy to see in progress area which steps are threaded
     my $index = 1;
     while($index <= $iterations) {
-      while(threads->list(threads::all) < $thread_count && $index <= $iterations) {
+      while(threads->list(threads::all()) < $thread_count && $index <= $iterations) {
         threads->create($function_ref, $index++, @params);
         last if($index > $iterations);
       }
-      sleep $self->thread_join_interval while(threads->list(threads::joinable) == 0);
-      for my $thr(threads->list(threads::joinable)) {
+      sleep $self->thread_join_interval while(threads->list(threads::joinable()) == 0);
+      for my $thr(threads->list(threads::joinable())) {
         $thr->join;
         if(my $err = $thr->error) { die "Thread error: $err\n"; }
       }
     }
     # last gasp for any remaining threads
-    sleep $self->thread_join_interval while(threads->list(threads::running) > 0);
-    for my $thr(threads->list(threads::joinable)) {
+    sleep $self->thread_join_interval while(threads->list(threads::running()) > 0);
+    for my $thr(threads->list(threads::joinable())) {
       $thr->join;
       if(my $err = $thr->error) { die "Thread error: $err\n"; }
     }
diff --git a/prerelease.sh b/prerelease.sh
index f8c817a..73d5aba 100755
--- a/prerelease.sh
+++ b/prerelease.sh
@@ -37,7 +37,7 @@ export HARNESS_PERL_SWITCHES=-MDevel::Cover=-db,reports,-select='^lib/*\.pm$',-i
 rm -rf reports docs pm_to_blib blib
 cover -delete
 mkdir -p docs/reports_text
-prove -w -I ./lib
+prove -w -j 9 -I ./lib
 
 echo -e '\n\n### Generating test/pod coverage reports ###\n'
 # removed 'condition' from coverage as '||' 'or' doesn't work properly
diff --git a/setup.sh b/setup.sh
index b04db40..481f630 100755
--- a/setup.sh
+++ b/setup.sh
@@ -1,21 +1,25 @@
 #!/bin/bash
 
-SOURCE_BWA="https://github.com/lh3/bwa/archive/0.7.12.tar.gz"
+SOURCE_BWA="https://github.com/lh3/bwa/archive/v0.7.15.tar.gz"
 
 SOURCE_SAMTOOLS="https://github.com/samtools/samtools/releases/download/1.3.1/samtools-1.3.1.tar.bz2"
 
-# for bamstats
-SOURCE_HTSLIB="https://github.com/samtools/htslib/archive/1.3.1.tar.gz"
+# for bamstats and Bio::DB::HTS
+SOURCE_HTSLIB="https://github.com/samtools/htslib/releases/download/1.3.1/htslib-1.3.1.tar.bz2"
+
+# Bio::DB::HTS
+SOURCE_BIOBDHTS="https://github.com/Ensembl/Bio-HTS/archive/2.3.tar.gz"
 
 # for bigwig
 SOURCE_JKENT_BIN="https://github.com/ENCODE-DCC/kentUtils/raw/master/bin/linux.x86_64"
 # for Bio::DB::BigWig
-SOURCE_KENTSRC="http://hgdownload.cse.ucsc.edu/admin/jksrc.zip"
+SOURCE_KENTSRC="ftp://ftp.sanger.ac.uk/pub/cancer/legacy-dependancies/jksrc.v334.zip"
+SOURCE_BIGFILE="http://www.cpan.org/authors/id/L/LD/LDS/Bio-BigFile-1.07.tar.gz"
 # for fast merging of per-chr BW files
-SOURCE_LIB_BW="https://github.com/dpryan79/libBigWig/archive/0.1.6.tar.gz"
+SOURCE_LIB_BW="https://github.com/dpryan79/libBigWig/archive/b36da5a06bffcc1b33c369e078b82f84625fd212.tar.gz"
 
 # for biobambam
-SOURCE_BBB_BIN_DIST="https://github.com/gt1/biobambam2/releases/download/2.0.50-release-20160705161609/biobambam2-2.0.50-release-20160705161609-x86_64-etch-linux-gnu.tar.gz"
+SOURCE_BBB_BIN_DIST="https://github.com/gt1/biobambam2/releases/download/2.0.54-release-20160802163650/biobambam2-2.0.54-release-20160802163650-x86_64-etch-linux-gnu.tar.gz"
 
 BIODBHTS_INSTALL="https://raw.githubusercontent.com/Ensembl/Bio-HTS/master/INSTALL.pl"
 
@@ -31,10 +35,11 @@ get_distro () {
     echo "I don't understand the file type for $1"
     exit 1
   fi
+  rm -f $1.$EXT
   if hash curl 2>/dev/null; then
-    curl -sS -o $1.$EXT -L $2
+    curl --retry 10 -sS -o $1.$EXT -L $2
   else
-    wget -nv -O $1.$EXT $2
+    wget --tries=10 -nv -O $1.$EXT $2
   fi
 }
 
@@ -98,10 +103,16 @@ if ! ( perl -MExtUtils::MakeMaker -e 1 >/dev/null 2>&1); then
     echo "WARNING: Your Perl installation does not seem to include a complete set of core modules.  Attempting to cope with this, but if installation fails please make sure that at least ExtUtils::MakeMaker is installed.  For most users, the best way to do this is to use your system's package manager: apt, yum, fink, homebrew, or similar."
 fi
 
-perlmods=( "File::ShareDir" "File::ShareDir::Install" "Const::Fast" "File::Which" )
-for i in "${perlmods[@]}" ; do
-  $CPANM --mirror http://cpan.metacpan.org -l $INST_PATH $i
-done
+if [ -e $SETUP_DIR/basePerlDeps.success ]; then
+  echo "Previously installed base perl deps..."
+else
+  perlmods=( "ExtUtils::CBuilder" "Module::Build~0.42" "File::ShareDir" "File::ShareDir::Install" "Const::Fast" "File::Which" "LWP::UserAgent" "Bio::Root::Version~1.006009001")
+  for i in "${perlmods[@]}" ; do
+    $CPANM -v --no-interactive --notest --mirror http://cpan.metacpan.org -l $INST_PATH $i
+  done
+  touch $SETUP_DIR/basePerlDeps.success
+fi
+
 
 # figure out the upgrade path
 COMPILE=`echo 'nothing' | perl -I lib -MPCAP -ne 'print PCAP::upgrade_path($_);'`
@@ -110,16 +121,51 @@ if [ -e "$INST_PATH/lib/perl5/PCAP.pm" ]; then
 fi
 COMPILE=",$COMPILE,"
 
-#Need to add CaVEMan stuff here... will depend on samtools too (for now).
+echo -n "Get htslib ..."
+if [ -e $SETUP_DIR/htslibGet.success ]; then
+  echo " already staged ...";
+else
+  echo
+  cd $SETUP_DIR
+  get_distro "htslib" $SOURCE_HTSLIB
+  touch $SETUP_DIR/htslibGet.success
+fi
+
+echo -n "Building Bio::DB::HTS ..."
+if [ -e $SETUP_DIR/biohts.success ]; then
+  echo " previously installed ...";
+else
+  echo
+  cd $SETUP_DIR
+  rm -rf bioDbHts
+  get_distro "bioDbHts" $SOURCE_BIOBDHTS
+  mkdir -p bioDbHts/htslib
+  tar --strip-components 1 -C bioDbHts -zxf bioDbHts.tar.gz
+  tar --strip-components 1 -C bioDbHts/htslib -jxf $SETUP_DIR/htslib.tar.bz2
+  cd bioDbHts/htslib
+  perl -pi -e 'if($_ =~ m/^CFLAGS/ && $_ !~ m/\-fPIC/i){chomp; s/#.+//; $_ .= " -fPIC -Wno-unused -Wno-unused-result\n"};' Makefile
+  make -j$CPU
+  rm -f libhts.so*
+  cd ../
+  env HTSLIB_DIR=$SETUP_DIR/bioDbHts/htslib perl Build.PL --install_base=$INST_PATH
+  ./Build test
+  ./Build install
+  cd $SETUP_DIR
+  rm -f bioDbHts.tar.gz
+  touch $SETUP_DIR/biohts.success
+fi
+
 
 echo -n "Building jkentUtils ..."
 if [ -e $SETUP_DIR/jkentUtils.success ]; then
-  echo -n " previously installed ...";
+  echo " previously installed ...";
 else
+  echo
   cd $SETUP_DIR
   if [[ `uname -m` == x86_64 ]] ; then
     get_file $INST_PATH/bin/wigToBigWig $SOURCE_JKENT_BIN/wigToBigWig
     chmod +x $INST_PATH/bin/wigToBigWig
+    touch $SETUP_DIR/jkentUtils.success
   else
     if [ ! -e $INST_DIR/bin/wigToBigWig ]; then
       echo "Binaries only available for x86_64, please install wigToBigWig from kentUtils: https://github.com/ENCODE-DCC/kentUtils"
@@ -127,68 +173,79 @@ else
     fi
   fi
 fi
-echo
 
 echo -n "Building htslib ..."
 if [ -e $SETUP_DIR/htslib.success ]; then
-  echo -n " previously installed ...";
+  echo " previously installed ...";
 else
-  cd $SETUP_DIR
-  get_distro "htslib" $SOURCE_HTSLIB
+  echo
   mkdir -p htslib
-  tar --strip-components 1 -C htslib -zxf htslib.tar.gz
-  make -C htslib -j$CPU
+  tar --strip-components 1 -C htslib -jxf htslib.tar.bz2
+  cd htslib
+  ./configure --enable-plugins --enable-libcurl --prefix=$INST_PATH
+  make -j$CPU
+  make install
+  cd $SETUP_DIR
   touch $SETUP_DIR/htslib.success
 fi
-echo
+
+export HTSLIB=$INST_PATH
+
+cd $INIT_DIR
+
+if [[ ",$COMPILE," == *,samtools,* ]] ; then
+  echo -n "Building samtools ..."
+  if [ -e $SETUP_DIR/samtools.success ]; then
+    echo " previously installed ...";
+  else
+  echo
+    cd $SETUP_DIR
+    rm -rf samtools
+    get_distro "samtools" $SOURCE_SAMTOOLS
+    mkdir -p samtools
+    tar --strip-components 1 -C samtools -xjf samtools.tar.bz2
+    cd samtools
+    ./configure --enable-plugins --enable-libcurl --prefix=$INST_PATH
+    make -j$CPU all all-htslib
+    make install all all-htslib
+    cd $SETUP_DIR
+    rm -f samtools.tar.bz2
+    touch $SETUP_DIR/samtools.success
+  fi
+else
+  echo "samtools - No change between PCAP versions"
+fi
 
 echo -n "Building libBigWig ..."
 if [ -e $SETUP_DIR/libBigWig.success ]; then
-  echo -n " previously installed ...";
+  echo " previously installed ...";
 else
+  echo
   cd $SETUP_DIR
   get_distro "libBigWig" $SOURCE_LIB_BW
   mkdir -p libBigWig
   tar --strip-components 1 -C libBigWig -zxf libBigWig.tar.gz
   make -C libBigWig -j$CPU install prefix=$INST_PATH
   rm -f $INST_PATH/lib/libBigWig.so
+  rm -f libBigWig.tar.gz
   touch $SETUP_DIR/libBigWig.success
 fi
-echo
-
-export HTSLIB="$SETUP_DIR/htslib"
-
-echo -n "Building bam_stats ..."
-if [ -e $SETUP_DIR/bam_stats.success ]; then
-  echo -n " previously installed ...";
-else
-  cd $INIT_DIR
-  make -C c clean
-  make -C c -j$CPU prefix=$INST_PATH
-  cp bin/bam_stats $INST_PATH/bin/.
-  cp bin/bwcat $INST_PATH/bin/.
-  cp bin/reheadSQ $INST_PATH/bin/.
-  touch $SETUP_DIR/bam_stats.success
-  # need to clean up as will clash with other version
-  rm -rf $SAMTOOLS
-  make -C c clean
-fi
-echo
 
 cd $SETUP_DIR
 if [[ ",$COMPILE," == *,bwa,* ]] ; then
   echo -n "Building BWA ..."
   if [ -e $SETUP_DIR/bwa.success ]; then
-    echo -n " previously installed ..."
+    echo " previously installed ..."
   else
-      get_distro "bwa" $SOURCE_BWA
-      mkdir -p bwa
-      tar --strip-components 1 -C bwa -zxf bwa.tar.gz
-      make -C bwa -j$CPU
-      cp bwa/bwa $INST_PATH/bin/.
-      touch $SETUP_DIR/bwa.success
+    echo
+    get_distro "bwa" $SOURCE_BWA
+    mkdir -p bwa
+    tar --strip-components 1 -C bwa -zxf bwa.tar.gz
+    make -C bwa -j$CPU
+    cp bwa/bwa $INST_PATH/bin/.
+    rm -f bwa.tar.gz
+    touch $SETUP_DIR/bwa.success
   fi
-  echo
 else
   echo "BWA - No change between PCAP versions"
 fi
@@ -198,6 +255,7 @@ if [[ ",$COMPILE," == *,biobambam,* ]] ; then
   if [ -e $SETUP_DIR/biobambam2.success ]; then
     echo " previously installed2 ..."
   else
+  echo
     cd $SETUP_DIR
     get_distro "biobambam2" $SOURCE_BBB_BIN_DIST
     mkdir -p biobambam2
@@ -208,8 +266,8 @@ if [[ ",$COMPILE," == *,biobambam,* ]] ; then
     cp -r biobambam2/etc/* $INST_PATH/etc/.
     cp -r biobambam2/lib/* $INST_PATH/lib/.
     cp -r biobambam2/share/* $INST_PATH/share/.
+    rm -f biobambam2.tar.gz
     touch $SETUP_DIR/biobambam2.success
-    echo
   fi
 else
   echo "biobambam - No change between PCAP versions"
@@ -217,79 +275,73 @@ fi
 
 cd $INIT_DIR
 
-if [[ ",$COMPILE," == *,samtools,* ]] ; then
-  echo -n "Building samtools ..."
-  if [ -e $SETUP_DIR/samtools.success ]; then
-    echo -n " previously installed ...";
-  else
-    cd $SETUP_DIR
-    get_distro "samtools" $SOURCE_SAMTOOLS
-    mkdir -p samtools
-    tar --strip-components 1 -C samtools -xjf samtools.tar.bz2
-    cd samtools
-    ./configure --enable-plugins --enable-libcurl --prefix=$INST_PATH
-    make all all-htslib
-    make install install-htslib
-    touch $SETUP_DIR/samtools.success
-  fi
-  echo
-else
-  echo "samtools - No change between PCAP versions"
-fi
-
-cd $INIT_DIR
-
-if [[ ",$COMPILE," == *,samtools,* ]] ; then
-  echo -n "Building Bio::DB::HTS ..."
-  if [ -e $SETUP_DIR/biohts.success ]; then
-    echo " previously installed ...";
-  else
-    cd $SETUP_DIR
-    $CPANM --mirror http://cpan.metacpan.org --notest -l $INST_PATH Module::Build Bio::Root::Version
-    # now Bio::DB::HTS
-    get_file "INSTALL.pl" $BIODBHTS_INSTALL
-    perl -I $PERL5LIB INSTALL.pl --prefix $INST_PATH --static
-    rm -f INSTALL.pl
-    touch $SETUP_DIR/biohts.success
-  fi
-  echo
-else
-  echo "Bio::DB::HTS - No change between PCAP versions" # based on samtools tag
-fi
-
 echo -n "Building kentsrc + Bio::DB::BigFile ..."
 if [ -e $SETUP_DIR/kentsrc.success ]; then
   echo " previously installed ...";
 else
+  echo
   cd $SETUP_DIR
+  rm -rf kent kentsrc.zip
   get_distro "kentsrc" $SOURCE_KENTSRC
   unzip -q kentsrc.zip
   perl -pi -e 's/(\s+CFLAGS=)$/${1}-fPIC/' kent/src/inc/common.mk
   cd kent/src/lib
   export MACHTYPE=i686    # for a 64-bit system
-  make
+  make -j$CPU
   cd ../
   export KENT_SRC=`pwd`
   cd $SETUP_DIR
-  $CPANM --mirror http://cpan.metacpan.org -l $INST_PATH Bio::DB::BigFile
+  mkdir -p bigfile
+  get_distro "bigfile" $SOURCE_BIGFILE
+  tar --strip-components 1 -C bigfile -zxf bigfile.tar.gz
+  cd bigfile
+  chmod u+w Build.PL
+  patch -p1 Build.PL < $INIT_DIR/dists/patch/Bio-BigFile_build.patch
+  perl Build.PL --install_base=$INST_PATH
+  ./Build
+  ./Build test
+  ./Build install
+  rm -f kentsrc.zip
+  touch $SETUP_DIR/kentsrc.success
 fi
 
 cd $INIT_DIR
 
-echo -n "Installing Perl prerequisites ..."
-$CPANM --mirror http://cpan.metacpan.org --notest -l $INST_PATH --installdeps .
-echo
+echo -n "Building PCAP-c ..."
+if [ -e $SETUP_DIR/bam_stats.success ]; then
+  echo " previously installed ...";
+else
+  echo
+  cd $INIT_DIR
+  make -C c clean
+  env HTSLIB=$SETUP_DIR/htslib make -C c -j$CPU prefix=$INST_PATH
+  cp bin/bam_stats $INST_PATH/bin/.
+  cp bin/bwcat $INST_PATH/bin/.
+  cp bin/reheadSQ $INST_PATH/bin/.
+  cp bin/bam2bedgraph $INST_PATH/bin/.
+  touch $SETUP_DIR/bam_stats.success
+  make -C c clean
+fi
+
+cd $INIT_DIR
+
+echo -n "Building PCAP_perlPrereq ..."
+if [ -e $SETUP_DIR/PCAP_perlPrereq.success ]; then
+  echo "PCAP_perlPrereq previously installed ...";
+else
+  echo
+  $CPANM -v --no-interactive --mirror http://cpan.metacpan.org --notest -l $INST_PATH --installdeps .
+  touch $SETUP_DIR/PCAP_perlPrereq.success
+fi
 
 echo -n "Installing PCAP ..."
-$CPANM --mirror http://cpan.metacpan.org -l $INST_PATH .
+$CPANM -v --no-interactive --mirror http://cpan.metacpan.org -l $INST_PATH .
 echo
 
 # cleanup all junk
 rm -rf $SETUP_DIR
 rm -rf $INIT_DIR/bin/biobambam
 
-
-
 echo
 echo
 echo "Please add the following to beginning of path:"