diff --git a/.dockerignore b/.dockerignore
index 0db1033..6236564 100644
--- a/.dockerignore
+++ b/.dockerignore
@@ -9,3 +9,4 @@
 /docs.tar.gz
 /setup.sh
 /prerelease.sh
+/blib
diff --git a/.gitignore b/.gitignore
index da0f63c..2a7d497 100644
--- a/.gitignore
+++ b/.gitignore
@@ -15,6 +15,8 @@ examples/cgp_gnos_pull.ini
 /c/c_tests/tests_log
 /bin/diff_bams
 /bin/reheadSQ
+/bin/mismatchQc
+/bin/mmFlagModifier
 /c/c_tests/01_bam_stats_output_tests
 /c/c_tests/02_bam_access_tests
 /c/c_tests/03_bam_stats_calcs_tests
diff --git a/CHANGES.md b/CHANGES.md
index 1217470..5b61995 100644
--- a/CHANGES.md
+++ b/CHANGES.md
@@ -1,5 +1,14 @@
 # CHANGES
 
+## 5.1.0
+
+* Base image updated to Focal (Ubuntu 20.04).
+* Majority of biobambam2 replaced with samtools functions.
+* Reads undergo full collate when mapping from BAM/CRAM (bwa-mem2 prep).
+* Duplicate marking `samtools markdup --mode` options exposed to `bwa_mem.pl`.
+  * Lanes mapped with earlier versions of PCAP-core cannot be merged without reporocessing to add "mate score tag" via `samtools fixmate`.
+* Scramble option for `bwa_mem.pl` deprecated, relevant option for fast CRAM random access exposed.
+
 ## 5.0.5
 
 * Add `noindex` commandline flag to `merge_or_mark.pl` for bammerge calls. Only permitted alongisde `qnamesort`
diff --git a/Dockerfile b/Dockerfile
index 68e5e0d..c112cfa 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,38 +1,42 @@
-FROM quay.io/wtsicgp/cgpbigwig:1.1.0 as builder
+FROM quay.io/wtsicgp/cgpbigwig:1.3.0 as builder
 
 USER  root
 
-ARG BBB2_URL="https://gitlab.com/german.tischler/biobambam2/uploads/178774a8ece96d2201fcd0b5249884c7/biobambam2-2.0.146-release-20191030105216-x86_64-linux-gnu.tar.xz"
+# ALL tool versions used by opt-build.sh
+# need to keep in sync with setup.sh
+
+# newer gitlab versions do not work
+ARG BBB2_URL="https://github.com/gt1/biobambam2/releases/download/2.0.87-release-20180301132713/biobambam2-2.0.87-release-20180301132713-x86_64-etch-linux-gnu.tar.gz"
 ARG BWAMEM2_URL="https://github.com/bwa-mem2/bwa-mem2/releases/download/v2.0pre2/bwa-mem2-2.0pre2_x64-linux.tar.bz2"
 ARG STADEN="https://iweb.dl.sourceforge.net/project/staden/staden/2.0.0b11/staden-2.0.0b11-2016-linux-x86_64.tar.gz"
 ARG VER_BIODBHTS="3.01"
 ARG VER_BWA="v0.7.17"
-ARG VER_HTSLIB="1.9"
-ARG VER_SAMTOOLS="1.9"
+ARG VER_HTSLIB="1.10.2"
+ARG VER_SAMTOOLS="1.10"
 
 RUN apt-get -yq update
-RUN apt-get install -yq --no-install-recommends\
-  apt-transport-https\
-  locales\
-  curl\
-  ca-certificates\
-  libperlio-gzip-perl\
-  make\
-  bzip2\
-  gcc\
-  psmisc\
-  time\
-  zlib1g-dev\
-  libbz2-dev\
-  liblzma-dev\
-  libcurl4-gnutls-dev\
-  libncurses5-dev\
-  nettle-dev\
-  libp11-kit-dev\
-  libtasn1-dev\
-  libgnutls-dev\
-  libgd-dev\
-  libdb-dev
+RUN apt-get install -yq --no-install-recommends apt-transport-https
+RUN apt-get install -yq --no-install-recommends locales
+RUN apt-get install -yq --no-install-recommends curl
+RUN apt-get install -yq --no-install-recommends ca-certificates
+RUN apt-get install -yq --no-install-recommends libperlio-gzip-perl
+RUN apt-get install -yq --no-install-recommends make
+RUN apt-get install -yq --no-install-recommends bzip2
+RUN apt-get install -yq --no-install-recommends gcc
+RUN apt-get install -yq --no-install-recommends psmisc
+RUN apt-get install -yq --no-install-recommends time
+RUN apt-get install -yq --no-install-recommends zlib1g-dev
+RUN apt-get install -yq --no-install-recommends libbz2-dev
+RUN apt-get install -yq --no-install-recommends liblzma-dev
+RUN apt-get install -yq --no-install-recommends libcurl4-gnutls-dev
+RUN apt-get install -yq --no-install-recommends libncurses5-dev
+RUN apt-get install -yq --no-install-recommends nettle-dev
+RUN apt-get install -yq --no-install-recommends libp11-kit-dev
+RUN apt-get install -yq --no-install-recommends libtasn1-dev
+RUN apt-get install -yq --no-install-recommends libdb-dev
+RUN apt-get install -yq --no-install-recommends libgnutls28-dev
+RUN apt-get install -yq --no-install-recommends xz-utils
+RUN apt-get install -yq --no-install-recommends libexpat1-dev
 
 RUN locale-gen en_US.UTF-8
 RUN update-locale LANG=en_US.UTF-8
@@ -54,11 +58,11 @@ RUN bash build/opt-build.sh $OPT
 COPY . .
 RUN bash build/opt-build-local.sh $OPT
 
-FROM  ubuntu:16.04
+FROM  ubuntu:20.04
 
 LABEL maintainer="cgphelp@sanger.ac.uk"\
       uk.ac.sanger.cgp="Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute" \
-      version="5.0.5" \
+      version="5.1.0" \
       description="pcap-core"
 
 ENV OPT /opt/wtsi-cgp
@@ -67,6 +71,7 @@ ENV PATH $OPT/bin:$PATH
 ENV PERL5LIB $OPT/lib/perl5
 ENV LD_LIBRARY_PATH $OPT/lib:$OPT/scramble/lib
 ENV LC_ALL C
+ENV GPERF_FOR_BWA /usr/lib/x86_64-linux-gnu/libtcmalloc_minimal.so.4
 
 RUN apt-get -yq update
 RUN apt-get install -yq --no-install-recommends \
@@ -82,8 +87,10 @@ zlib1g \
 liblzma5 \
 libncurses5 \
 p11-kit \
-libcurl3 \
+libcurl3-gnutls \
+libcurl4 \
 moreutils \
+google-perftools \
 unattended-upgrades && \
 unattended-upgrade -d -v && \
 apt-get remove -yq unattended-upgrades && \
diff --git a/README.md b/README.md
index 9f5b418..8773658 100644
--- a/README.md
+++ b/README.md
@@ -29,18 +29,12 @@ Available programs are described in the [wiki][wiki].
 
 ## Docker, Singularity and Dockstore
 
-There are docker and dockstore.org wrappers for this project at [dockstore-cgpmap][dockstore-cgpmap].
+There are dockstore.org CWL and wrappers for this project at [dockstore-cgpmap][dockstore-cgpmap].
 
-The docker image is held on [quay.io][quay-io-cgpmap].
-
-The CWL bindings of `dockstore-cgpmap` specifically target execution of the BWA mem mapping flow,
-however all tools are contained in the image and can be used if you construct the relevant docker
-commands.
+The docker image is held on [quay.io][quay-io-pcap-core].
 
 The docker image is know to work correctly after import into a singularity image.
 
-See the [dockstore-cgpmap][dockstore-cgpmap] documentation for more detail.
-
 ## Dependencies/Install
 
 Please be aware that this expects basic C compilation libraries and tools to be available, most are listed in `INSTALL`.
@@ -69,13 +63,10 @@ Please see the respective licence for each before use.
 ### Cutting the release
 
 1. Update `lib/PCAP.pm` to the correct version.
-2. Ensure upgrade path for new version number is added to `lib/PCAP.pm`.
+2. Update `Dockerfile` to the correct version.
 3. Update `CHANGES.md` to show major items.
-4. Run `./prerelease.sh`
-5. Check all tests and coverage reports are acceptable.
-6. Commit the updated docs tree and updated module/version.
-7. Push commits.
-8. Use the GitHub tools to draft a release.
+4. Push commits and verify with Sanger internal CI.
+5. Use the GitHub tools to draft a release.
 
 <!-- References -->
 
@@ -87,7 +78,7 @@ Please see the respective licence for each before use.
 [cancerit_github]: https://github.com/cancerit
 [old_repo]: https://github.com/ICGC-TCGA-PanCancer/PCAP-core
 [dockstore-cgpmap]: https://github.com/cancerit/dockstore-cgpmap
-[quay-io-cgpmap]: https://quay.io/repository/wtsicgp/dockstore-cgpmap
+[quay-io-pcap-core]: https://quay.io/repository/wtsicgp/pcap-core
 
 <!-- Travis -->
 [travis-base]: https://travis-ci.org/cancerit/PCAP-core
diff --git a/bin/bwa_mem.pl b/bin/bwa_mem.pl
index e80f8aa..6f7afe4 100755
--- a/bin/bwa_mem.pl
+++ b/bin/bwa_mem.pl
@@ -52,15 +52,14 @@
   my $options = setup();
 
  	my $threads = PCAP::Threaded->new($options->{'threads'});
-  &PCAP::Threaded::disable_out_err if(exists $options->{'index'});
 
   # register processes
-	$threads->add_function('split', \&PCAP::Bwa::split_in);
-	$threads->add_function('bwamem', \&PCAP::Bwa::bwa_mem, exists $options->{'index'} ? 1 : $options->{'map_threads'});
+  $threads->add_function('split', \&PCAP::Bwa::split_in, split_threads($options));
+  $threads->add_function('bwamem', \&PCAP::Bwa::bwa_mem, exists $options->{'index'} ? 1 : $options->{'map_threads'});
 
   PCAP::Bwa::mem_setup($options) if(!exists $options->{'process'} || $options->{'process'} eq 'setup');
 
-	$threads->run($options->{'max_split'}, 'split', $options) if(!exists $options->{'process'} || $options->{'process'} eq 'split');
+  $threads->run($options->{'max_split'}, 'split', $options) if(!exists $options->{'process'} || $options->{'process'} eq 'split');
 
   if(!exists $options->{'process'} || $options->{'process'} eq 'bwamem') {
     $options->{'max_index'} = PCAP::Bwa::mem_mapmax($options);
@@ -78,6 +77,24 @@
   }
 }
 
+sub split_threads {
+  my $options = shift;
+  my $div = 1;
+  my $threads_per_split = 1;
+  if(exists $options->{index}) {
+    $div = 1;
+    $threads_per_split = $options->{threads};
+  }
+  elsif($options->{raw_files}->[0] =~ m/(bam|cram)$/) {
+    my $inputs = scalar @{$options->{raw_files}};
+    $threads_per_split = int ($options->{threads} / $inputs);
+    $threads_per_split = 1 if($threads_per_split < 1);
+    $div = $threads_per_split;
+  }
+  $options->{threads_per_split} = $threads_per_split; # so can be used later
+  return $div; # so can be used as return
+}
+
 sub cleanup {
   my $options = shift;
   my $tmpdir = $options->{'tmp'};
@@ -91,6 +108,8 @@ sub setup {
               'mmqcfrac' => 0.05,
               'threads' => 1,
               'fragment' => 10,
+              'dupmode' => 't',
+              'seqslice' => 10000,
               'csi' => undef,
              );
 
@@ -116,6 +135,8 @@ sub setup {
               'q|mmqc' => \$opts{'mmqc'},
               'qf|mmqcfrac:f' => \$opts{'mmqcfrac'},
               'bm2|bwamem2' => \$opts{'bwamem2'},
+              'd|dupmode:s' => \$opts{'dupmode'},
+              'ss|seqslice:i' => $opts{'seqslice'},
   ) or pod2usage(2);
 
   pod2usage(-verbose => 1, -exitval => 0) if(defined $opts{'h'});
@@ -145,10 +166,14 @@ sub setup {
     die "ERROR: Please generate $opts{dict}, e.g.\n\t\$ samtools dict -a \$ASSEMBLY -s \$SPECIES $opts{reference} > $opts{dict}\n";
   }
 
+  if(defined $opts{'scramble'}) {
+    die "ERROR: -scramble option is deprecated, please see -seqslice\n";
+  }
+
   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'});
+  delete $opts{'scramble'};
   delete $opts{'bwa_pl'} unless(defined $opts{'bwa_pl'});
   delete $opts{'mmqc'} unless(defined $opts{'mmqc'});
   delete $opts{'csi'} unless(defined $opts{'csi'});
@@ -220,11 +245,12 @@ =head1 SYNOPSIS
   Optional parameters:
     -bwamem2     -bm2  Use bwa-mem2 instead of bwa.
     -fragment    -f    Split input into fragments of X million repairs [10]
+                        - only applies to fastq[.gz] input
     -nomarkdup   -n    Don't mark duplicates [flag]
     -csi               Use CSI index instead of BAI for BAM files [flag].
     -cram        -c    Output cram, see '-sc' [flag]
-    -scramble    -sc   Single quoted string of parameters to pass to Scramble when '-c' used
-                       - '-I,-O' are used internally and should not be provided
+    -seqslice    -ss   seqs_per_slice for CRAM compression [samtools default: 10000]
+    -scramble    -sc   DEPRECATED
     -bwa         -b    Single quoted string of additional parameters to pass to BWA
                         - '-t,-p,-R' are used internally and should not be provided.
                         - '-v' is set to 1 unless '-bwa' is set.
@@ -234,12 +260,15 @@ =head1 SYNOPSIS
     -mmqc        -q    Mark reads as QCFAIL (0x200, 512) if mismatch rate exceeded [flag]
                         - Please see 'bwa_mem.pl -m'
     -mmqcfrac    -qf   Mismatch fraction for -mmqc [0.05]
+    -dupmode     -d    see "samtools markdup -m" [t]
 
   Targeted processing:
     -process     -p    Only process this step then exit, optionally set -index
+                         setup - checks and configure workspace (-index N/A)
+                         split - split data by readgroup and chunk size (if applicable)
                         bwamem - only applicable if input is bam
                           mark - Run duplicate marking (-index N/A)
-                         stats - Generates the *.bas file for the final BAM.
+                         stats - Generates the *.bas file for the final BAM  (-index N/A)
 
     -index       -i    Optionally restrict '-p' to single job
                         bwamem - 1..<lane_count>
@@ -249,6 +278,7 @@ =head1 SYNOPSIS
                        https://github.com/gperftools/ (assuming number of cores not exceeded)
                        If available specify the path to 'gperftools/lib/libtcmalloc_minimal.so'.
                        - NOT APPLIED TO bwa-mem2
+                       Falls back to environment variable GPERF_FOR_BWA when not set, or nothing.
 
   Other:
     -jobs        -j   For a parallel step report the number of jobs required
diff --git a/bin/merge_or_mark.pl b/bin/merge_or_mark.pl
index 11616dd..a87c48f 100755
--- a/bin/merge_or_mark.pl
+++ b/bin/merge_or_mark.pl
@@ -39,7 +39,6 @@
 use PCAP::Bwa;
 use version;
 
-const my $COORD_SORT_ORDER => 'coordinate';
 const my $QUERYNAME_SORT_ORDER => 'queryname';
 const my @VALID_PROCESS => qw(setup mark stats);
 const my %INDEX_FACTOR => ( 'setup' => 1,
@@ -72,7 +71,8 @@ sub setup {
   my %opts = (
               'threads' => 1,
               'csi' => undef,
-              'sortorder' => $COORD_SORT_ORDER,
+              'dupmode' => 't',
+              'seqslice' => 10000,
              );
 
   GetOptions( 'h|help' => \$opts{'h'},
@@ -84,11 +84,13 @@ sub setup {
               's|sample=s' => \$opts{'sample'},
               'n|nomarkdup' => \$opts{'nomarkdup'},
               'p|process=s' => \$opts{'process'},
-              'q|querynamesort' => \$opts{'qnamesort'},
+              'q|qnamesort' => \$opts{'qnamesort'},
               'i|noindex' => \$opts{'noindex'},
               'csi' => \$opts{'csi'},
               'c|cram' => \$opts{'cram'},
               'sc|scramble=s' => \$opts{'scramble'},
+              'd|dupmode:s' => \$opts{'dupmode'},
+              'ss|seqslice:i' => $opts{'seqslice'},
   ) or pod2usage(2);
 
   pod2usage(-verbose => 1, -exitval => 0) if(defined $opts{'h'});
@@ -113,9 +115,13 @@ sub setup {
     die "ERROR: Please generate $opts{dict}, e.g.\n\t\$ samtools dict -a \$ASSEMBLY -s \$SPECIES $opts{reference} > $opts{dict}\n";
   }
 
+  if(defined $opts{'scramble'}) {
+    die "ERROR: -scramble option is deprecated, please see -seqslice\n";
+  }
+
   delete $opts{'process'} unless(defined $opts{'process'});
   delete $opts{'index'} unless(defined $opts{'index'});
-  delete $opts{'scramble'} unless(defined $opts{'scramble'});
+  delete $opts{'scramble'};
   delete $opts{'csi'} unless(defined $opts{'csi'});
   if($opts{'qnamesort'} && !$opts{'nomarkdup'}){
       die "ERROR: -qnamesort can only be used in conjunction with -nomarkdups\n";
@@ -123,7 +129,6 @@ sub setup {
   if($opts{'noindex'} && !$opts{'qnamesort'}){
       die "ERROR: -noindex can only be used in conjunction with -qnamesort\n";
   }
-  $opts{'sortorder'} = $QUERYNAME_SORT_ORDER if($opts{'qnamesort'});
 
   if($opts{'threads'} > 4) {
     warn "Setting 'threads' to 4 as higher values are of limited value\n";
@@ -172,18 +177,19 @@ =head1 SYNOPSIS
     -nomarkdup   -n   Don't mark duplicates [flag]
     -qnamesort   -q   Use queryname sorting flag in bammerge rather than coordinate. [flag].
                       To be used in conjunction with -nomarkdup only
-    -noindex     -i   Don't attempt to index the merged file. Only available in conjunction with 
+    -noindex     -i   Don't attempt to index the merged file. Only available in conjunction with
                       -qnamesort.
     -csi              Use CSI index instead of BAI for BAM files [flag].
     -cram        -c   Output cram, see '-sc' [flag]
-    -scramble    -sc  Single quoted string of parameters to pass to Scramble when '-c' used
-                      - '-I,-O' are used internally and should not be provided
+    -seqslice    -ss   seqs_per_slice for CRAM compression [samtools default: 10000]
+    -scramble    -sc   DEPRECATED
+    -dupmode     -d    see "samtools markdup -m" [t]
 
   Targeted processing:
-    -process     -p   Only process this step then exit, optionally set -index
-                        bwamem - only applicable if input is bam
-                          mark - Run duplicate marking (-index N/A)
-                         stats - Generates the *.bas file for the final BAM.
+    -process     -p   Only process this step then exit
+                         setup - only applicable if input is bam
+                          mark - Run duplicate marking
+                         stats - Generates the *.bas file for the final BAM
 
   Other:
     -help        -h   Brief help message.
@@ -261,6 +267,8 @@ =head2 OPTIONAL parameters
 
 =item B<-scramble>
 
+DEPRECATED - see -seqslice
+
 Single quoted string of parameters to pass to Scramble when '-c' used.  Please see the Scramble
 documentation for details.
 
diff --git a/build/opt-build-local.sh b/build/opt-build-local.sh
index 2e0abfa..7d13a48 100644
--- a/build/opt-build-local.sh
+++ b/build/opt-build-local.sh
@@ -40,9 +40,11 @@ mkdir -p $INST_PATH/bin
 
 # make sure tools installed can see the install loc of libraries
 set +u
+BB_INST=$INST_PATH/biobambam2
 export LD_LIBRARY_PATH=`echo $INST_PATH/lib:$LD_LIBRARY_PATH | perl -pe 's/:\$//;'`
-export PATH=`echo $INST_PATH/bin:$PATH | perl -pe 's/:\$//;'`
-export MANPATH=`echo $INST_PATH/man:$INST_PATH/share/man:$MANPATH | perl -pe 's/:\$//;'`
+export PATH=`echo $INST_PATH/bin:$BB_INST/bin:$PATH | perl -pe 's/:\$//;'`
+export MANPATH=`echo $INST_PATH/man:$BB_INST/man:$INST_PATH/share/man:$MANPATH | perl -pe 's/:\$//;'`
+export PERL5LIB=`echo $INST_PATH/lib/perl5:$PERL5LIB | perl -pe 's/:\$//;'`
 set -u
 
 ##### PCAP-core installation
diff --git a/build/opt-build.sh b/build/opt-build.sh
index 036b78b..874a46c 100755
--- a/build/opt-build.sh
+++ b/build/opt-build.sh
@@ -13,7 +13,6 @@ if [ "$#" -lt "1" ] ; then
   exit 1
 fi
 
-
 # get path to this script
 SCRIPT_PATH=`dirname $0`;
 SCRIPT_PATH=`(cd $SCRIPT_PATH && pwd)`
@@ -42,12 +41,20 @@ mkdir -p $SETUP_DIR/distro # don't delete the actual distro directory until the
 mkdir -p $INST_PATH/bin
 cd $SETUP_DIR
 
+# make sure tools installed can see the install loc of libraries
+set +u
+export LD_LIBRARY_PATH=`echo $INST_PATH/lib:$LD_LIBRARY_PATH | perl -pe 's/:\$//;'`
+export PATH=`echo $INST_PATH/bin:$BB_INST/bin:$PATH | perl -pe 's/:\$//;'`
+export MANPATH=`echo $INST_PATH/man:$BB_INST/man:$INST_PATH/share/man:$MANPATH | perl -pe 's/:\$//;'`
+export PERL5LIB=`echo $INST_PATH/lib/perl5:$PERL5LIB | perl -pe 's/:\$//;'`
+set -u
+
 ## biobambam2 first
 BB_INST=$INST_PATH/biobambam2
 if [ ! -e $SETUP_DIR/bbb2.sucess ]; then
   curl -sSL --retry 10 $BBB2_URL > distro.tar.gz
   mkdir -p $BB_INST
-  tar --strip-components 3 -C $BB_INST -Jxf distro.tar.gz
+  tar --strip-components 3 -C $BB_INST -zxf distro.tar.gz
   rm -f $BB_INST/bin/curl # don't let this file in SSL doesn't work
   rm -rf distro.* distro/*
   touch $SETUP_DIR/bbb2.success
@@ -70,7 +77,7 @@ rm -f $SETUP_DIR/cpanm
 ## scramble (from staden)
 if [ ! -e $SETUP_DIR/staden.success ]; then
   curl -sSL --retry 10 $STADEN > distro.tar.gz
-  rm -rf distro/*
+  rm -rf distro/* $OPT/scramble
   mkdir -p $OPT/scramble
   tar --strip-components 1 -C distro -xzf distro.tar.gz
   cp -r distro/* $OPT/scramble
@@ -121,6 +128,7 @@ fi
 if [ ! -e $SETUP_DIR/Bio-DB-HTS.success ]; then
   ## add perl deps
   cpanm --no-wget --no-interactive --notest --mirror http://cpan.metacpan.org -l $INST_PATH Module::Build
+  cpanm --no-wget --no-interactive --notest --mirror http://cpan.metacpan.org -l $INST_PATH XML::Parser
   cpanm --no-wget --no-interactive --notest --mirror http://cpan.metacpan.org -l $INST_PATH Bio::Root::Version
 
   curl -sSL --retry 10 https://github.com/Ensembl/Bio-DB-HTS/archive/${VER_BIODBHTS}.tar.gz > distro.tar.gz
@@ -137,4 +145,3 @@ if [ ! -e $SETUP_DIR/Bio-DB-HTS.success ]; then
 fi
 
 cd $HOME
-rm -rf $SETUP_DIR
diff --git a/c/mismatchQc.c b/c/mismatchQc.c
index 3da8656..216d4e7 100644
--- a/c/mismatchQc.c
+++ b/c/mismatchQc.c
@@ -369,9 +369,9 @@ int main(int argc, char *argv[]){
   hts_opt_free(out_opts);
 
   //Add program line to header
-  SAM_hdr *cram_head = bam_header_to_cram(head);
+  SAM_hdr *cram_head = sam_hdr_dup(head);
   check(cram_head != NULL,"Error converting bam header to cram for PG add.");
-  int chk_h = sam_hdr_add_PG(cram_head,prog_id,"CL",prog_cl,"DS",prog_desc,"VN",VERSION,NULL);
+  int chk_h = sam_hdr_add_pg(cram_head,prog_id,"CL",prog_cl,"DS",prog_desc,"VN",VERSION,NULL);
   check(chk_h==0,"Error adding PG line to header.");
   //Reference setup if CRAM output
   if (wflags & W_CRAM) {
@@ -398,7 +398,7 @@ int main(int argc, char *argv[]){
     hts_set_opt(output, HTS_OPT_THREAD_POOL, &p);
   }
 
-  new_head = cram_header_to_bam(cram_head);
+  new_head = sam_hdr_dup(cram_head);
   int hd_chk = sam_hdr_write(output, new_head);
   check(hd_chk!=-1,"Error writing header to output file.");
 
diff --git a/c/mmFlagModifier.c b/c/mmFlagModifier.c
index 4a43476..eda8157 100644
--- a/c/mmFlagModifier.c
+++ b/c/mmFlagModifier.c
@@ -272,9 +272,9 @@ int main(int argc, char *argv[]){
   hts_opt_free(out_opts);
 
   //Add program line to header
-  SAM_hdr *cram_head = bam_header_to_cram(head);
+  SAM_hdr *cram_head = sam_hdr_dup(head);
   check(cram_head != NULL,"Error converting bam header to cram for PG add.");
-  int chk_h = sam_hdr_add_PG(cram_head,prog_id,"CL",prog_cl,"DS",prog_desc,"VN",VERSION,NULL);
+  int chk_h = sam_hdr_add_pg(cram_head,prog_id,"CL",prog_cl,"DS",prog_desc,"VN",VERSION,NULL);
   check(chk_h==0,"Error adding PG line to header.");
   //Reference setup if CRAM output
   if (wflags & W_CRAM) {
@@ -302,7 +302,7 @@ int main(int argc, char *argv[]){
     hts_set_opt(output, HTS_OPT_THREAD_POOL, &p);
   }
 
-  new_head = cram_header_to_bam(cram_head);
+  new_head = sam_hdr_dup(cram_head);
   int hd_chk = sam_hdr_write(output, new_head);
   check(hd_chk!=-1,"Error writing header to output file.");
 
@@ -325,7 +325,7 @@ int main(int argc, char *argv[]){
     }
     //Check to see if the read has the mm tag required.
     int has_tag = 0;
-    has_tag = check_mm_tag(b); 
+    has_tag = check_mm_tag(b);
     check(has_tag>=0,"Error checking for mm tag in read.");
     if(has_tag){
       marked_count++;
@@ -340,7 +340,7 @@ int main(int argc, char *argv[]){
     int res = sam_write1(output,new_head,b);
     check(res>=0,"Error writing read to output file.");
   }//End of iteration through each read in the xam file
-  
+
   bam_destroy1(b);
   bam_hdr_destroy(head);
   bam_hdr_destroy(new_head);
diff --git a/docs.tar.gz b/docs.tar.gz
deleted file mode 100644
index abb2424..0000000
Binary files a/docs.tar.gz and /dev/null differ
diff --git a/lib/PCAP.pm b/lib/PCAP.pm
index fbdcfcd..d75980c 100644
--- a/lib/PCAP.pm
+++ b/lib/PCAP.pm
@@ -28,7 +28,7 @@ use FindBin qw($Bin);
 use File::Which qw(which);
 # don't use autodie, only core perl in here
 
-our $VERSION = '5.0.5';
+our $VERSION = '5.1.0';
 our @EXPORT = qw($VERSION _which);
 
 const my $LICENSE =>
diff --git a/lib/PCAP/Bam.pm b/lib/PCAP/Bam.pm
index 16f556a..19ba85b 100644
--- a/lib/PCAP/Bam.pm
+++ b/lib/PCAP/Bam.pm
@@ -36,19 +36,6 @@ 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 $MISMATCHQC => q{| %s -l 0 -t %.2f -p };
-const my $BAMBAM_DUP => q{%s level=0 %s | %s tmpfile=%s level=0 markthreads=%d M=%s.met %s| pee '%s tmpfile=%s index=1 md5=1 numthreads=%d md5filename=%s.md5 indexfilename=%s.%s > %s' '%s -o %s.bas -@ %d'};
-const my $BAMBAM_MERGE => q{%s %s tmpfile=%s level=0 %s| pee '%s tmpfile=%s index=1 md5=1 numthreads=%d md5filename=%s.md5 indexfilename=%s.%s > %s' '%s -o %s.bas -@ %d'};
-const my $BAMBAM_DUP_CRAM => q{%s level=0 %s | %s tmpfile=%s M=%s.met markthreads=%s level=0 %s| %s -r %s -t %d -I bam -O cram %s | tee %s | %s index - %s.crai};
-const my $BAMBAM_MERGE_CRAM => q{%s %s tmpfile=%s level=0 %s| %s -r %s -t %d -I bam -O cram %s | tee %s | %s index - %s.crai};
-
-const my $LANE_BAMBAM_MERGE => q{%s SO=%s %s tmpfile=%s level=0 | pee '%s tmpfile=%s index=1 md5=1 numthreads=%d md5filename=%s.md5 indexfilename=%s.%s > %s' '%s -o %s.bas -@ %d'};
-const my $LANE_BAMBAM_MERGE_CRAM => q{%s SO=%s %s tmpfile=%s level=0 | %s -r %s -t %d -I bam -O cram %s | tee %s | %s index - %s.crai};
-const my $LANE_BAMBAM_MERGE_NOIDX => q{%s SO=%s %s tmpfile=%s level=0 | pee '%s tmpfile=%s md5=1 numthreads=%d md5filename=%s.md5 > %s' '%s -o %s.bas -@ %d'};
-const my $LANE_BAMBAM_MERGE_CRAM_NOIDX => q{%s SO=%s %s tmpfile=%s level=0 | %s -r %s -t %d -I bam -O cram %s %s};
-
-const my $LANE_BAMBAM_DUP => q{%s level=0 %s | %s -l 0 -m | %s tmpfile=%s level=0 markthreads=%d M=%s.met | %s -l 0 -p | pee '%s tmpfile=%s index=1 md5=1 numthreads=%d md5filename=%s.md5 indexfilename=%s.%s > %s' '%s -o %s.bas -@ %d'};
-const my $LANE_BAMBAM_DUP_CRAM => q{%s level=0 %s | %s -l 0 -m | %s tmpfile=%s level=0 markthreads=%d M=%s.met | %s -l 0 -p | %s -r %s -t %d -I bam -O cram %s | tee %s | %s 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 -@ %d};
@@ -107,143 +94,81 @@ sub bam_to_grouped_bam {
 }
 
 sub merge_or_mark_lanes {
-  my ($options, @sorted_bams) = @_;
+  my ($options, @bams) = @_;
   my $tmp = $options->{'tmp'};
-  my $marked = File::Spec->catdir($options->{'outdir'}, $options->{'sample'});
 
+  my $marked = File::Spec->catdir($options->{'outdir'}, $options->{'sample'});
   if($options->{'cram'}) { $marked .= '.cram'; }
   else { $marked .= '.bam'; }
 
-  my @commands;
   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 = ' I='.join(' I=', sort @sorted_bams);
+  my @commands = ('set -o pipefail');
+
+  my $helper_threads = $options->{'threads'};
 
-  my $bbb_tmp = File::Spec->catfile($tmp, 'biormdup');
+  my $input_str = join q{ }, sort @bams;
+
+  my $strmd_tmp = File::Spec->catfile($tmp, 'strmdup');
   my $brc_tmp = File::Spec->catfile($tmp, 'brcTmp');
 
   my %tools;
-  for my $tool(qw(bam_stats bammerge bammarkduplicates2 bamrecompress scramble samtools mmFlagModifier)) {
+  for my $tool(qw(bam_stats samtools md5sum)) {
     $tools{$tool} = _which($tool) || die "Unable to find '$tool' in path";
   }
 
+  my $out_fmt = 'bam';
   my $idx_type = 'bai';
-  $idx_type = 'csi' if(exists $options->{'csi'});
+  my $idx_csi_flag = q{};
+  if($options->{'cram'}) {
+    $idx_type = 'crai';
+    $out_fmt = 'cram';
+    $out_fmt .= ',seqs_per_slice='.$options->{'seqslice'};
+  }
+  elsif(exists $options->{'csi'}) {
+    # only valid for bam
+    $idx_type = 'csi';
+    $idx_csi_flag = '-c';
+  }
 
-  # subtly different, as need to strip mmQc before dup-rem, and then reapply
   if(defined $options->{'nomarkdup'} && $options->{'nomarkdup'} == 1) {
-      if(defined $options->{'noindex'} && $options->{'noindex'} == 1){
-        if($options->{'cram'}) {
-            my $add_sc = $options->{'scramble'} || q{};
-            $commands[0] = sprintf $LANE_BAMBAM_MERGE_CRAM_NOIDX,
-                              $tools{'bammerge'},
-                              $options->{'sortorder'},
-                              $input_str,
-                              $bbb_tmp,
-                              $tools{'scramble'},
-                              $options->{'reference'},
-                              $helper_threads,
-                              $add_sc,
-                              $marked;
-        }
-        else {
-            $commands[0] = sprintf $LANE_BAMBAM_MERGE_NOIDX,
-                              $tools{'bammerge'},
-                              $options->{'sortorder'},
-                              $input_str,
-                              $bbb_tmp,
-                              $tools{'bamrecompress'},
-                              $brc_tmp,
-                              $helper_threads,
-                              $marked,
-                              $marked,
-                              $tools{'bam_stats'},
-                              $marked,
-                              $helper_threads;
-        }
+      my $idx = q{};
+      unless($options->{'noindex'}) {
+        $idx = sprintf q{%s index -@ %d %s - %s.%s},
+                        $tools{samtools}, $helper_threads, $idx_csi_flag, $marked, $idx_type;
       }
-      else{
-        if($options->{'cram'}) {
-            my $add_sc = $options->{'scramble'} || q{};
-            $commands[0] = sprintf $LANE_BAMBAM_MERGE_CRAM,
-                                $tools{'bammerge'},
-                                $options->{'sortorder'},
-                                $input_str,
-                                $bbb_tmp,
-                                $tools{'scramble'},
-                                $options->{'reference'},
-                                $helper_threads,
-                                $add_sc,
-                                $marked,
-                                $tools{'samtools'},
-                                $marked;
-        }
-        else {
-            $commands[0] = sprintf $LANE_BAMBAM_MERGE,
-                                $tools{'bammerge'},
-                                $options->{'sortorder'},
-                                $input_str,
-                                $bbb_tmp,
-                                $tools{'bamrecompress'},
-                                $brc_tmp,
-                                $helper_threads,
-                                $marked,
-                                $marked, $idx_type,
-                                $marked,
-                                $tools{'bam_stats'},
-                                $marked,
-                                $helper_threads;
-        }
-    }
+
+      my $namesrt = q{};
+      $namesrt = q{-n} if($options->{'qnamesort'});
+
+      my $merge    = sprintf q{%s merge %s -u -@ %d - %s},
+                              $tools{samtools}, $namesrt, $helper_threads, $input_str;
+      my $compress = sprintf q{%s view -T %s --output-fmt %s -@ %d -},
+                              $tools{samtools}, $options->{reference}, $out_fmt, $helper_threads;
+      my $md5      = sprintf q{%s -b > %s.md5},
+                            $tools{md5sum}, $marked;
+      my $stats    = sprintf q{%s -o %s.bas -@ %d},
+                              $tools{bam_stats}, $marked, $helper_threads;
+      push @commands, qq{$merge | pee "$stats" "$compress | pee '$idx' '$md5' 'cat > $marked'"};
   }
   else {
-    if($options->{'cram'}) {
-      my $add_sc = $options->{'scramble'} || q{};
-      $commands[0] = sprintf $LANE_BAMBAM_DUP_CRAM,
-                              $tools{'bammerge'},
-                              $input_str,
-                              $tools{'mmFlagModifier'},
-                              $tools{'bammarkduplicates2'},
-                              $bbb_tmp,
-                              $helper_threads,
-                              $marked,
-                              $tools{'mmFlagModifier'},
-                              $tools{'scramble'},
-                              $options->{'reference'},
-                              $helper_threads,
-                              $add_sc,
-                              $marked,
-                              $tools{'samtools'},
-                              $marked;
-    }
-    else {
-      $commands[0] = sprintf $LANE_BAMBAM_DUP,
-                              $tools{'bammerge'},
-                              $input_str,
-                              $tools{'mmFlagModifier'},
-                              $tools{'bammarkduplicates2'},
-                              $bbb_tmp,
-                              $helper_threads,
-                              $marked,
-                              $tools{'mmFlagModifier'},
-                              $tools{'bamrecompress'},
-                              $brc_tmp,
-                              $helper_threads,
-                              $marked,
-                              $marked, $idx_type,
-                              $marked,
-                              $tools{'bam_stats'},
-                              $marked,
-                              $helper_threads;
-    }
+    my $merge    = sprintf q{%s merge -u -@ %d - %s},
+                           $tools{samtools}, $helper_threads, $input_str;
+    my $markdup  = sprintf q{%s markdup --mode %s --output-fmt bam,level=0 -S --include-fails -T %s -@ %d -f %s.met - -},
+                           $tools{samtools}, $options->{dupmode}, $strmd_tmp, $helper_threads, $marked;
+    my $compress = sprintf q{%s view -T %s --output-fmt %s -@ %d -},
+                           $tools{samtools}, $options->{reference}, $out_fmt, $helper_threads;
+    my $idx      = sprintf q{%s index -@ %d %s - %s.%s},
+                           $tools{samtools}, $helper_threads, $idx_csi_flag, $marked, $idx_type;
+    my $md5      = sprintf q{%s -b > %s.md5},
+                           $tools{md5sum}, $marked;
+    my $stats    = sprintf q{%s -o %s.bas -@ %d},
+                           $tools{bam_stats}, $marked, $helper_threads;
+    push @commands, qq{$merge | $markdup | pee "$compress | pee 'cat > $marked' '$idx' '$md5'" "$stats" };
   }
 
   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($tmp, 'logs'), \@commands, 0);
@@ -255,135 +180,95 @@ sub merge_and_mark_dup {
   # uncoverable subroutine
   my ($options, $source) = @_;
   my $tmp = $options->{'tmp'};
-  my $marked = File::Spec->catdir($options->{'outdir'}, $options->{'sample'});
-
-  my @commands;
 
-  if($options->{'cram'}) {
-    $marked .= '.cram';
-  }
-  else {
-    $marked .= '.bam';
-  }
+  my $marked = File::Spec->catdir($options->{'outdir'}, $options->{'sample'});
+  if($options->{'cram'}) { $marked .= '.cram'; }
+  else { $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 @commands = ('set -o pipefail');
 
-  my @sorted_bams;
-  my $input_str = q{};
+  my $helper_threads = $options->{'threads'};
+
+  my @bams;
   if(defined $source) {
     opendir(my $dh, $source);
     while(my $file = readdir $dh) {
       next unless($file =~ m/_sorted\.bam$/);
-      push @sorted_bams, File::Spec->catfile($source, $file);
+      push @bams, File::Spec->catfile($source, $file);
     }
     closedir $dh;
 
   }
   else {
     for(@{$options->{'meta_set'}}) {
-      push @sorted_bams, $_->tstub.'_sorted.bam';
+      push @bams, $_->tstub.'_sorted.bam';
     }
   }
-  $input_str = ' I='.join(' I=', sort @sorted_bams);
 
-  my $bbb_tmp = File::Spec->catfile($tmp, 'biormdup');
+  my $input_str = join q{ }, sort @bams;
+
+  my $strmd_tmp = File::Spec->catfile($tmp, 'strmdup');
   my $brc_tmp = File::Spec->catfile($tmp, 'brcTmp');
 
   my %tools;
-  for my $tool(qw(bammerge bammarkduplicates2 bamrecompress scramble samtools bam_stats mismatchQc)) {
+  for my $tool(qw(samtools bam_stats mismatchQc md5sum)) {
     $tools{$tool} = _which($tool) || die "Unable to find '$tool' in path";
   }
 
   my $mismatchQc = q{};
   if(defined $options->{'mmqc'}) {
-    $mismatchQc = sprintf $MISMATCHQC,
+    $mismatchQc = sprintf q{ | %s -l 0 -t %.2f -p},
                       $tools{'mismatchQc'},
                       $options->{'mmqcfrac'};
   }
 
+  my $out_fmt = 'bam';
   my $idx_type = 'bai';
-  $idx_type = 'csi' if(exists $options->{'csi'});
+  my $idx_csi_flag = q{};
+  if($options->{'cram'}) {
+    $idx_type = 'crai';
+    $out_fmt = 'cram';
+    $out_fmt .= ',seqs_per_slice='.$options->{'seqslice'};
+  }
+  elsif(exists $options->{'csi'}) {
+    # only valid for bam
+    $idx_type = 'csi';
+    $idx_csi_flag = '-c';
+  }
 
   if(defined $options->{'nomarkdup'} && $options->{'nomarkdup'} == 1) {
-    if($options->{'cram'}) {
-      my $add_sc = $options->{'scramble'} || q{};
-      $commands[0] = sprintf $BAMBAM_MERGE_CRAM,
-                              $tools{'bammerge'},
-                              $input_str,
-                              $bbb_tmp,
-                              $mismatchQc,
-                              $tools{'scramble'},
-                              $options->{'reference'},
-                              $helper_threads,
-                              $add_sc,
-                              $marked,
-                              $tools{'samtools'},
-                              $marked;
-    }
-    else {
-      $commands[0] = sprintf $BAMBAM_MERGE,
-                              $tools{'bammerge'},
-                              $input_str,
-                              $bbb_tmp,
-                              $mismatchQc,
-                              $tools{'bamrecompress'},
-                              $brc_tmp,
-                              $helper_threads,
-                              $marked,
-                              $marked, $idx_type,
-                              $marked,
-                              $tools{'bam_stats'},
-                              $marked,
-                              $helper_threads;
-    }
+    my $merge    = sprintf q{%s merge -u -@ %d - %s},
+                            $tools{samtools}, $helper_threads, $input_str;
+    my $compress = sprintf q{%s view -T %s --output-fmt %s -@ %d -},
+                            $tools{samtools}, $options->{reference}, $out_fmt, $helper_threads;
+    my $idx      = sprintf q{%s index -@ %d %s - %s.%s},
+                          $tools{samtools}, $helper_threads, $idx_csi_flag, $marked, $idx_type;
+    my $md5      = sprintf q{%s -b > %s.md5},
+                           $tools{md5sum}, $marked;
+    my $stats    = sprintf q{%s -o %s.bas -@ %d},
+                            $tools{bam_stats}, $marked, $helper_threads;
+    push @commands, qq{$merge $mismatchQc | pee "$stats" "$compress | pee '$idx' '$md5' 'cat > $marked'"};
   }
   else {
-    if($options->{'cram'}) {
-      my $add_sc = $options->{'scramble'} || q{};
-      $commands[0] = sprintf $BAMBAM_DUP_CRAM,
-                              $tools{'bammerge'},
-                              $input_str,
-                              $tools{'bammarkduplicates2'},
-                              $bbb_tmp,
-                              $marked,
-                              $helper_threads,
-                              $mismatchQc,
-                              $tools{'scramble'},
-                              $options->{'reference'},
-                              $helper_threads,
-                              $add_sc,
-                              $marked,
-                              $tools{'samtools'},
-                              $marked;
-    }
-    else {
-      $commands[0] = sprintf $BAMBAM_DUP,
-                              $tools{'bammerge'},
-                              $input_str,
-                              $tools{'bammarkduplicates2'},
-                              $bbb_tmp,
-                              $helper_threads,
-                              $marked,
-                              $mismatchQc,
-                              $tools{'bamrecompress'},
-                              $brc_tmp,
-                              $helper_threads,
-                              $marked,
-                              $marked, $idx_type,
-                              $marked,
-                              $tools{'bam_stats'},
-                              $marked,
-                              $helper_threads;
-    }
+    my $merge    = sprintf q{%s merge -u -@ %d - %s},
+                           $tools{samtools}, $helper_threads, $input_str;
+    my $markdup  = sprintf q{%s markdup --mode %s --output-fmt bam,level=0 -S --include-fails -T %s -@ %d -f %s.met - -},
+                           $tools{samtools}, $options->{dupmode}, $strmd_tmp, $helper_threads, $marked;
+    my $compress = sprintf q{%s view -T %s --output-fmt %s -@ %d -},
+                           $tools{samtools}, $options->{reference}, $out_fmt, $helper_threads;
+    my $idx      = sprintf q{%s index -@ %d %s - %s.%s},
+                           $tools{samtools}, $helper_threads, $idx_csi_flag, $marked, $idx_type;
+    my $md5      = sprintf q{%s -b > %s.md5},
+                           $tools{md5sum}, $marked;
+    my $stats    = sprintf q{%s -o %s.bas -@ %d},
+                           $tools{bam_stats}, $marked, $helper_threads;
+    push @commands, qq{$merge $mismatchQc | $markdup | pee "$compress | pee 'cat > $marked' '$idx' '$md5'" "$stats" };
   }
 
   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);
@@ -395,17 +280,12 @@ sub bam_stats {
   # uncoverable subroutine
   my $options = shift;
   my $tmp = $options->{'tmp'};
+  # leagacy method, not needed
   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);
-  if($options->{'cram'}) {
-    # Only needed for cram output
-    my $command = _which('bam_stats') || die "Unable to find 'bam_stats' in path";
-    $command .= sprintf $BAM_STATS, $xam, $bas, $options->{'threads'};
-    PCAP::Threaded::external_process_handler(File::Spec->catdir($tmp, 'logs'), $command, 0);
-  }
   PCAP::Threaded::touch_success(File::Spec->catdir($tmp, 'progress'), 0);
   return $bas;
 }
diff --git a/lib/PCAP/Bwa.pm b/lib/PCAP/Bwa.pm
index 3ef6b97..a963fb9 100644
--- a/lib/PCAP/Bwa.pm
+++ b/lib/PCAP/Bwa.pm
@@ -27,7 +27,7 @@ use autodie qw(:all);
 use English qw( -no_match_vars );
 use warnings FATAL => 'all';
 use Const::Fast qw(const);
-use File::Path qw(make_path);
+use File::Path qw(make_path remove_tree);
 use File::Spec;
 use Capture::Tiny qw(capture);
 use File::Copy qw(copy);
@@ -36,11 +36,9 @@ use PCAP::Bwa::Meta;
 use PCAP::Bam;
 
 const my $BWA_ALN => q{ aln%s -t %s -f %s_%s.sai %s %s.%s};
-const my $BAMFASTQ => q{%s view -F 2816 -T %s -u %s| %s exclude=QCFAIL,SECONDARY,SUPPLEMENTARY tryoq=1 gz=1 level=1 outputperreadgroup=1 outputperreadgroupsuffixF=_i.fq outputperreadgroupsuffixF2=_i.fq T=%s outputdir=%s split=%s};
-const my $CRAMFASTQ => q{%s reference=%s inputformat=cram exclude=QCFAIL,SECONDARY,SUPPLEMENTARY tryoq=1 gz=1 level=1 outputperreadgroup=1 outputperreadgroupsuffixF=_i.fq outputperreadgroupsuffixF2=_i.fq T=%s outputdir=%s split=%s filename=%s};
-const my $BWA_MEM => q{ mem %s %s -R %s -t %s %s};
 const my $ALN_TO_SORTED => q{ sampe -P -a 1000 -r '%s' %s %s_1.sai %s_2.sai %s.%s %s.%s | %s fixmate=1 inputformat=sam level=1 tmpfile=%s_tmp O=%s_sorted.bam};
-const my $BAMSORT => q{ fixmate=1 inputformat=sam level=1 tmpfile=%s_tmp O=%s_sorted.bam outputthreads=%s calmdnm=1 calmdnmrecompindetonly=1 calmdnmreference=%s sortthreads=%s};
+
+const my $TAG_STRIP => q{-x AM -x MD -x NM -x RT -x SM -x X0 -x X1 -x XA -x XG -x XM -x XN -x XO -x XT -x mm};
 
 const my $FALSE_RG => q{@RG\tID:%s\tSM:%s\tLB:default\tPL:ILLUMINA};
 
@@ -92,9 +90,6 @@ sub mem_setup {
       copy("$options->{reference}.fai", "$options->{tmp}/decomp.fa.fai") unless(-e "$options->{decomp_ref}.fai");
     }
   }
-  # do some checking to ensure input BAM/CRAM hasn't been through mismatchQc
-  # if it has check for use of at least bammaskflags
-  PCAP::Bam::mismatchQc_checks($options->{'raw_files'}) unless($skip_mmqc_check);
   return 1;
 }
 
@@ -136,6 +131,7 @@ sub mem_mapmax {
       next if($file =~ m/^\./);
       next if($file =~ m/^pairedfq2\.[[:digit:]]+/); # captured by 1.*
       next if($file =~ m/s[.]fq[.]gz_[[:digit:]]+[.]gz$/);
+      next if($file eq 'unknown.bam');
       if($file =~ m/o[12][.]fq[.]gz_[[:digit:]]+[.]gz$/) {
         warn "Orphan reads found, your input BAM appears to have had duplicates 'removed' rather than 'marked': $folder/$file\n\tWARNING: This will give a sub-optimal result\n";
         next;
@@ -171,7 +167,6 @@ sub split_in {
     make_path($split_folder) unless(-d $split_folder);
     make_path($sort_folder) unless(-d $sort_folder);
 
-
     my $fragment_size = $options->{'fragment'};
     $fragment_size ||= $READPAIR_SPLITSIZE;
 
@@ -213,28 +208,19 @@ sub split_in {
     }
     # if bam|cram input
     else {
-      my $bam2fq = _which('bamtofastq') || die "Unable to find 'bamtofastq' in path";
-      my $cmd;
-      if($input->bam_or_cram eq 'cram') {
-        $cmd = sprintf $CRAMFASTQ, $bam2fq,
-                                  $options->{'reference'},
-                                  File::Spec->catfile($tmp, "bamtofastq.$index"),
-                                  $split_folder,
-                                  $fragment_size * $MILLION * $BAM_MULT,
-                                  $input->in;
-      }
-      else {
-        my $samtools = _which('samtools') || die "Unable to find 'samtools' in path";
-        $cmd = sprintf $BAMFASTQ, $samtools,
-                                  $options->{'reference'},
-                                  $input->in,
-                                  $bam2fq,
-                                  File::Spec->catfile($tmp, "bamtofastq.$index"),
-                                  $split_folder,
-                                  $fragment_size * $MILLION * $BAM_MULT;
-      }
+      my $helpers = $options->{threads_per_split};
+      my $collate_folder = File::Spec->catdir($options->{'tmp'}, 'collate', $index);
+      make_path($collate_folder) unless(-d $collate_folder);
+      my $samtools = _which('samtools') || die "Unable to find 'samtools' in path";
+      my $mmQcStrip = sprintf '%s --remove -l 0 -@ %d -i %s', _which('mmFlagModifier'), $helpers, $input->in;
+      my $view = sprintf '%s view %s -bu -T %s -F 2816 -@ %d -', $samtools, $TAG_STRIP, $options->{'reference'}, $helpers; # leave
+      my $collate = sprintf '%s collate -Ou -@ %d - %s/collate', $samtools, $helpers, $collate_folder;
+      my $split = sprintf '%s split --output-fmt bam,level=1 -@ %d -u %s/unknown.bam -f %s/%%!_i.bam -', $samtools, $helpers, $split_folder, $split_folder;
+      my $cmd = sprintf '%s | %s | %s | %s', $mmQcStrip, $view, $collate, $split;
       # treat as interleaved fastq
+      push @commands, 'set -o pipefail';
       push @commands, $cmd;
+      push @commands, "rm -rf $collate_folder"; # cleanup temp folder
     }
 
     PCAP::Threaded::external_process_handler(File::Spec->catdir($tmp, 'logs'), \@commands, $index);
@@ -250,6 +236,7 @@ sub bwa_mem {
   my $tmp = $options->{'tmp'};
   return 1 if PCAP::Threaded::success_exists(File::Spec->catdir($tmp, 'progress'), $index);
 
+
   my $input_meta = $options->{'meta_set'};
   my $to_map = $options->{'to_map'};
   my $iter = 1;
@@ -272,7 +259,7 @@ sub bwa_mem {
       $rg_line = q{'}.$input->rg_header(q{\t}).q{'};
     }
     else {
-      my ($rg) = $split =~ m|/split/[[:digit:]]+/(.+)_i.fq_[[:digit:]]+.gz$|;
+      my ($rg) = $split =~ m{/split/[[:digit:]]+/(.+)_i\.(?:fq_[[:digit:]]+\.)?(?:gz|bam)$};
       ($rg_line, undef) = PCAP::Bam::rg_line_for_output($input->in, $options->{'sample'}, undef, $rg);
       if($rg_line) {
         $rg_line =~ s/('+)/'"$1"'/g;
@@ -293,12 +280,18 @@ sub bwa_mem {
     else {
       if(exists $options->{'bwa_pl'}) {
         $bwa .= 'LD_PRELOAD='.$options->{'bwa_pl'}.' ';
+      } elsif(exists $ENV{GPERF_FOR_BWA}) {
+        $bwa .= 'LD_PRELOAD='.$ENV{GPERF_FOR_BWA}.' ';
       }
       $bwa .= _which('bwa') || die "Unable to find 'bwa' in path";
     }
 
     $ENV{SHELL} = '/bin/bash'; # ensure bash to allow pipefail
-    my $command = 'set -o pipefail; ';
+
+    my %tools;
+    for my $tool(qw(samtools reheadSQ)) {
+      $tools{$tool} = _which($tool) || die "Unable to find '$tool' in path";
+    }
 
     my $interleaved_fq = q{};
     # uncoverable branch true
@@ -307,41 +300,40 @@ sub bwa_mem {
 
     my $add_options = q{-v 1}; # minimise output
     $add_options = $options->{'bwa'} if(exists $options->{'bwa'});
-    $bwa .= sprintf $BWA_MEM, $add_options, $interleaved_fq, $rg_line, $threads, $options->{'reference'};
+    $bwa .= sprintf q{ mem %s %s -R %s -t %s %s}, $add_options, $interleaved_fq, $rg_line, $threads, $options->{'reference'};
 
     # uncoverable branch true
     # uncoverable branch false
-    if($input->paired_fq) {
-      $split =~ s/'/\\'/g;
-      my $split2 = $split;
-      $split2 =~ s/pairedfq1(\.[[:digit:]]+)/pairedfq2$1/;
+    $split =~ s/'/\\'/g;
+    if($input->fastq) {
       $bwa .= ' '.$split;
-      $bwa .= ' '.$split2;
+      if($input->paired_fq) {
+        my $split2 = $split;
+        $split2 =~ s/pairedfq1(\.[[:digit:]]+)/pairedfq2$1/;
+        $bwa .= ' '.$split2;
+      }
     }
     else {
-      $split =~ s/'/\\'/g;
-      $bwa .= ' '.$split;
+      # bam/cram
+      my $tofastq = sprintf '%s fastq -@ %d -N %s', $tools{samtools}, $threads, $split;
+      $bwa = sprintf '%s | %s /dev/stdin', $tofastq, $bwa;
     }
-    $command .= $bwa;
-
-    # now add the code for reheadSQ
-    my $rehead_sq = sprintf '%s -d %s', _which('reheadSQ'), $options->{'dict'};
-    $command .= ' | '.$rehead_sq;
-
-    my $helpers = 1;
-    # uncoverable branch true
-    # uncoverable branch false
-    $helpers = $threads - 1 if($threads > 1);
 
     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";
-    $sort .= sprintf $BAMSORT, File::Spec->catfile($tmp, "bamsort.$index"), $sorted_bam_stub, $helpers, $ref, $helpers;
 
-    $command .= " | $sort";
+    my $rehead_sq = sprintf '%s -d %s',
+                            $tools{reheadSQ}, $options->{'dict'};
+    my $fixmate   = sprintf q{%s fixmate -m --output-fmt bam,level=0 -@ %d - -},
+                            $tools{samtools}, $threads;
+    my $sort      = sprintf q{%s sort -m 2G --output-fmt bam,level=0 -T %s_tmp -@ %d -},
+                            $tools{samtools}, File::Spec->catfile($tmp, "bamsort.$index"), $threads;
+    my $calmd     = sprintf q{%s calmd --output-fmt bam,level=1 -Q -@ %d - %s > %s_sorted.bam},
+                            $tools{samtools}, $threads, $ref, $sorted_bam_stub;
+    my $command .= "set -o pipefail; $bwa | $rehead_sq | $fixmate | $sort | $calmd";
 
     PCAP::Threaded::external_process_handler(File::Spec->catdir($tmp, 'logs'), $command, $index);
     PCAP::Threaded::touch_success(File::Spec->catdir($tmp, 'progress'), $index);
diff --git a/prerelease.sh b/prerelease.sh
deleted file mode 100755
index 92ac79c..0000000
--- a/prerelease.sh
+++ /dev/null
@@ -1,70 +0,0 @@
-#!/bin/bash
-
-set -eu # exit on first error or undefined value in subtitution
-set -o pipefail
-
-# get current directory
-INIT_DIR=`pwd`
-
-rm -rf blib
-
-# get location of this file
-MY_PATH="`dirname \"$0\"`"              # relative
-MY_PATH="`( cd \"$MY_PATH\" && pwd )`"  # absolutized and normalized
-if [ -z "$MY_PATH" ] ; then
-  # error; for some reason, the path is not accessible
-  # to the script (e.g. permissions re-evaled after suid)
-  echo Failed to determine location of script >2
-  exit 1  # fail
-fi
-# change into the location of the script
-cd $MY_PATH
-
-echo -e '\n### Compile/Test C ###\n'
-set +u
-if [ "x$HTSLIB" == "x" ] || [ "x$LIBBIGWIG" == "x" ]; then
-  echo -e '\n\t$HTSLIB or $LIBBIGWIG not defined skipping C compile/test\n'
-else
-  make -C c clean
-  make -C c
-  make -C c clean
-fi
-set -u
-
-echo -e '\n\n### Running perl tests ###\n'
-
-export HARNESS_PERL_SWITCHES=-MDevel::Cover=-db,reports,-select='^lib/*\.pm$',-ignore,'^t/'
-rm -rf reports docs pm_to_blib blib
-cover -delete
-mkdir -p docs/reports_text
-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
-cover -coverage branch,subroutine,pod -report_c0 50 -report_c1 85 -report_c2 100 -report html_basic reports -silent |& grep -v '^Perltidy' | grep -v '^##' | grep -v '^1:'
-# grep on last command to cleanup an oddity in perltidy
-cover -coverage branch,subroutine,pod -report text reports -silent > docs/reports_text/coverage.txt
-rm -rf reports/structure reports/digests reports/cover.13 reports/runs
-cp reports/coverage.html reports/index.html
-mv reports docs/reports_html
-unset HARNESS_PERL_SWITCHES
-
-echo '### Generating POD ###'
-mkdir -p docs/pod_html
-perl -MPod::Simple::HTMLBatch -e 'Pod::Simple::HTMLBatch::go' lib:bin docs/pod_html > /dev/null
-
-echo '### Archiving docs folder ###'
-tar cz -C $INIT_DIR -f docs.tar.gz docs
-
-# generate manifest, and cleanup
-echo '### Generating MANIFEST ###'
-# delete incase any files are moved, the make target just adds stuff
-rm -f MANIFEST
-# cleanup things which could break the manifest
-rm -rf install_tmp
-perl Makefile.PL > /dev/null
-make manifest &> /dev/null
-rm -f Makefile MANIFEST.bak pm_to_blib
-
-# change back to original dir
-cd $INIT_DIR
diff --git a/setup.sh b/setup.sh
index 8aabf6d..1dfb91f 100755
--- a/setup.sh
+++ b/setup.sh
@@ -1,279 +1,62 @@
 #!/bin/bash
 
-SOURCE_BWA="https://github.com/lh3/bwa/archive/v0.7.17.tar.gz"
-SOURCE_BWAMEM2="https://github.com/bwa-mem2/bwa-mem2/releases/download/v2.0pre2/bwa-mem2-2.0pre2_x64-linux.tar.bz2"
-
-# for bamstats and Bio::DB::HTS
-SOURCE_HTSLIB="https://github.com/samtools/htslib/releases/download/1.7/htslib-1.7.tar.bz2"
-SOURCE_SAMTOOLS="https://github.com/samtools/samtools/releases/download/1.7/samtools-1.7.tar.bz2"
-
-# Bio::DB::HTS
-SOURCE_BIOBDHTS="https://github.com/Ensembl/Bio-HTS/archive/2.10.tar.gz"
-
-# for biobambam
-SOURCE_BBB_BIN_DIST="https://github.com/gt1/biobambam2/releases/download/2.0.86-release-20180228171821/biobambam2-2.0.86-release-20180228171821-x86_64-etch-linux-gnu.tar.gz"
-
-get_distro () {
-  EXT=""
-  if [[ $2 == *.tar.bz2* ]] ; then
-    EXT="tar.bz2"
-  elif [[ $2 == *.zip* ]] ; then
-    echo "ERROR: zip archives are not supported by default, if pulling from github replace .zip with .tar.gz"
-    exit 1
-  elif [[ $2 == *.tar.gz* ]] ; then
-    EXT="tar.gz"
-  else
-    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 --retry 10 -sS -o $1.$EXT -L $2
-  else
-    echo "ERROR: curl not found"
-    exit 1
-  fi
-}
-
-get_file () {
-# output, source
-  if hash curl 2>/dev/null; then
-    curl -sS -o $1 -L $2
-  else
-    wget -nv -O $1 $2
-  fi
-}
-
-if [ "$#" -ne "1" ] ; then
-  echo "Please provide an installation path  such as /opt/ICGC"
-  exit 0
+# ALL tool versions used by opt-build.sh
+# need to keep in sync with Dockerfile
+
+# newer gitlab versions do not work
+export BBB2_URL="https://github.com/gt1/biobambam2/releases/download/2.0.87-release-20180301132713/biobambam2-2.0.87-release-20180301132713-x86_64-etch-linux-gnu.tar.gz"
+export BWAMEM2_URL="https://github.com/bwa-mem2/bwa-mem2/releases/download/v2.0pre2/bwa-mem2-2.0pre2_x64-linux.tar.bz2"
+export STADEN="https://iweb.dl.sourceforge.net/project/staden/staden/2.0.0b11/staden-2.0.0b11-2016-linux-x86_64.tar.gz"
+export VER_BIODBHTS="3.01"
+export VER_BWA="v0.7.17"
+export VER_HTSLIB="1.10.2"
+export VER_SAMTOOLS="1.10"
+
+
+if [[ ($# -ne 1 && $# -ne 2) ]] ; then
+  echo "Please provide an installation path and optionally perl lib paths to allow, e.g."
+  echo "  ./setup.sh /opt/myBundle"
+  echo "OR all elements versioned:"
+  echo "  ./setup.sh /opt/cgpPinel-X.X.X /opt/cgpVcf-X.X.X/lib/perl:/opt/PCAP-core-X.X.X/lib/perl"
+  exit 1
 fi
 
-set -e
+INST_PATH=$1
 
-CPU=`grep -c ^processor /proc/cpuinfo`
-if [ $? -eq 0 ]; then
-  if [ "$CPU" -gt "6" ]; then
-    CPU=6
-  fi
-else
-  CPU=1
+if [[ $# -eq 2 ]] ; then
+  CGP_PERLLIBS=$2
 fi
-echo "Max compilation CPUs set to $CPU"
-
-INST_PATH=$1
 
 # get current directory
 INIT_DIR=`pwd`
 
+set -e
+
 # cleanup inst_path
-mkdir -p $INST_PATH
+mkdir -p $INST_PATH/bin
 cd $INST_PATH
 INST_PATH=`pwd`
-mkdir -p $INST_PATH/bin
 cd $INIT_DIR
 
 # make sure that build is self contained
-unset PERL5LIB
-ARCHNAME=`perl -e 'use Config; print $Config{archname};'`
 PERLROOT=$INST_PATH/lib/perl5
-export PERL5LIB="$PERLROOT"
-export PATH="$INST_PATH/biobambam2/bin:$INST_PATH/bin:$PATH"
-
-#create a location to build dependencies
-SETUP_DIR=$INIT_DIR/install_tmp
-mkdir -p $SETUP_DIR
-
-# check for cgpBigWig
-if [ -e "$INST_PATH/bin/detectExtremeDepth" ]; then
-  echo -e "\tcgpBigWig installation found";
-else
-  echo -e "\tERROR: Please see README.md and install cgpBigWig";
-  exit 1
-fi
-
-## grab cpanm and stick in workspace, then do a self upgrade into bin:
-get_file $SETUP_DIR/cpanm https://cpanmin.us/
-perl $SETUP_DIR/cpanm --no-wget -l $INST_PATH App::cpanminus
-CPANM=`which cpanm`
-echo $CPANM
-
-if ! ( perl -MExtUtils::MakeMaker -e 1 >/dev/null 2>&1); then
-    echo
-    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
-
-if [ -e $SETUP_DIR/basePerlDeps.success ]; then
-  echo "Previously installed base perl deps..."
-else
-  perlmods=( "ExtUtils::CBuilder" "Module::Build~0.42" "Const::Fast" "File::Which" "LWP::UserAgent" "Bio::Root::Version~1.006924")
-  for i in "${perlmods[@]}" ; do
-    $CPANM --no-wget --no-interactive --notest --mirror http://cpan.metacpan.org -l $INST_PATH $i
-  done
-  touch $SETUP_DIR/basePerlDeps.success
-fi
-
-
-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 htslib ..."
-if [ -e $SETUP_DIR/htslib.success ]; then
-  echo " previously installed ...";
+# allows user to knowingly specify other PERL5LIB areas.
+if [ -z ${CGP_PERLLIBS+x} ]; then
+  export PERL5LIB="$PERLROOT"
 else
-  echo
-  mkdir -p htslib
-  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 $SETUP_DIR/htslib.success
+  export PERL5LIB="$PERLROOT:$CGP_PERLLIBS"
 fi
 
-export HTSLIB=$INST_PATH
-
-CHK=`perl -le 'eval "require $ARGV[0]" and print $ARGV[0]->VERSION' Bio::DB::HTS`
-if [[ "x$CHK" == "x" ]] ; then
-  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" $SOURCE_BIOBDHTS
-    mkdir -p bioDbHts
-    tar --strip-components 1 -C bioDbHts -zxf bioDbHts.tar.gz
-    cd bioDbHts
-    perl Build.PL --htslib=$HTSLIB --install_base=$INST_PATH
-    ./Build
-    ./Build test
-    ./Build install
-    cd $SETUP_DIR
-    rm -f bioDbHts.tar.gz
-    touch $SETUP_DIR/biohts.success
-  fi
-else
-  echo "Bio::DB::HTS already installed ..."
-fi
-
-cd $INIT_DIR
-
-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
-
-
-cd $SETUP_DIR
-echo -n "Building BWA ..."
-if [ -e $SETUP_DIR/bwa.success ]; then
-  echo " previously installed ..."
-else
-  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
-
-## build BWA-mem2 (tar.gz)
-cd $SETUP_DIR
-echo -n "Building bwa-mem2 ..."
-if [ ! -e $SETUP_DIR/bwa2.success ]; then
-  get_distro "bwa2" $SOURCE_BWAMEM2
-  mkdir -p bwa2
-  tar --strip-components 1 -C bwa2 -jxf bwa2.tar.bz2
-  cp bwa2/bwa-mem2* $INST_PATH/bin/.
-  rm -rf bwa2.* bwa2/*
-  touch $SETUP_DIR/bwa2.success
-fi
-
-echo -n "Building biobambam2 ..."
-if [ -e $SETUP_DIR/biobambam2.success ]; then
-  echo " previously installed ..."
-else
-echo
-  cd $SETUP_DIR
-  get_distro "biobambam2" $SOURCE_BBB_BIN_DIST
-  mkdir -p $INST_PATH/biobambam2
-  tar -m --strip-components 3 -C $INST_PATH/biobambam2 -zxf biobambam2.tar.gz
-  rm -f $INST_PATH/biobambam2/bin/curl # don't let this file in SSL doesn't work
-  rm -f biobambam2.tar.gz
-  touch $SETUP_DIR/biobambam2.success
-fi
-
-cd $INIT_DIR
-
-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
-  if [ -z ${REF_PATH+x} ]; then
-    export REF_CACHE=$INIT_DIR/t/data/ref_cache/%2s/%2s/%s
-    export REF_PATH=$REF_CACHE
-  fi
-  env HTSLIB=$SETUP_DIR/htslib make -C c -j$CPU prefix=$INST_PATH
-  cp bin/bam_stats $INST_PATH/bin/.
-  cp bin/reheadSQ $INST_PATH/bin/.
-  cp bin/diff_bams $INST_PATH/bin/.
-  cp bin/mismatchQc $INST_PATH/bin/.
-  cp bin/mmFlagModifier $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 --no-wget --no-interactive --notest --mirror http://cpan.metacpan.org --notest -l $INST_PATH --installdeps .
-  touch $SETUP_DIR/PCAP_perlPrereq.success
-fi
-
-echo -n "Installing PCAP ..."
-$CPANM --no-wget -v --no-interactive --mirror http://cpan.metacpan.org -l $INST_PATH .
-echo
+export OPT=$INST_PATH
 
-# cleanup all junk
-rm -rf $SETUP_DIR
+bash build/opt-build.sh $INST_PATH
+bash build/opt-build-local.sh $INST_PATH
 
 echo
 echo
 echo "Please add the following to beginning of path:"
-echo "  $INST_PATH/biobambam2/bin:$INST_PATH/bin"
+echo "  $INST_PATH/bin"
 echo "Please add the following to beginning of PERL5LIB:"
 echo "  $PERLROOT"
 echo
diff --git a/t/3_external_progs.t b/t/3_external_progs.t
index e329960..8f53e5b 100644
--- a/t/3_external_progs.t
+++ b/t/3_external_progs.t
@@ -32,9 +32,10 @@ use Data::Dumper;
 use version 0.77;
 
 const my @REQUIRED_PROGRAMS => qw(bamcollate2 bammarkduplicates2 bamsort bwa samtools);
-const my $BIOBAMBAM2_VERSION => '2.0.86';
-const my $BWA_VERSION => '0.7.12';
-const my $SAMTOOLS_VERSION => '1.7';
+# left-pad all subelements to 3 digits
+const my $BIOBAMBAM2_VERSION => '2.000.086'; # 2.0.86
+const my $BWA_VERSION => '0.007.012'; # 0.7.12
+const my $SAMTOOLS_VERSION => '1.010'; # 1.10
 
 # can't put regex in const
 my %EXPECTED_VERSION = (
@@ -89,7 +90,14 @@ subtest 'External programs have expected version' => sub {
     }
 
     my $reg = $details->{'match'};
-    my ($version) = $stream =~ /$reg/m;
+    my $version;
+    # have to fix problem numbering
+    ($version) = $stream =~ /$reg/m;
+    my ($maj, $min, $hot) = split /\./, $version;
+    $version = sprintf '%d.%03d', $maj, $min;
+    if(defined $hot) {
+      $version .= sprintf '.%03d', $hot;
+    }
     version->parse($version);
 
     ok(version->parse($version) >= $details->{'version'}, sprintf 'Expect minimum version of %s for %s, got %s', $details->{'version'}, $prog, $version);