This would do a full switch to bwa-mem2, probably want it to be optio…

…nal, but default

bin/bwa_mem.pl

@@ -125,7 +125,7 @@ sub setup {
     exit 0;
   }
 
-  my $version = PCAP::Bwa::bwa_version();
+  my $version = PCAP::Bwa::bwamem2_version();
   die "bwa mem can only be used with bwa version 0.7+, the version found in path is: $version\n" unless(version->parse($version) >= version->parse('0.7.0'));
 
   # then check for no args:

build/opt-build.sh

@@ -107,6 +107,16 @@ if [ ! -e $SETUP_DIR/bwa.success ]; then
   touch $SETUP_DIR/bwa.success
 fi
 
+## build BWA-mem2 (tar.gz)
+if [ ! -e $SETUP_DIR/bwa2.success ]; then
+  curl -sSL https://github.com/bwa-mem2/bwa-mem2/releases/download/v2.0pre2/bwa-mem2-2.0pre2_x64-linux.tar.bz2 > distro.tar.bz2
+  rm -rf distro/*
+  tar --strip-components 1 -C distro -jxf distro.tar.bz2
+  cp distro/bwa-mem2* $INST_PATH/bin/.
+  rm -rf distro.* distro/*
+  touch $SETUP_DIR/bwa2.success
+fi
+
 ## Bio::DB::HTS (tar.gz)
 if [ ! -e $SETUP_DIR/Bio-DB-HTS.success ]; then
   ## add perl deps

lib/PCAP/Bwa.pm

@@ -56,6 +56,17 @@ sub bwa_mem_max_cores {
   return $BWA_MEM_MAX_CORES;
 }
 
+sub bwamem2_version {
+  my $bwa = _which('bwa-mem2');
+  my $version;
+  {
+    my ($stdout, $stderr, $exit) = capture{ system("$bwa version"); };
+    chomp $stdout;
+    ($version) = $stdout =~ /([[:digit:]\.]+)/m;
+  }
+  return $version;
+}
+
 sub bwa_version {
   my $bwa = _which('bwa');
   my $version;
@@ -279,7 +290,8 @@ sub bwa_mem {
     if(exists $options->{'bwa_pl'}) {
       $bwa .= 'LD_PRELOAD='.$options->{'bwa_pl'}.' ';
     }
-    $bwa .= _which('bwa') || die "Unable to find 'bwa' in path";
+    # may want to test for chipset abilities
+    $bwa .= _which('bwa-mem2') || die "Unable to find 'bwa-mem2' in path";
 
     $ENV{SHELL} = '/bin/bash'; # ensure bash to allow pipefail
     my $command = 'set -o pipefail; ';

t/pcapBwa.t

@@ -32,6 +32,7 @@ subtest 'Initialisation checks' => sub {
 
 subtest 'Non object checks' => sub {
   ok(PCAP::Bwa::bwa_version(), 'Version returned for BWA');
+  ok(PCAP::Bwa::bwamem2_version(), 'Version returned for bwa-mem2');
 };
 
 done_testing();