Index: head/biology/ngs-sdk/Makefile
===================================================================
--- head/biology/ngs-sdk/Makefile	(revision 510394)
+++ head/biology/ngs-sdk/Makefile	(revision 510395)
@@ -1,40 +1,40 @@
 # $FreeBSD$
 
 PORTNAME=	ngs
-DISTVERSION=	2.9.6
+DISTVERSION=	2.10.0
 CATEGORIES=	biology
 PKGNAMESUFFIX=	-sdk
 
 MAINTAINER=	yuri@FreeBSD.org
 COMMENT=	Tools and libraries for using data in the INSDC Sequence Read Archives
 
 LICENSE=	PD
 LICENSE_FILE=	${WRKSRC}/LICENSE
 
 BROKEN_aarch64=		fails to configure: unsupported architecture 'FreeBSD'
 NOT_FOR_ARCHS=		powerpc64
 NOT_FOR_ARCHS_REASON=	os-arch.prl needs to be taught about powerpc64
 
 USES=		gmake perl5
 GNU_CONFIGURE=	yes
 USE_GITHUB=	yes
 GH_ACCOUNT=	ncbi
 ALL_TARGET=	default
 USE_LDCONFIG=	yes
 
 CFLAGS+=	-I${WRKSRC}/ngs-sdk/ngs/unix/${ARCH}/
 
 post-patch:
 	@cd ${WRKSRC}/ngs-sdk/ngs/unix && ${LN} -s x86_64 amd64
 
 do-install:
 	cd ${WRKSRC}/ngs-sdk && ${COPYTREE_SHARE} ngs ${STAGEDIR}/${PREFIX}/include
 	${INSTALL_PROGRAM} ${WRKSRC}/ngs-sdk/${ARCH}-portbld-*/ngs-sdk/FreeBSD/clang/${ARCH}/rel/lib/libngs-sdk.so.${DISTVERSION} ${STAGEDIR}${PREFIX}/lib/
 	cd ${STAGEDIR}${PREFIX}/lib/ && \
 		${LN} -s libngs-sdk.so.${DISTVERSION} libngs-sdk.so.${DISTVERSION:R:R} && \
 		${LN} -s libngs-sdk.so.${DISTVERSION:R:R} libngs-sdk.so
 .for l in libngs-c++.a libngs-adapt-c++.a
 	${INSTALL_LIB} ${WRKSRC}/ngs-sdk/${ARCH}-portbld-*/ngs-sdk/FreeBSD/clang/${ARCH}/rel/lib/${l}.${PORTVERSION} ${STAGEDIR}${PREFIX}/lib/${l}
 .endfor
 
 .include <bsd.port.mk>
Index: head/biology/ngs-sdk/distinfo
===================================================================
--- head/biology/ngs-sdk/distinfo	(revision 510394)
+++ head/biology/ngs-sdk/distinfo	(revision 510395)
@@ -1,3 +1,3 @@
-TIMESTAMP = 1554002979
-SHA256 (ncbi-ngs-2.9.6_GH0.tar.gz) = 4be42f4d62b2376dc2fc4cd992822525bd99f8e1193008c2dab387a2f291405b
-SIZE (ncbi-ngs-2.9.6_GH0.tar.gz) = 1092167
+TIMESTAMP = 1567263810
+SHA256 (ncbi-ngs-2.10.0_GH0.tar.gz) = 4139adff83af213d7880bc80d1c0f5ee9b00c6c4e615d00aa47aaa267e40ed25
+SIZE (ncbi-ngs-2.10.0_GH0.tar.gz) = 1093883
Index: head/biology/ngs-sdk/files/patch-ngs-sdk_setup_konfigure.perl
===================================================================
--- head/biology/ngs-sdk/files/patch-ngs-sdk_setup_konfigure.perl	(revision 510394)
+++ head/biology/ngs-sdk/files/patch-ngs-sdk_setup_konfigure.perl	(revision 510395)
@@ -1,72 +1,72 @@
---- ngs-sdk/setup/konfigure.perl.orig	2018-02-23 22:53:52 UTC
+--- ngs-sdk/setup/konfigure.perl.orig	2019-08-20 18:05:02 UTC
 +++ ngs-sdk/setup/konfigure.perl
-@@ -202,7 +202,7 @@ print "checking system type... " unless 
+@@ -202,7 +202,7 @@ print "checking system type... " unless ($AUTORUN);
  my ($OS, $ARCH, $OSTYPE, $MARCH, @ARCHITECTURES) = OsArch();
  println $OSTYPE unless ($AUTORUN);
  
 -unless ($OSTYPE =~ /linux/i || $OSTYPE =~ /darwin/i || $OSTYPE eq 'win') {
 +unless ($OSTYPE =~ /linux/i || $OSTYPE =~ /darwin/i || $OSTYPE eq 'win' || $OSTYPE eq 'FreeBSD') {
      println "configure: error: unsupported system '$OSTYPE'";
      exit 1;
  }
-@@ -215,6 +215,10 @@ if ($OS eq 'linux') {
+@@ -221,6 +221,10 @@ if ($OS eq 'linux') {
      println $OS_DISTRIBUTOR unless ($AUTORUN);
  }
  
 +if ($MARCH eq 'amd64') {
 +    $MARCH = 'x86_64';
 +}
 +
  print "checking machine architecture... " unless ($AUTORUN);
  println $MARCH unless ($AUTORUN);
  unless ($MARCH =~ /x86_64/i || $MARCH =~ /i?86/i) {
-@@ -326,6 +330,16 @@ if ($OSTYPE =~ /linux/i) {
+@@ -332,6 +336,16 @@ if ($OSTYPE =~ /linux/i) {
      $EXEX = '';
      $OSINC = 'unix';
      $TOOLS = 'gcc' unless ($TOOLS);
 +} elsif ($OSTYPE =~ /freebsd/i) {
 +    $BITS = '';
 +    $LPFX = 'lib';
 +    $OBJX = 'o';
 +    $LOBX = 'pic.o';
 +    $LIBX = 'a';
 +    $SHLX = 'so';
 +    $EXEX = '';
 +    $OSINC = 'unix';
 +    $TOOLS = 'clang' unless ($TOOLS);
  } elsif ($OSTYPE =~ /darwin/i) {
      $LPFX = 'lib';
      $OBJX = 'o';
-@@ -371,11 +385,11 @@ if ($TOOLS =~ /gcc$/) {
+@@ -377,11 +391,11 @@ if ($TOOLS =~ /gcc$/) {
  } elsif ($TOOLS eq 'clang') {
      $CPP  = 'clang++' unless ($CPP);
      $CC   = 'clang -c';
--    my $versionMin = '-mmacosx-version-min=10.6';
+-    my $versionMin = '-mmacosx-version-min=10.10';
 +    my $versionMin = '';
      $CP   = "$CPP -c $versionMin";
      if ($BITS ne '32_64') {
          $ARCH_FL = '-arch i386' if ($BITS == 32);
 -        $OPT = '-O3';
 +        $OPT = $ENV{'CXXFLAGS'};
          $AR      = 'ar rc';
          $LD      = "clang $ARCH_FL";
          $LP      = "$CPP $versionMin $ARCH_FL";
-@@ -463,7 +477,7 @@ foreach my $href (DEPENDS()) {
+@@ -478,7 +492,7 @@ foreach my $href (DEPENDS()) {
              $I = $t if (-e $t);
          }
          push ( @L, File::Spec->catdir($OPT{$o}, 'lib') );
 -        push ( @L, File::Spec->catdir($OPT{$o}, 'lib64') );
 +        #push ( @L, File::Spec->catdir($OPT{$o}, 'lib64') );
      }
      my ($i, $l) = find_lib($_, $I, @L);
      if (defined $i || $l) {
-@@ -881,8 +895,7 @@ EndText
+@@ -898,8 +912,7 @@ EndText
      L($F, "PIC     = $PIC") if ($PIC);
      if ($PKG{LNG} eq 'C') {
          if ($TOOLS =~ /clang/i) {
 -   L($F, 'SONAME  = -install_name ' .
 -               '$(INST_LIBDIR)$(BITS)/$(subst $(VERSION),$(MAJVERS),$(@F)) \\');
 +   L($F, 'SONAME = -Wl,-soname=$(subst $(VERSION),$(MAJVERS),$(@F)) \\');
     L($F, '    -compatibility_version $(MAJMIN) -current_version $(VERSION) \\');
     L($F, '    -flat_namespace -undefined suppress');
          } else {
Index: head/biology/ngs-sdk/pkg-plist
===================================================================
--- head/biology/ngs-sdk/pkg-plist	(revision 510394)
+++ head/biology/ngs-sdk/pkg-plist	(revision 510395)
@@ -1,95 +1,95 @@
 include/ngs/Alignment.hpp
 include/ngs/AlignmentIterator.hpp
 include/ngs/ErrorMsg.hpp
 include/ngs/Fragment.hpp
 include/ngs/FragmentIterator.hpp
 include/ngs/Package.hpp
 include/ngs/Pileup.hpp
 include/ngs/PileupEvent.hpp
 include/ngs/PileupEventIterator.hpp
 include/ngs/PileupIterator.hpp
 include/ngs/Read.hpp
 include/ngs/ReadCollection.hpp
 include/ngs/ReadGroup.hpp
 include/ngs/ReadGroupIterator.hpp
 include/ngs/ReadIterator.hpp
 include/ngs/Reference.hpp
 include/ngs/ReferenceIterator.hpp
 include/ngs/ReferenceSequence.hpp
 include/ngs/Statistics.hpp
 include/ngs/StringRef.hpp
 include/ngs/adapter/AlignmentItf.hpp
 include/ngs/adapter/ErrorMsg.hpp
 include/ngs/adapter/FragmentItf.hpp
 include/ngs/adapter/PileupEventItf.hpp
 include/ngs/adapter/PileupItf.hpp
 include/ngs/adapter/ReadCollectionItf.hpp
 include/ngs/adapter/ReadGroupItf.hpp
 include/ngs/adapter/ReadItf.hpp
 include/ngs/adapter/Refcount.hpp
 include/ngs/adapter/ReferenceItf.hpp
 include/ngs/adapter/ReferenceSequenceItf.hpp
 include/ngs/adapter/StatisticsItf.hpp
 include/ngs/adapter/StringItf.hpp
 include/ngs/adapter/defs.h
 include/ngs/inl/Alignment.hpp
 include/ngs/inl/AlignmentIterator.hpp
 include/ngs/inl/Fragment.hpp
 include/ngs/inl/FragmentIterator.hpp
 include/ngs/inl/Package.hpp
 include/ngs/inl/Pileup.hpp
 include/ngs/inl/PileupEvent.hpp
 include/ngs/inl/PileupEventIterator.hpp
 include/ngs/inl/PileupIterator.hpp
 include/ngs/inl/Read.hpp
 include/ngs/inl/ReadCollection.hpp
 include/ngs/inl/ReadGroup.hpp
 include/ngs/inl/ReadGroupIterator.hpp
 include/ngs/inl/ReadIterator.hpp
 include/ngs/inl/Reference.hpp
 include/ngs/inl/ReferenceIterator.hpp
 include/ngs/inl/ReferenceSequence.hpp
 include/ngs/inl/Statistics.hpp
 include/ngs/inl/StringRef.hpp
 include/ngs/itf/AlignmentItf.h
 include/ngs/itf/AlignmentItf.hpp
 include/ngs/itf/ErrBlock.h
 include/ngs/itf/ErrBlock.hpp
 include/ngs/itf/ErrorMsg.hpp
 include/ngs/itf/FragmentItf.h
 include/ngs/itf/FragmentItf.hpp
 include/ngs/itf/PackageItf.hpp
 include/ngs/itf/PileupEventItf.h
 include/ngs/itf/PileupEventItf.hpp
 include/ngs/itf/PileupItf.h
 include/ngs/itf/PileupItf.hpp
 include/ngs/itf/ReadCollectionItf.h
 include/ngs/itf/ReadCollectionItf.hpp
 include/ngs/itf/ReadGroupItf.h
 include/ngs/itf/ReadGroupItf.hpp
 include/ngs/itf/ReadItf.h
 include/ngs/itf/ReadItf.hpp
 include/ngs/itf/Refcount.h
 include/ngs/itf/Refcount.hpp
 include/ngs/itf/ReferenceItf.h
 include/ngs/itf/ReferenceItf.hpp
 include/ngs/itf/ReferenceSequenceItf.h
 include/ngs/itf/ReferenceSequenceItf.hpp
 include/ngs/itf/StatisticsItf.h
 include/ngs/itf/StatisticsItf.hpp
 include/ngs/itf/StringItf.h
 include/ngs/itf/StringItf.hpp
 include/ngs/itf/VTable.h
 include/ngs/itf/VTable.hpp
 include/ngs/itf/defs.h
 include/ngs/unix/amd64
 include/ngs/unix/fat86/atomic32.h
 include/ngs/unix/i386/atomic32.h
 include/ngs/unix/x86_64/atomic32.h
 include/ngs/win/atomic32.h
 include/ngs/win/stdbool.h
 lib/libngs-adapt-c++.a
 lib/libngs-c++.a
 lib/libngs-sdk.so
 lib/libngs-sdk.so.2
-lib/libngs-sdk.so.2.9.6
+lib/libngs-sdk.so.2.10.0