biology/bamtools: API and toolkit for handling BAM files

Approved by:    jrm
Differential Revision:  https://reviews.freebsd.org/D14877

7 files changed, 76 insertions, 0 deletions

diff --git a/biology/Makefile b/biology/Makefile
index 8fdd4c1311b0..53733c94937b 100644
--- a/biology/Makefile
+++ b/biology/Makefile
@@ -7,6 +7,7 @@
     SUBDIR += artemis
     SUBDIR += avida
     SUBDIR += babel
+    SUBDIR += bamtools
     SUBDIR += bcftools
     SUBDIR += bedtools
     SUBDIR += biococoa
diff --git a/biology/bamtools/Makefile b/biology/bamtools/Makefile
new file mode 100644
index 000000000000..02f454bb79b2
--- /dev/null
+++ b/biology/bamtools/Makefile
@@ -0,0 +1,22 @@
+# $FreeBSD$
+
+PORTNAME=	bamtools
+DISTVERSIONPREFIX=	v
+DISTVERSION=	2.5.1
+CATEGORIES=	biology
+
+MAINTAINER=	jwb@FreeBSD.org
+COMMENT=	API and toolkit for handling BAM files
+
+LICENSE=	MIT
+
+LIB_DEPENDS+=	libjsoncpp.so:devel/jsoncpp
+
+USES=		cmake:outsource
+USE_LDCONFIG=	yes
+USE_GITHUB=	yes
+GH_ACCOUNT=	pezmaster31
+
+CMAKE_ON+=	BUILD_SHARED_LIBS
+
+.include <bsd.port.mk>
diff --git a/biology/bamtools/distinfo b/biology/bamtools/distinfo
new file mode 100644
index 000000000000..070895fe7681
--- /dev/null
+++ b/biology/bamtools/distinfo
@@ -0,0 +1,3 @@
+TIMESTAMP = 1520126058
+SHA256 (pezmaster31-bamtools-v2.5.1_GH0.tar.gz) = 4abd76cbe1ca89d51abc26bf43a92359e5677f34a8258b901a01f38c897873fc
+SIZE (pezmaster31-bamtools-v2.5.1_GH0.tar.gz) = 549750
diff --git a/biology/bamtools/files/patch-src_api_internal_io_HostInfo__p.cpp b/biology/bamtools/files/patch-src_api_internal_io_HostInfo__p.cpp
new file mode 100644
index 000000000000..e38d728f8f7e
--- /dev/null
+++ b/biology/bamtools/files/patch-src_api_internal_io_HostInfo__p.cpp
@@ -0,0 +1,11 @@
+--- src/api/internal/io/HostInfo_p.cpp.orig	2015-06-16 16:50:53 UTC
++++ src/api/internal/io/HostInfo_p.cpp
+@@ -11,6 +11,8 @@
+ using namespace BamTools;
+ using namespace BamTools::Internal;
+ 
++#include <netinet/in.h>
++
+ // platorm-specifics
+ #ifdef _WIN32
+ #  include "api/internal/io/NetWin_p.h"
diff --git a/biology/bamtools/files/patch-src_api_internal_io_TcpSocketEngine__unix__p.cpp b/biology/bamtools/files/patch-src_api_internal_io_TcpSocketEngine__unix__p.cpp
new file mode 100644
index 000000000000..557e8c55d6ba
--- /dev/null
+++ b/biology/bamtools/files/patch-src_api_internal_io_TcpSocketEngine__unix__p.cpp
@@ -0,0 +1,11 @@
+--- src/api/internal/io/TcpSocketEngine_unix_p.cpp.orig	2015-06-16 16:50:53 UTC
++++ src/api/internal/io/TcpSocketEngine_unix_p.cpp
+@@ -12,6 +12,8 @@
+ using namespace BamTools;
+ using namespace BamTools::Internal;
+ 
++#include <netinet/in.h>
++
+ #ifdef SUN_OS
+ #include <sys/filio.h> 
+ #endif
diff --git a/biology/bamtools/pkg-descr b/biology/bamtools/pkg-descr
new file mode 100644
index 000000000000..36a70c47131e
--- /dev/null
+++ b/biology/bamtools/pkg-descr
@@ -0,0 +1,4 @@
+BamTools provides both a programmer's API and an end-user's toolkit for
+handling BAM files.
+
+WWW: https://github.com/pezmaster31/bamtools
diff --git a/biology/bamtools/pkg-plist b/biology/bamtools/pkg-plist
new file mode 100644
index 000000000000..e1d16b9653e7
--- /dev/null
+++ b/biology/bamtools/pkg-plist
@@ -0,0 +1,24 @@
+bin/bamtools
+include/bamtools/api/BamAlgorithms.h
+include/bamtools/api/BamAlignment.h
+include/bamtools/api/BamAux.h
+include/bamtools/api/BamConstants.h
+include/bamtools/api/BamIndex.h
+include/bamtools/api/BamMultiReader.h
+include/bamtools/api/BamReader.h
+include/bamtools/api/BamWriter.h
+include/bamtools/api/IBamIODevice.h
+include/bamtools/api/SamConstants.h
+include/bamtools/api/SamHeader.h
+include/bamtools/api/SamProgram.h
+include/bamtools/api/SamProgramChain.h
+include/bamtools/api/SamReadGroup.h
+include/bamtools/api/SamReadGroupDictionary.h
+include/bamtools/api/SamSequence.h
+include/bamtools/api/SamSequenceDictionary.h
+include/bamtools/api/algorithms/Sort.h
+include/bamtools/api/api_global.h
+include/bamtools/shared/bamtools_global.h
+lib/libbamtools.so
+lib/libbamtools.so.2.5.1
+libdata/pkgconfig/bamtools-1.pc