Date: Wed, 28 Mar 2018 13:26:31 +0000 (UTC) From: "Jason W. Bacon" <jwb@FreeBSD.org> To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r465808 - in head/biology: . bamtools bamtools/files Message-ID: <201803281326.w2SDQVl6065909@repo.freebsd.org>
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Author: jwb Date: Wed Mar 28 13:26:31 2018 New Revision: 465808 URL: https://svnweb.freebsd.org/changeset/ports/465808 Log: biology/bamtools: API and toolkit for handling BAM files Approved by: jrm Differential Revision: https://reviews.freebsd.org/D14877 Added: head/biology/bamtools/ head/biology/bamtools/Makefile (contents, props changed) head/biology/bamtools/distinfo (contents, props changed) head/biology/bamtools/files/ head/biology/bamtools/files/patch-src_api_internal_io_HostInfo__p.cpp (contents, props changed) head/biology/bamtools/files/patch-src_api_internal_io_TcpSocketEngine__unix__p.cpp (contents, props changed) head/biology/bamtools/pkg-descr (contents, props changed) head/biology/bamtools/pkg-plist (contents, props changed) Modified: head/biology/Makefile Modified: head/biology/Makefile ============================================================================== --- head/biology/Makefile Wed Mar 28 13:26:15 2018 (r465807) +++ head/biology/Makefile Wed Mar 28 13:26:31 2018 (r465808) @@ -7,6 +7,7 @@ SUBDIR += artemis SUBDIR += avida SUBDIR += babel + SUBDIR += bamtools SUBDIR += bcftools SUBDIR += bedtools SUBDIR += biococoa Added: head/biology/bamtools/Makefile ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/bamtools/Makefile Wed Mar 28 13:26:31 2018 (r465808) @@ -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> Added: head/biology/bamtools/distinfo ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/bamtools/distinfo Wed Mar 28 13:26:31 2018 (r465808) @@ -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 Added: head/biology/bamtools/files/patch-src_api_internal_io_HostInfo__p.cpp ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/bamtools/files/patch-src_api_internal_io_HostInfo__p.cpp Wed Mar 28 13:26:31 2018 (r465808) @@ -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" Added: head/biology/bamtools/files/patch-src_api_internal_io_TcpSocketEngine__unix__p.cpp ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/bamtools/files/patch-src_api_internal_io_TcpSocketEngine__unix__p.cpp Wed Mar 28 13:26:31 2018 (r465808) @@ -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 Added: head/biology/bamtools/pkg-descr ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/bamtools/pkg-descr Wed Mar 28 13:26:31 2018 (r465808) @@ -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 Added: head/biology/bamtools/pkg-plist ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/bamtools/pkg-plist Wed Mar 28 13:26:31 2018 (r465808) @@ -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
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