diff --git a/biology/bamtools/Makefile b/biology/bamtools/Makefile index b5757d08a16f..61904dae747a 100644 --- a/biology/bamtools/Makefile +++ b/biology/bamtools/Makefile @@ -1,21 +1,20 @@ PORTNAME= bamtools DISTVERSIONPREFIX= v -DISTVERSION= 2.5.1 -PORTREVISION= 2 +DISTVERSION= 2.5.2 CATEGORIES= biology MAINTAINER= jwb@FreeBSD.org COMMENT= API and toolkit for handling BAM files LICENSE= MIT LIB_DEPENDS+= libjsoncpp.so:devel/jsoncpp USES= cmake USE_LDCONFIG= yes USE_GITHUB= yes GH_ACCOUNT= pezmaster31 CMAKE_ON+= BUILD_SHARED_LIBS .include diff --git a/biology/bamtools/distinfo b/biology/bamtools/distinfo index 070895fe7681..e36197452212 100644 --- a/biology/bamtools/distinfo +++ b/biology/bamtools/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1520126058 -SHA256 (pezmaster31-bamtools-v2.5.1_GH0.tar.gz) = 4abd76cbe1ca89d51abc26bf43a92359e5677f34a8258b901a01f38c897873fc -SIZE (pezmaster31-bamtools-v2.5.1_GH0.tar.gz) = 549750 +TIMESTAMP = 1625529459 +SHA256 (pezmaster31-bamtools-v2.5.2_GH0.tar.gz) = 4d8b84bd07b673d0ed41031348f10ca98dd6fa6a4460f9b9668d6f1d4084dfc8 +SIZE (pezmaster31-bamtools-v2.5.2_GH0.tar.gz) = 245729 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 deleted file mode 100644 index 557e8c55d6ba..000000000000 --- a/biology/bamtools/files/patch-src_api_internal_io_TcpSocketEngine__unix__p.cpp +++ /dev/null @@ -1,11 +0,0 @@ ---- 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 -+ - #ifdef SUN_OS - #include - #endif diff --git a/biology/bamtools/pkg-descr b/biology/bamtools/pkg-descr index 36a70c47131e..b2ed0122cd5a 100644 --- a/biology/bamtools/pkg-descr +++ b/biology/bamtools/pkg-descr @@ -1,4 +1,9 @@ BamTools provides both a programmer's API and an end-user's toolkit for handling BAM files. +BAM is the binary alternative to the sequence alignment/map (SAM) format used +for storing genetic sequence data. It uses BGZF block compression implemented +on top of the standard gzip file format to provide good compression while +allowing efficient random access for indexed queries. + WWW: https://github.com/pezmaster31/bamtools diff --git a/biology/bamtools/pkg-plist b/biology/bamtools/pkg-plist index e1d16b9653e7..a976799fd806 100644 --- a/biology/bamtools/pkg-plist +++ b/biology/bamtools/pkg-plist @@ -1,24 +1,25 @@ 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/api/bamtools_api_export.h include/bamtools/shared/bamtools_global.h lib/libbamtools.so -lib/libbamtools.so.2.5.1 +lib/libbamtools.so.2.5.2 libdata/pkgconfig/bamtools-1.pc