Date: Tue, 6 Jul 2021 18:12:59 GMT From: "Jason W. Bacon" <jwb@FreeBSD.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org Subject: git: 814a894e9012 - main - biology/bamtools: Update to 2.5.2 Message-ID: <202107061812.166ICxGF079553@gitrepo.freebsd.org>
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The branch main has been updated by jwb: URL: https://cgit.FreeBSD.org/ports/commit/?id=814a894e90121538d402f40d5d1311adb2eda00f commit 814a894e90121538d402f40d5d1311adb2eda00f Author: Jason W. Bacon <jwb@FreeBSD.org> AuthorDate: 2021-07-06 18:10:54 +0000 Commit: Jason W. Bacon <jwb@FreeBSD.org> CommitDate: 2021-07-06 18:10:54 +0000 biology/bamtools: Update to 2.5.2 Code clean up Changes: https://github.com/pezmaster31/bamtools/releases/tag/v2.5.2 Reported by: portscout --- biology/bamtools/Makefile | 3 +-- biology/bamtools/distinfo | 6 +++--- .../patch-src_api_internal_io_TcpSocketEngine__unix__p.cpp | 11 ----------- biology/bamtools/pkg-descr | 5 +++++ biology/bamtools/pkg-plist | 3 ++- 5 files changed, 11 insertions(+), 17 deletions(-) diff --git a/biology/bamtools/Makefile b/biology/bamtools/Makefile index b5757d08a16f..61904dae747a 100644 --- a/biology/bamtools/Makefile +++ b/biology/bamtools/Makefile @@ -1,7 +1,6 @@ PORTNAME= bamtools DISTVERSIONPREFIX= v -DISTVERSION= 2.5.1 -PORTREVISION= 2 +DISTVERSION= 2.5.2 CATEGORIES= biology MAINTAINER= jwb@FreeBSD.org 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 <netinet/in.h> -+ - #ifdef SUN_OS - #include <sys/filio.h> - #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 @@ -18,7 +18,8 @@ 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
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