git: 814a894e9012 - main - biology/bamtools: Update to 2.5.2

[Jason W. Bacon]

The branch main has been updated by jwb:

URL: https://cgit.FreeBSD.org/ports/commit/?id=814a894e90121538d402f40d5d1311adb2eda00f

commit 814a894e90121538d402f40d5d1311adb2eda00f
Author:     Jason W. Bacon <jwb at FreeBSD.org>
AuthorDate: 2021-07-06 18:10:54 +0000
Commit:     Jason W. Bacon <jwb at 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 at 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