bamtools: Update to 2.5.3

[Jason W. Bacon (via pkgsrc-wip) <commit-notify%pkgsrc.org@localhost>]

Module Name:	pkgsrc-wip
Committed By:	Jason W. Bacon <bacon4000%gmail.com@localhost>
Pushed By:	outpaddling
Date:		Mon May 19 16:38:53 2025 -0500
Changeset:	1d2a686afc31b7996d3c71069137edf3c1dc396a

Modified Files:
	bamtools/Makefile
	bamtools/PLIST
	bamtools/distinfo
	bamtools/patches/patch-src_api_internal_io_TcpSocketEngine__unix__p.cpp

Log Message:
bamtools: Update to 2.5.3

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=1d2a686afc31b7996d3c71069137edf3c1dc396a

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.

diffstat:
 bamtools/Makefile                                     |  8 +++-----
 bamtools/PLIST                                        |  1 +
 bamtools/distinfo                                     |  8 ++++----
 ...h-src_api_internal_io_TcpSocketEngine__unix__p.cpp | 19 ++++++++++---------
 4 files changed, 18 insertions(+), 18 deletions(-)

diffs:
diff --git a/bamtools/Makefile b/bamtools/Makefile
index a1a79d4354..7d37a61882 100644
--- a/bamtools/Makefile
+++ b/bamtools/Makefile
@@ -1,12 +1,12 @@
 # $NetBSD$
 
-DISTNAME=	bamtools-${PORTVERSION}
+DISTNAME=	bamtools-2.5.3
 CATEGORIES=	biology
 MASTER_SITES=	${MASTER_SITE_GITHUB:=pezmaster31/}
 GITHUB_PROJECT=	bamtools
-GITHUB_TAG=	v${PORTVERSION}
+GITHUB_TAG=	v${PKGVERSION_NOREV}
 
-MAINTAINER=	dsiercks%uwm.edu@localhost
+MAINTAINER=	bacon%NetBSD.org@localhost
 HOMEPAGE=	https://github.com/pezmaster31/bamtools
 COMMENT=	API and toolkit for handling BAM files
 LICENSE=	mit
@@ -17,8 +17,6 @@ CMAKE_CONFIGURE_ARGS+=	-DBUILD_SHARED_LIBS:BOOL=ON
 CMAKE_ARG_PATH=	..
 CONFIGURE_DIRS=	_build
 
-PORTVERSION=	2.5.1
-
 post-extract:
 	${RUN} mkdir -p ${WRKSRC}/_build
 
diff --git a/bamtools/PLIST b/bamtools/PLIST
index 1f9b86c832..4546c128dc 100644
--- a/bamtools/PLIST
+++ b/bamtools/PLIST
@@ -19,6 +19,7 @@ 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.${PKGVERSION}
diff --git a/bamtools/distinfo b/bamtools/distinfo
index 1677f24526..15ffe026d8 100644
--- a/bamtools/distinfo
+++ b/bamtools/distinfo
@@ -1,7 +1,7 @@
 $NetBSD$
 
-RMD160 (bamtools-2.5.1.tar.gz) = 2f4ad157f56c8511463212432d1ec6b1b0a71326
-SHA512 (bamtools-2.5.1.tar.gz) = f2c761c5bf923cf2f3db3dc54e40b4781307106b9177784f930aab619bd11fae3b343f3cfd232524580d39f0526a2a2f18efcf820fe4d9c951406bdb6b953afb
-Size (bamtools-2.5.1.tar.gz) = 549750 bytes
+BLAKE2s (bamtools-2.5.3.tar.gz) = fd0dd4de76283a6f26c45d193282d568cd8e2bd59083ba1117374e4a57d1c0bf
+SHA512 (bamtools-2.5.3.tar.gz) = bde9d98048d9f30d7f3c4e75db97e610ab58148dedadd09a36ad2421a6357b24510abda2451452d1fb9b40e22e1b8fe6f4e4c6ee1c529c426055a050a24b52d8
+Size (bamtools-2.5.3.tar.gz) = 245648 bytes
 SHA1 (patch-src_api_internal_io_HostInfo__p.cpp) = c5d466337e25c4d63a477f509169270c396b6c09
-SHA1 (patch-src_api_internal_io_TcpSocketEngine__unix__p.cpp) = e42fb04c8405587b239ef3bfcdc710d584700151
+SHA1 (patch-src_api_internal_io_TcpSocketEngine__unix__p.cpp) = 6df3fabc4ea9bb87704fd0e84e3639d886598b57
diff --git a/bamtools/patches/patch-src_api_internal_io_TcpSocketEngine__unix__p.cpp b/bamtools/patches/patch-src_api_internal_io_TcpSocketEngine__unix__p.cpp
index 7e3b9a2c13..60a1ccb6b4 100644
--- a/bamtools/patches/patch-src_api_internal_io_TcpSocketEngine__unix__p.cpp
+++ b/bamtools/patches/patch-src_api_internal_io_TcpSocketEngine__unix__p.cpp
@@ -1,13 +1,14 @@
 $NetBSD$
-#add netinit
---- src/api/internal/io/TcpSocketEngine_unix_p.cpp.orig	2018-03-12 15:14:05.061616533 +0000
+
+# Portability
+
+--- src/api/internal/io/TcpSocketEngine_unix_p.cpp.orig	2025-05-19 21:34:43.789320412 +0000
 +++ src/api/internal/io/TcpSocketEngine_unix_p.cpp
-@@ -12,6 +12,8 @@
- using namespace BamTools;
- using namespace BamTools::Internal;
+@@ -7,6 +7,7 @@
+ // Provides low-level implementation of TCP I/O for all UNIX-like systems
+ // ***************************************************************************
  
 +#include <netinet/in.h>
-+
- #ifdef SUN_OS
- #include <sys/filio.h>
- #endif
+ #include "api/internal/io/NetUnix_p.h"
+ #include "api/internal/io/TcpSocketEngine_p.h"
+ using namespace BamTools;