bedtools: samtools isn't really necessary

[Jason Bacon <bacon%NetBSD.org@localhost>]

Module Name:	pkgsrc-wip
Committed By:	Jason Bacon <bacon%NetBSD.org@localhost>
Pushed By:	outpaddling
Date:		Sun Jan 24 14:00:08 2021 -0600
Changeset:	5c4a16b8f4430b4bf4d418921e31ee14bddc4738

Modified Files:
	bedtools/Makefile
	bedtools/distinfo
Added Files:
	bedtools/patches/patch-src_utils_BamTools_include_SamHeader.hpp

Log Message:
bedtools: samtools isn't really necessary

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=5c4a16b8f4430b4bf4d418921e31ee14bddc4738

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

diffstat:
 bedtools/Makefile                                  |  2 --
 bedtools/distinfo                                  |  1 +
 .../patch-src_utils_BamTools_include_SamHeader.hpp | 27 ++++++++++++++++++++++
 3 files changed, 28 insertions(+), 2 deletions(-)

diffs:
diff --git a/bedtools/Makefile b/bedtools/Makefile
index 439a5d5958..1904da9748 100644
--- a/bedtools/Makefile
+++ b/bedtools/Makefile
@@ -11,8 +11,6 @@ HOMEPAGE=	https://bedtools.readthedocs.io/en/latest/
 COMMENT=	Swiss army knife for genome arithmetic
 LICENSE=	mit
 
-DEPENDS=	samtools>0:../../biology/samtools
-
 USE_LANGUAGES=	c c++
 USE_TOOLS+=	gmake
 REPLACE_SH+=	scripts/vcfsort.sh
diff --git a/bedtools/distinfo b/bedtools/distinfo
index 9ba694c9cc..1c7a14939b 100644
--- a/bedtools/distinfo
+++ b/bedtools/distinfo
@@ -5,4 +5,5 @@ RMD160 (bedtools-2.30.0.tar.gz) = 1cc30e5bc3df12f38d8f1e055ff2f939d7608395
 SHA512 (bedtools-2.30.0.tar.gz) = 3d69d6a53d3e5d15597dfefa26f7895231adbf3c1fe3b16ee4213e497ef01a20698add2f0e6f03d8eb7cd7c70709955f0ebdf897a025a83d31ef17e2c91f9856
 Size (bedtools-2.30.0.tar.gz) = 20639858 bytes
 SHA1 (patch-Makefile) = d6a76cb23e623842d6d5c60d67eff928b45b091c
+SHA1 (patch-src_utils_BamTools_include_SamHeader.hpp) = 7ab168b247b5edf7f3eccd9ef7329a5e1605c787
 SHA1 (patch-src_utils_htslib_Makefile) = ba513efa59eed05321c176185fb576f4892ea7a5
diff --git a/bedtools/patches/patch-src_utils_BamTools_include_SamHeader.hpp b/bedtools/patches/patch-src_utils_BamTools_include_SamHeader.hpp
new file mode 100644
index 0000000000..9e3641a3aa
--- /dev/null
+++ b/bedtools/patches/patch-src_utils_BamTools_include_SamHeader.hpp
@@ -0,0 +1,27 @@
+$NetBSD$
+
+# Silence compiler warnings
+
+--- src/utils/BamTools/include/SamHeader.hpp.orig	2021-01-24 16:15:06 UTC
++++ src/utils/BamTools/include/SamHeader.hpp
+@@ -7,6 +7,7 @@
+ #include <string.h>
+ #include <api/BamAux.h>
+ #include <stdlib.h>
++#include <sysexits.h>
+ 
+ 
+ #ifdef WITH_HTS_CB_API
+@@ -29,7 +30,11 @@ namespace htslib_future {
+ 		ops.cb_data = buffer;
+ 		samFile* fp = hts_open_callback(NULL, &ops, "w");
+ 
+-		sam_hdr_write(fp, hdr);
++		if ( sam_hdr_write(fp, hdr) != 0 )
++		{
++			fputs("sam_hdr_rebuild: Error: sam_hdr_write() failed.\n", stderr);
++			exit(EX_IOERR);
++		}
+ 
+ 		hts_close(fp);
+