<pre style='margin:0'>
Chih-Hsuan Yen (yan12125) pushed a commit to branch master
in repository macports-ports.
</pre>
<p><a href="https://github.com/macports/macports-ports/commit/57c818ec3aed5fda1be3cdbc0d2a472b3684c65b">https://github.com/macports/macports-ports/commit/57c818ec3aed5fda1be3cdbc0d2a472b3684c65b</a></p>
<pre style="white-space: pre; background: #F8F8F8">The following commit(s) were added to refs/heads/master by this push:
<span style='display:block; white-space:pre;color:#404040;'> new 57c818e bedtools: update to 2.28.0 (and remove universal variant)
</span>57c818e is described below
<span style='display:block; white-space:pre;color:#808000;'>commit 57c818ec3aed5fda1be3cdbc0d2a472b3684c65b
</span>Author: Arjan van der Velde <vandervelde.ag@gmail.com>
AuthorDate: Tue Mar 26 14:22:17 2019 -0400
<span style='display:block; white-space:pre;color:#404040;'> bedtools: update to 2.28.0 (and remove universal variant)
</span>---
science/bedtools/Portfile | 23 ++++++++---------
science/bedtools/files/patch-docs-conf.py.diff | 30 ----------------------
...rc-utils-BamTools-include-BamAlignment.hpp.diff | 12 +++++++++
...h-src-utils-BamTools-include-SamHeader.hpp.diff | 12 +++++++++
4 files changed, 35 insertions(+), 42 deletions(-)
<span style='display:block; white-space:pre;color:#808080;'>diff --git a/science/bedtools/Portfile b/science/bedtools/Portfile
</span><span style='display:block; white-space:pre;color:#808080;'>index 087469f..aaf3367 100644
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>--- a/science/bedtools/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>+++ b/science/bedtools/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -2,8 +2,9 @@
</span>
PortSystem 1.0
PortGroup github 1.0
<span style='display:block; white-space:pre;background:#e0ffe0;'>+PortGroup cxx11 1.1
</span>
<span style='display:block; white-space:pre;background:#ffe0e0;'>-github.setup arq5x bedtools2 2.27.1 v
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+github.setup arq5x bedtools2 2.28.0 v
</span>
name bedtools
categories science
<span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -18,25 +19,23 @@ long_description The BEDTools utilities allow one to address common genomics
</span> The utilities are largely based on four widely-used file formats: \
BED, GFF/GTF, VCF, and SAM/BAM.
<span style='display:block; white-space:pre;background:#ffe0e0;'>-checksums rmd160 2a0fc10ce07f6228ee006e297577560bc24e35af \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- sha256 eb7028247d0e4732f113076fdbd580b8601365f7830cf19649d4d3116af08dfd
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+checksums rmd160 0807fc84acd6d80f646ee387943ff6345203396a \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ sha256 511d8623038836ac8d1f9e260016867494b9040de65d0f0f1eb7feac7b698bbd \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ size 20565042
</span>
depends_build port:py27-sphinx
<span style='display:block; white-space:pre;background:#ffe0e0;'>-depends_lib port:zlib
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+depends_lib-append port:zlib port:lzma
</span>
use_configure no
<span style='display:block; white-space:pre;background:#ffe0e0;'>-patchfiles patch-docs-conf.py.diff
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+build.args-append CC=${configure.cc} \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ CXX=${configure.cxx}
</span>
<span style='display:block; white-space:pre;background:#ffe0e0;'>-variant universal {}
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+use_parallel_build yes
</span>
<span style='display:block; white-space:pre;background:#ffe0e0;'>-configure.optflags -O2
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-configure.cxxflags-append -Wall -D_FILE_OFFSET_BITS=64 -fPIC
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-build.args CXX=${configure.cxx} \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- CXXFLAGS="${configure.cxxflags} [get_canonical_archflags cxx]"
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-use_parallel_build no
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+patchfiles patch-src-utils-BamTools-include-BamAlignment.hpp.diff \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ patch-src-utils-BamTools-include-SamHeader.hpp.diff
</span>
post-build {
system -W ${worksrcpath}/docs "${build.cmd} SPHINXBUILD=${prefix}/bin/sphinx-build-2.7 html man"
<span style='display:block; white-space:pre;color:#808080;'>diff --git a/science/bedtools/files/patch-docs-conf.py.diff b/science/bedtools/files/patch-docs-conf.py.diff
</span>deleted file mode 100644
<span style='display:block; white-space:pre;color:#808080;'>index c956dad..0000000
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>--- a/science/bedtools/files/patch-docs-conf.py.diff
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>+++ /dev/null
</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -1,30 +0,0 @@
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>---- docs/conf.py.orig 2017-09-06 19:16:13.000000000 -0400
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+++ docs/conf.py 2017-09-05 16:54:48.000000000 -0400
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-@@ -26,7 +26,7 @@
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- # coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- extensions = ['sphinx.ext.autodoc', 'sphinx.ext.doctest',
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- 'sphinx.ext.intersphinx', 'sphinx.ext.todo',
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- 'sphinx.ext.coverage', 'sphinx.ext.pngmath',
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ 'sphinx.ext.coverage',
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- 'sphinx.ext.ifconfig', 'sphinx.ext.viewcode',
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- 'matplotlib.sphinxext.plot_directive']
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-@@ -225,7 +225,7 @@
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- # Example configuration for intersphinx: refer to the Python standard library.
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- intersphinx_mapping = {'bedtools': ('http://bedtools.readthedocs.org/en/latest/', None)}
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>--class Mock(object):
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+class Mock(list):
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- def __init__(self, *args, **kwargs):
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- pass
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-@@ -241,6 +241,9 @@
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- else:
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- return Mock()
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ def setup(self, *args, **kargs):
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ pass
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- MOCK_MODULES = ['numpy', 'matplotlib', 'matplotlib.pyplot',
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- 'matplotlib.sphinxext', 'matplotlib.sphinxext.plot_directive']
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- for mod_name in MOCK_MODULES:
</span><span style='display:block; white-space:pre;color:#808080;'>diff --git a/science/bedtools/files/patch-src-utils-BamTools-include-BamAlignment.hpp.diff b/science/bedtools/files/patch-src-utils-BamTools-include-BamAlignment.hpp.diff
</span>new file mode 100644
<span style='display:block; white-space:pre;color:#808080;'>index 0000000..4190f37
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>--- /dev/null
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>+++ b/science/bedtools/files/patch-src-utils-BamTools-include-BamAlignment.hpp.diff
</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -0,0 +1,12 @@
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+diff --git src/utils/BamTools/include/BamAlignment.hpp src/utils/BamTools/include/BamAlignment.hpp
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+index f7da717d..db01a2f4 100644
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+--- src/utils/BamTools/include/BamAlignment.hpp
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++++ src/utils/BamTools/include/BamAlignment.hpp
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+@@ -3,6 +3,7 @@
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ #include <stdint.h>
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ #include <memory>
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ #include <cstring>
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++#include <stdlib.h>
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ namespace BamTools {
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ const static char cigar_ops_as_chars[] = { 'M', 'I', 'D', 'N', 'S', 'H', 'P', '=', 'X', 'B' };
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ static inline std::string _mkstr(const uint8_t* what) { return std::string((const char*)what + 1); }
</span><span style='display:block; white-space:pre;color:#808080;'>diff --git a/science/bedtools/files/patch-src-utils-BamTools-include-SamHeader.hpp.diff b/science/bedtools/files/patch-src-utils-BamTools-include-SamHeader.hpp.diff
</span>new file mode 100644
<span style='display:block; white-space:pre;color:#808080;'>index 0000000..cd2dacf
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>--- /dev/null
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>+++ b/science/bedtools/files/patch-src-utils-BamTools-include-SamHeader.hpp.diff
</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -0,0 +1,12 @@
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+diff --git src/utils/BamTools/include/SamHeader.hpp src/utils/BamTools/include/SamHeader.hpp
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+index 1024370e..06d22be6 100644
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+--- src/utils/BamTools/include/SamHeader.hpp
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++++ src/utils/BamTools/include/SamHeader.hpp
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+@@ -6,6 +6,7 @@
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ #include <vector>
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ #include <string.h>
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ #include <api/BamAux.h>
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++#include <stdlib.h>
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ namespace BamTools {
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ typedef std::vector<RefData> RefVector;
</span></pre><pre style='margin:0'>
</pre>