<pre style='margin:0'>
Zero King (l2dy) pushed a commit to branch master
in repository macports-ports.
</pre>
<p><a href="https://github.com/macports/macports-ports/commit/dccf3d9417ee833fe0a72d9f109288b51c3a251d">https://github.com/macports/macports-ports/commit/dccf3d9417ee833fe0a72d9f109288b51c3a251d</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 dccf3d9 bedtools: update to v2.27.0
</span>dccf3d9 is described below
<span style='display:block; white-space:pre;color:#808000;'>commit dccf3d9417ee833fe0a72d9f109288b51c3a251d
</span>Author: Arjan van der Velde <vandervelde.ag@gmail.com>
AuthorDate: Tue Dec 12 18:06:55 2017 -0500
<span style='display:block; white-space:pre;color:#404040;'> bedtools: update to v2.27.0
</span><span style='display:block; white-space:pre;color:#404040;'>
</span><span style='display:block; white-space:pre;color:#404040;'> This update bedtools from v2.26.0 to v2.27.0 and also fixes issue
</span><span style='display:block; white-space:pre;color:#404040;'> https://github.com/arq5x/bedtools2/issues/594, a performance issue that
</span><span style='display:block; white-space:pre;color:#404040;'> was introduced by regression in v2.27.0 but fixed in the next commit.
</span>---
science/bedtools/Portfile | 9 ++-
science/bedtools/files/patch-Makefile.diff | 32 +++++++++++
...ls-FileRecordTools-Records-StrandQueue.cpp.diff | 67 ----------------------
...tils-FileRecordTools-Records-StrandQueue.h.diff | 35 -----------
4 files changed, 36 insertions(+), 107 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 a60717d..1a01edc 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;'>@@ -3,7 +3,7 @@
</span> PortSystem 1.0
PortGroup github 1.0
<span style='display:block; white-space:pre;background:#ffe0e0;'>-github.setup arq5x bedtools2 2.26.0 v
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+github.setup arq5x bedtools2 2.27.0 v
</span>
name bedtools
categories science
<span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -18,8 +18,8 @@ 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 880f6c0711f500f24a5f0161ef209c739c3cc735 \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- sha256 ed9e9305ed88838125de53abee0b65ef5decbd75beeeb3adb0cb656b87a965b2
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+checksums rmd160 7ad91cda54b8cc0ea3f0694bb0dbdf2276ae13e5 \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ sha256 b2ee7cd29983dad1665e60d194b5d6920ca5785cb1021692487ed1823b7491dc
</span>
depends_build port:py27-sphinx
<span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -28,8 +28,7 @@ depends_lib port:zlib
</span> use_configure no
patchfiles patch-docs-conf.py.diff \
<span style='display:block; white-space:pre;background:#ffe0e0;'>- patch-src-utils-FileRecordTools-Records-StrandQueue.cpp.diff \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- patch-src-utils-FileRecordTools-Records-StrandQueue.h.diff
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ patch-Makefile.diff
</span>
variant universal {}
<span style='display:block; white-space:pre;color:#808080;'>diff --git a/science/bedtools/files/patch-Makefile.diff b/science/bedtools/files/patch-Makefile.diff
</span>new file mode 100644
<span style='display:block; white-space:pre;color:#808080;'>index 0000000..ecf508b
</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-Makefile.diff
</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -0,0 +1,32 @@
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+--- Makefile.orig 2017-12-06 12:22:40.000000000 -0500
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++++ Makefile 2017-12-12 17:50:11.000000000 -0500
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+@@ -16,7 +16,7 @@
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ export BIN_DIR = bin
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ export SRC_DIR = src
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ export UTIL_DIR = src/utils
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-export CXX ?= g++
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++export CXX = g++
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ ifeq ($(DEBUG),1)
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ export CXXFLAGS = -Wall -Wextra -DDEBUG -D_DEBUG -g -O0 -D_FILE_OFFSET_BITS=64 -fPIC $(INCLUDES)
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ else
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+@@ -25,10 +25,9 @@
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ # If the user has specified to do so, tell the compile to use rand() (instead of mt19937).
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ ifeq ($(USE_RAND),1)
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-export CXXFLAGS = -DUSE_RAND
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++export CXXFLAGS += -DUSE_RAND
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ else
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-# Although we really want c++11, g++ 4.6.3 (as used by Travis) uses 'gnu++0x'
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-export CXXFLAGS = -std=gnu++0x
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++export CXXFLAGS += -std=c++11
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ endif
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ export LIBS = -lz
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+@@ -165,6 +164,7 @@
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ print_banner:
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ @echo "Building BEDTools:"
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ @echo "========================================================="
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++ $(info $$CXXFLAGS is [${CXXFLAGS}])
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ .PHONY: print_banner
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ # make the "obj/" and "bin/" directories, if they don't exist
</span><span style='display:block; white-space:pre;color:#808080;'>diff --git a/science/bedtools/files/patch-src-utils-FileRecordTools-Records-StrandQueue.cpp.diff b/science/bedtools/files/patch-src-utils-FileRecordTools-Records-StrandQueue.cpp.diff
</span>deleted file mode 100644
<span style='display:block; white-space:pre;color:#808080;'>index 9caecf6..0000000
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>--- a/science/bedtools/files/patch-src-utils-FileRecordTools-Records-StrandQueue.cpp.diff
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>+++ /dev/null
</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -1,67 +0,0 @@
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>---- src/utils/FileRecordTools/Records/StrandQueue.cpp.orig
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+++ src/utils/FileRecordTools/Records/StrandQueue.cpp
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-@@ -25,11 +25,11 @@ StrandQueue::~StrandQueue() {
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- }
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- }
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>--Record *StrandQueue::top() const
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+Record *StrandQueue::top()
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- {
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- int minIdx = getMinIdx();
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- if (minIdx == -1) return NULL;
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- return const_cast<Record *>(_queues[minIdx]->top());
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ return _queues[minIdx]->top();
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- }
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- void StrandQueue::pop() {
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-@@ -38,8 +38,8 @@ void StrandQueue::pop() {
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- _queues[minIdx]->pop();
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- }
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>--Record * StrandQueue::top(Record::strandType strand) const {
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- const Record *record = NULL;
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+Record * StrandQueue::top(Record::strandType strand) {
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ Record *record = NULL;
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- switch (strand) {
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- case Record::FORWARD:
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- if (_queues[0]->empty()) return NULL;
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-@@ -57,10 +57,10 @@ Record * StrandQueue::top(Record::strandType strand) const {
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- default:
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- break;
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- }
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- return const_cast<Record *>(record);
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ return record;
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- }
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>--void StrandQueue::pop(Record::strandType strand) const {
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+void StrandQueue::pop(Record::strandType strand) {
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- switch (strand) {
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- case Record::FORWARD:
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- if (_queues[0]->empty()) return;
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-@@ -95,7 +95,7 @@ void StrandQueue::push(Record *record) {
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- }
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- }
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>--size_t StrandQueue::size() const {
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+size_t StrandQueue::size() {
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- size_t sumSize = 0;
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- for (int i = 0; i < NUM_QUEUES; i++) {
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- sumSize += _queues[i]->size();
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-@@ -103,7 +103,7 @@ size_t StrandQueue::size() const {
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- return sumSize;
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- }
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>--bool StrandQueue::empty() const {
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+bool StrandQueue::empty() {
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- for (int i = 0; i < NUM_QUEUES; i++) {
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- if (!_queues[i]->empty()) {
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- return false;
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-@@ -113,7 +113,7 @@ bool StrandQueue::empty() const {
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- }
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>--int StrandQueue::getMinIdx() const {
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+int StrandQueue::getMinIdx() {
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- if (empty()) return -1;
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- const Record *minRec = NULL;
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- int minIdx = -1;
</span><span style='display:block; white-space:pre;color:#808080;'>diff --git a/science/bedtools/files/patch-src-utils-FileRecordTools-Records-StrandQueue.h.diff b/science/bedtools/files/patch-src-utils-FileRecordTools-Records-StrandQueue.h.diff
</span>deleted file mode 100644
<span style='display:block; white-space:pre;color:#808080;'>index bf914af..0000000
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>--- a/science/bedtools/files/patch-src-utils-FileRecordTools-Records-StrandQueue.h.diff
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>+++ /dev/null
</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -1,35 +0,0 @@
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>---- src/utils/FileRecordTools/Records/StrandQueue.h.orig
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+++ src/utils/FileRecordTools/Records/StrandQueue.h
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-@@ -20,17 +20,17 @@ class StrandQueue {
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- StrandQueue();
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- ~StrandQueue();
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- Record * top() const;
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ Record * top();
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- void pop();
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- Record * top(Record::strandType strand) const;
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- void pop(Record::strandType strand) const;
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ Record * top(Record::strandType strand);
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ void pop(Record::strandType strand);
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- void push(Record *record);
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- size_t size() const;
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- bool empty() const;
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ size_t size();
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ bool empty();
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- private:
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- // static RecordPtrSortFunctor _recSortFunctor;
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- typedef priority_queue<Record *, vector<const Record *>, RecordPtrSortDescFunctor > queueType;
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ typedef priority_queue<Record *, vector<Record *>, RecordPtrSortDescFunctor > queueType;
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- vector<queueType *> _queues;
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- static const int NUM_QUEUES = 3;
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-@@ -39,7 +39,7 @@ class StrandQueue {
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- //do, so we'll use a suggestion found in a forum, and put the enum values into a vector.
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- vector<Record::strandType> _strandIdxs;
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-- int getMinIdx() const; //will return the idx of queue with the current min val.
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-+ int getMinIdx(); //will return the idx of queue with the current min val.
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- };
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-
</span></pre><pre style='margin:0'>
</pre>