gnu: bedtools: Add patch to fix compilation on 32 bit systems.

* gnu/packages/patches/bedtools-32bit-compilation.patch: New file.
* gnu/packages/bioinformatics.scm (bedtools)[source]: Add patch.
* gnu-system.am (dist_patch_DATA): Register patch.

Signed-off-by: Andreas Enge <andreas@enge.fr>

3 files changed, 174 insertions, 1 deletions

diff --git a/gnu-system.am b/gnu-system.am
index f4e121af26..d6635fe636 100644
--- a/gnu-system.am
+++ b/gnu-system.am
@@ -392,6 +392,7 @@ dist_patch_DATA =						\
   gnu/packages/patches/avahi-localstatedir.patch		\
   gnu/packages/patches/avrdude-fix-libusb.patch			\
   gnu/packages/patches/bash-completion-directories.patch	\
+  gnu/packages/patches/bedtools-32bit-compilation.patch         \
   gnu/packages/patches/bowtie-fix-makefile.patch		\
   gnu/packages/patches/bigloo-gc-shebangs.patch			\
   gnu/packages/patches/binutils-ld-new-dtags.patch		\
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 92b93948f4..06037c1bbf 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -204,7 +204,8 @@ computational cluster.")
               (file-name (string-append name "-" version ".tar.gz"))
               (sha256
                (base32
-                "0lnxrjvs3nnmb4bmskag1wg3h2hd80przz5q3xd0bvs7vyxrvpbl"))))
+                "0lnxrjvs3nnmb4bmskag1wg3h2hd80przz5q3xd0bvs7vyxrvpbl"))
+              (patches (list (search-patch "bedtools-32bit-compilation.patch")))))
     (build-system gnu-build-system)
     (native-inputs `(("python" ,python-2)))
     (inputs `(("samtools" ,samtools)
diff --git a/gnu/packages/patches/bedtools-32bit-compilation.patch b/gnu/packages/patches/bedtools-32bit-compilation.patch
new file mode 100644
index 0000000000..bc567f3f6b
--- /dev/null
+++ b/gnu/packages/patches/bedtools-32bit-compilation.patch
@@ -0,0 +1,171 @@
+Fixed in upstream, see
+https://github.com/arq5x/bedtools2/issues/271
+
+From b47dbefcb57f8e6c4fe397f64346338620740b71 Mon Sep 17 00:00:00 2001
+From: arq5x <arq5x@virginia.edu>
+Date: Wed, 15 Jul 2015 15:15:23 -0600
+Subject: [PATCH] settle on uint32_t signature for QuickString. Resolves #267
+ and #271?
+
+---
+ src/coverageFile/coverageFile.cpp | 24 ++++++++++++------------
+ src/utils/general/QuickString.cpp | 27 ++++++++++++++-------------
+ src/utils/general/QuickString.h   |  6 +++---
+ 3 files changed, 29 insertions(+), 28 deletions(-)
+
+diff --git a/src/coverageFile/coverageFile.cpp b/src/coverageFile/coverageFile.cpp
+index 859cfdc..0fb544b 100644
+--- a/src/coverageFile/coverageFile.cpp
++++ b/src/coverageFile/coverageFile.cpp
+@@ -83,11 +83,11 @@ void CoverageFile::giveFinalReport(RecordOutputMgr *outputMgr) {
+ 		float depthPct = (float)basesAtDepth / (float)_totalQueryLen;
+ 
+ 		_finalOutput = "all\t";
+-		_finalOutput.append(depth);
++		_finalOutput.append(static_cast<uint32_t>(depth));
+ 		_finalOutput.append("\t");
+-		_finalOutput.append(basesAtDepth);
++		_finalOutput.append(static_cast<uint32_t>(basesAtDepth));
+ 		_finalOutput.append("\t");
+-		_finalOutput.append(_totalQueryLen);
++		_finalOutput.append(static_cast<uint32_t>(_totalQueryLen));
+ 		_finalOutput.append("\t");
+ 		format(depthPct);
+ 
+@@ -138,7 +138,7 @@ size_t CoverageFile::countBasesAtDepth(size_t depth) {
+ 
+ void CoverageFile::doCounts(RecordOutputMgr *outputMgr, RecordKeyVector &hits)
+ {
+-	_finalOutput = hits.size();
++	_finalOutput = static_cast<uint32_t>(hits.size());
+ 	outputMgr->printRecord(hits.getKey(), _finalOutput);
+ }
+ 
+@@ -147,9 +147,9 @@ void CoverageFile::doPerBase(RecordOutputMgr *outputMgr, RecordKeyVector &hits)
+ 	//loop through all bases in query, printing full record and metrics for each
+ 	const Record * queryRec = hits.getKey();
+ 	for (size_t i= 0; i < _queryLen; i++) {
+-		_finalOutput = i +1;
++		_finalOutput = static_cast<uint32_t>(i+1);
+ 		_finalOutput.append("\t");
+-		_finalOutput.append(_depthArray[i]);
++		_finalOutput.append(static_cast<uint32_t>(_depthArray[i]));
+ 
+ 		outputMgr->printRecord(queryRec, _finalOutput);
+ 	}
+@@ -181,11 +181,11 @@ void CoverageFile::doHist(RecordOutputMgr *outputMgr, RecordKeyVector &hits)
+ 		size_t numBasesAtDepth = iter->second;
+ 		float coveredBases = (float)numBasesAtDepth / (float)_queryLen;
+ 
+-		_finalOutput = depth;
++		_finalOutput = static_cast<uint32_t>(depth);
+ 		_finalOutput.append("\t");
+-		_finalOutput.append(numBasesAtDepth);
++		_finalOutput.append(static_cast<uint32_t>(numBasesAtDepth));
+ 		_finalOutput.append("\t");
+-		_finalOutput.append(_queryLen);
++		_finalOutput.append(static_cast<uint32_t>(_queryLen));
+ 		_finalOutput.append("\t");
+ 		format(coveredBases);
+ 
+@@ -199,11 +199,11 @@ void CoverageFile::doDefault(RecordOutputMgr *outputMgr, RecordKeyVector &hits)
+ 	size_t nonZeroBases = _queryLen - countBasesAtDepth(0);
+ 	float coveredBases = (float)nonZeroBases / (float)_queryLen;
+ 
+-	_finalOutput = hits.size();
++	_finalOutput = static_cast<uint32_t>(hits.size());
+ 	_finalOutput.append("\t");
+-	_finalOutput.append(nonZeroBases);
++	_finalOutput.append(static_cast<uint32_t>(nonZeroBases));
+ 	_finalOutput.append("\t");
+-	_finalOutput.append(_queryLen);
++	_finalOutput.append(static_cast<uint32_t>(_queryLen));
+ 	_finalOutput.append("\t");
+ 	format(coveredBases);
+ 
+diff --git a/src/utils/general/QuickString.cpp b/src/utils/general/QuickString.cpp
+index 0757009..a83263e 100644
+--- a/src/utils/general/QuickString.cpp
++++ b/src/utils/general/QuickString.cpp
+@@ -105,11 +105,11 @@ QuickString &QuickString::operator = (uint32_t val) {
+ 	return *this;
+ }
+ 
+-QuickString &QuickString::operator = (size_t val) {
+-	clear();
+-	append(val);
+-	return *this;
+-}
++// QuickString &QuickString::operator = (size_t val) {
++// 	clear();
++// 	append(val);
++// 	return *this;
++// }
+ 
+ QuickString &QuickString::operator = (float val) {
+ 	clear();
+@@ -158,10 +158,11 @@ QuickString &QuickString::operator += (uint32_t num) {
+ 	return *this;
+ }
+ 
+-QuickString &QuickString::operator += (size_t num) {
+-	append(num);
+-	return *this;
+-}
++// QuickString &QuickString::operator += (size_t num) {
++// 	append(num);
++// 	return *this;
++// }
++
+ QuickString &QuickString::operator += (float num) {
+ 	append(num);
+ 	return *this;
+@@ -273,12 +274,12 @@ void QuickString::append(int num) {
+ }
+ 
+ void QuickString::append(uint32_t num) {
+-	int2str((int)num, *this, true);
++ 	int2str((int)num, *this, true);
+ }
+ 
+-void QuickString::append(size_t num) {
+-	int2str((int)num, *this, true);
+-}
++// void QuickString::append(size_t num) {
++// 	int2str((int)num, *this, true);
++// }
+ 
+ void QuickString::append(float num) {
+ 	append(ToString(num));
+diff --git a/src/utils/general/QuickString.h b/src/utils/general/QuickString.h
+index b43fdfc..6e6fa94 100644
+--- a/src/utils/general/QuickString.h
++++ b/src/utils/general/QuickString.h
+@@ -38,7 +38,7 @@ class QuickString {
+ 	QuickString &operator = (char);
+ 	QuickString &operator = (int);
+ 	QuickString &operator = (uint32_t);
+-	QuickString &operator = (size_t);
++	//QuickString &operator = (size_t);
+ 	QuickString &operator = (float);
+ 	QuickString &operator = (double);
+ 	QuickString &operator += (const QuickString &);
+@@ -47,7 +47,7 @@ class QuickString {
+ 	QuickString &operator += (char);
+ 	QuickString &operator += (int);
+ 	QuickString &operator += (uint32_t);
+-	QuickString &operator += (size_t);
++	//QuickString &operator += (size_t);
+ 	QuickString &operator += (float);
+ 	QuickString &operator += (double);
+ 
+@@ -74,7 +74,7 @@ class QuickString {
+ 	//for better performance.
+ 	void append(int num);
+ 	void append(uint32_t num);
+-	void append(size_t num);
++	//void append(size_t num);
+ 	void append(float num);
+ 	void append(double num);
+ 
+