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-rw-r--r--gnu/packages/bioinformatics.scm3
-rw-r--r--gnu/packages/patches/bedtools-32bit-compilation.patch171
2 files changed, 173 insertions, 1 deletions
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);
+
+
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