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author | Ben Woodcroft <donttrustben@gmail.com> | 2015-07-25 23:32:55 +1000 |
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committer | Andreas Enge <andreas@enge.fr> | 2015-07-25 19:16:49 +0200 |
commit | b81cb1f2f3c9eaa7faea60d42d9a24ada8b5a290 (patch) | |
tree | b7b56efd0afcddfc9de7dabc85a07e62505de87a /gnu/packages/patches | |
parent | c6c86cd7a50ba1f2801f5f74bf712ea2a3acadc2 (diff) | |
download | guix-patches-b81cb1f2f3c9eaa7faea60d42d9a24ada8b5a290.tar guix-patches-b81cb1f2f3c9eaa7faea60d42d9a24ada8b5a290.tar.gz |
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>
Diffstat (limited to 'gnu/packages/patches')
-rw-r--r-- | gnu/packages/patches/bedtools-32bit-compilation.patch | 171 |
1 files changed, 171 insertions, 0 deletions
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); + + |