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commit: 71fb540e91fd211248ed97daee867d9bfe77fa4d |
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Author: David Seifert <soap <AT> gentoo <DOT> org> |
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AuthorDate: Thu May 5 18:11:32 2016 +0000 |
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Commit: David Seifert <soap <AT> gentoo <DOT> org> |
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CommitDate: Thu May 5 18:11:49 2016 +0000 |
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URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=71fb540e |
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|
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sci-biology/allpathslg: replace isnan macro with proper std::isnan function |
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|
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Gentoo-Bug: 580086 |
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|
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Package-Manager: portage-2.2.28 |
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|
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.../allpathslg-52488_remove-namespace-std.patch | 22 +++++++++++++++++++++- |
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1 file changed, 21 insertions(+), 1 deletion(-) |
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|
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diff --git a/sci-biology/allpathslg/files/allpathslg-52488_remove-namespace-std.patch b/sci-biology/allpathslg/files/allpathslg-52488_remove-namespace-std.patch |
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index a094c53..56d0406 100644 |
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--- a/sci-biology/allpathslg/files/allpathslg-52488_remove-namespace-std.patch |
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+++ b/sci-biology/allpathslg/files/allpathslg-52488_remove-namespace-std.patch |
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@@ -890,10 +890,12 @@ https://bugs.gentoo.org/show_bug.cgi?id=568440 |
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bool IsBubbleEdge(int eid, const HyperBasevector& hb, const vec<int>& to_left, |
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--- allpathslg-52488/src/paths/long/VariantReadSupport.cc |
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+++ allpathslg-52488/src/paths/long/VariantReadSupport.cc |
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-@@ -23,6 +23,11 @@ |
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+@@ -23,6 +23,13 @@ |
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#include "paths/long/ReadOriginTracker.h" |
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#include "paths/long/EvalByReads.h" |
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|
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++#include <cmath> |
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++ |
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+using std::get; |
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+using std::make_tuple; |
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+using std::ignore; |
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@@ -902,6 +904,24 @@ https://bugs.gentoo.org/show_bug.cgi?id=568440 |
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namespace { |
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void CalcLengthProbSimple(vec<double>&vOut,const double dProbIns_len, const double dProbDel_len, const uint64_t org_length){ |
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const double dProbIns=dProbIns_len; |
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+@@ -158,7 +165,7 @@ |
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+ for(uint64_t ff=1;ff<nFlavors;++ff){ |
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+ for( size_t ll = 2 ; ll <= get<0>(n_q_len[ff]) ; ++ll){ dFactor /= (long double)(ll); } |
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+ } |
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+- if( dFactor==std::numeric_limits<long double>::infinity() || isnan(dFactor) ){ dFactor=1.0; } |
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++ if( dFactor==std::numeric_limits<long double>::infinity() || std::isnan(dFactor) ){ dFactor=1.0; } |
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+ if(verbosity>0) std::cout << "dFactor " << dFactor << std::endl; |
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+ |
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+ long double dDenom=0.0; |
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+@@ -193,7 +200,7 @@ |
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+ } |
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+ } |
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+ if(verbosity>0) std::cout <<"denom: " << dDenom<< std::endl; |
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+- if( dDenom < std::numeric_limits<long double>::epsilon() * 100 || isnan(dDenom)) return; |
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++ if( dDenom < std::numeric_limits<long double>::epsilon() * 100 || std::isnan(dDenom)) return; |
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+ ForceAssert(dDenom>0); |
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+ if(verbosity>0){ |
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+ for( uint64_t row=0;row<nFlavors;++row){ |
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--- allpathslg-52488/src/paths/long/VariantReadSupport.h |
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+++ allpathslg-52488/src/paths/long/VariantReadSupport.h |
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@@ -5,6 +5,8 @@ |
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