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commit f803fe06df2058ddc74ea108661ad69a469d4ee3 Author: Fabian Klötzl <[email protected]> Date: Mon Sep 4 14:58:52 2017 +0200 fix json name clash --- debian/patches/fix_json_name_clash.patch | 85 ++++++++++++++++++++++++++++++++ debian/patches/series | 1 + 2 files changed, 86 insertions(+) diff --git a/debian/patches/fix_json_name_clash.patch b/debian/patches/fix_json_name_clash.patch new file mode 100644 index 0000000..4549c1d --- /dev/null +++ b/debian/patches/fix_json_name_clash.patch @@ -0,0 +1,85 @@ +Author: Fabian Klötzl <[email protected]> +Date: Mon, 4 Sep 2017 12:27:38 +0200 +Acked-by: Andreas Tille <[email protected]> +Description: Fix a "json" name clash + htslib exports an enum value called `json`. That clashes with the + definition of a friend function. For simplicity we resolve this by + renaming the local function and ask htslib to prefix their symbols in + the future. + +--- + src/Allele.cpp | 10 +++++----- + src/Allele.h | 10 +++++----- + src/Sample.cpp | 2 +- + 3 files changed, 11 insertions(+), 11 deletions(-) + +diff --git a/src/Allele.cpp b/src/Allele.cpp +index 2c58c79..8645704 100644 +--- a/src/Allele.cpp ++++ b/src/Allele.cpp +@@ -332,19 +332,19 @@ string stringForAlleles(vector<Allele> &alleles) { + return out.str(); + } + +-string json(vector<Allele*> &alleles) { ++string to_json(vector<Allele*> &alleles) { + stringstream out; + vector<Allele*>::iterator a = alleles.begin(); +- out << "[" << (*a)->json(); ++a; ++ out << "[" << (*a)->to_json(); ++a; + for (; a != alleles.end(); ++a) +- out << "," << (*a)->json(); ++ out << "," << (*a)->to_json(); + out << "]"; + return out.str(); + } + +-string json(Allele*& allele) { return allele->json(); } ++string to_json(Allele*& allele) { return allele->to_json(); } + +-string Allele::json(void) { ++string Allele::to_json(void) { + stringstream out; + if (!genotypeAllele) { + out << "{\"id\":\"" << readID << "\"" +diff --git a/src/Allele.h b/src/Allele.h +index 3f0125f..ff41c10 100644 +--- a/src/Allele.h ++++ b/src/Allele.h +@@ -96,10 +96,10 @@ class Allele { + friend ostream &operator<<(ostream &out, Allele &a); + friend ostream &operator<<(ostream &out, Allele* &a); + +- friend string json(vector<Allele*> &alleles, long int &position); +- friend string json(vector<Allele*> &alleles); +- friend string json(Allele &allele, long int &position); +- friend string json(Allele* &allele); ++ friend string to_json(vector<Allele*> &alleles, long int &position); ++ friend string to_json(vector<Allele*> &alleles); ++ friend string to_json(Allele &allele, long int &position); ++ friend string to_json(Allele* &allele); + + public: + +@@ -262,7 +262,7 @@ public: + // this is used to update cached data in the allele prior to presenting the allele for analysis + // for the current base, just use allele.currentBase + +- string json(void); ++ string to_json(void); + unsigned int getLengthOnReference(void); + int referenceLengthFromCigar(void); + +diff --git a/src/Sample.cpp b/src/Sample.cpp +index 06207cd..a6e3886 100644 +--- a/src/Sample.cpp ++++ b/src/Sample.cpp +@@ -264,7 +264,7 @@ string Sample::json(void) { + vector<Allele*>& alleles = g->second; + for (vector<Allele*>::iterator a = alleles.begin(); a != alleles.end(); ++a) { + if (!first) { out << ","; } else { first = false; } +- out << (*a)->json(); ++ out << (*a)->to_json(); + } + } + out << "]"; diff --git a/debian/patches/series b/debian/patches/series index 2b2a98d..ea7ec8f 100644 --- a/debian/patches/series +++ b/debian/patches/series @@ -5,3 +5,4 @@ use_debian_packaged_libjsoncpp.patch fix_test.patch vcffirstheader.patch use_cpp11.patch +fix_json_name_clash.patch -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/freebayes.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
