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commit: b2afaced4f1f7c81e59293698518d9b4f6f8b414 |
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Author: Michał Górny <mgorny <AT> gentoo <DOT> org> |
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AuthorDate: Sat Dec 9 23:12:24 2017 +0000 |
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Commit: Michał Górny <mgorny <AT> gentoo <DOT> org> |
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CommitDate: Sat Dec 9 23:13:08 2017 +0000 |
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URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=b2afaced |
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|
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sci-biology/allpathslg: [QA] Move patches to a distfile |
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|
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Closes: https://bugs.gentoo.org/620610 |
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|
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sci-biology/allpathslg/Manifest | 3 +- |
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sci-biology/allpathslg/allpathslg-52488-r2.ebuild | 9 +- |
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.../files/allpathslg-52488_fix-buildsystem.patch | 33 - |
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.../allpathslg-52488_remove-namespace-std.patch | 1770 -------------------- |
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4 files changed, 7 insertions(+), 1808 deletions(-) |
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|
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diff --git a/sci-biology/allpathslg/Manifest b/sci-biology/allpathslg/Manifest |
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index c87071a8893..22364d00b07 100644 |
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--- a/sci-biology/allpathslg/Manifest |
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+++ b/sci-biology/allpathslg/Manifest |
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@@ -1 +1,2 @@ |
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-DIST allpathslg-52488.tar.gz 3121949 SHA256 035b49cb21b871a6b111976757d7aee9c2513dd51af04678f33375e620998542 SHA512 c44ef1a3ed5b343bf096663309cc399e79d65e83175232743cf330fd0d426633bd0d388922fd0c73ac0927d85ea9005549c8e4f7711c79fea7107068510ef30d WHIRLPOOL c63a13450c55fce8f2c5399bdd5d8f32939e31d9d13a120835b1d826ae96e251fea81caa134d5d45ad857af0777c22e4ad1d894c81a74db6d83a7d9ad83b12b4 |
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+DIST allpathslg-52488-patchset.tar.bz2 11405 BLAKE2B 7a4c36884ac95a4eb23291720e422ce1ec41d0bea3a0b10582aa1d8154234971eb8d06979a969e65c1ec1eab031d2500a1ec40809019c8b4aa1d1d2e81427dbe SHA512 a1d58c131afeef04a9d7a2520fcd28a853317323fdcab1a253cb2548546bbc559993c74a68a8032a5d0e865ac2c2d53ff6b4c149aade2d1f87a2ab4116ebe4cc |
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+DIST allpathslg-52488.tar.gz 3121949 BLAKE2B b75904f9e8256a14c97abae45a0cb41718f95d27a4a072b6144bd125abb57682faa180de6a18399ab4fa43988344c436ca1eab8412433353fcc746c432c33031 SHA512 c44ef1a3ed5b343bf096663309cc399e79d65e83175232743cf330fd0d426633bd0d388922fd0c73ac0927d85ea9005549c8e4f7711c79fea7107068510ef30d |
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|
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diff --git a/sci-biology/allpathslg/allpathslg-52488-r2.ebuild b/sci-biology/allpathslg/allpathslg-52488-r2.ebuild |
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index e4c4d95288f..e68430e2462 100644 |
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--- a/sci-biology/allpathslg/allpathslg-52488-r2.ebuild |
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+++ b/sci-biology/allpathslg/allpathslg-52488-r2.ebuild |
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@@ -1,4 +1,4 @@ |
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-# Copyright 1999-2016 Gentoo Foundation |
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+# Copyright 1999-2017 Gentoo Foundation |
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# Distributed under the terms of the GNU General Public License v2 |
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|
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EAPI=6 |
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@@ -8,7 +8,8 @@ inherit autotools flag-o-matic toolchain-funcs |
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DESCRIPTION="De novo assembly of whole-genome shotgun microreads" |
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# see also http://www.broadinstitute.org/software/allpaths-lg/blog/?page_id=12 |
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HOMEPAGE="http://www.broadinstitute.org/science/programs/genome-biology/crd" |
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-SRC_URI="ftp://ftp.broadinstitute.org/pub/crd/ALLPATHS/Release-LG/latest_source_code/${P}.tar.gz" |
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+SRC_URI="ftp://ftp.broadinstitute.org/pub/crd/ALLPATHS/Release-LG/latest_source_code/${P}.tar.gz |
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+ https://dev.gentoo.org/~mgorny/dist/${P}-patchset.tar.bz2" |
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|
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LICENSE="MIT" |
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SLOT="0" |
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@@ -22,8 +23,8 @@ DEPEND=" |
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dev-libs/boost:=" |
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|
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PATCHES=( |
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- "${FILESDIR}/${P}_fix-buildsystem.patch" |
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- "${FILESDIR}/${P}_remove-namespace-std.patch" |
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+ "${WORKDIR}/${P}-patchset/${P}_fix-buildsystem.patch" |
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+ "${WORKDIR}/${P}-patchset/${P}_remove-namespace-std.patch" |
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) |
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|
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pkg_pretend() { |
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|
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diff --git a/sci-biology/allpathslg/files/allpathslg-52488_fix-buildsystem.patch b/sci-biology/allpathslg/files/allpathslg-52488_fix-buildsystem.patch |
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deleted file mode 100644 |
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index 7944eb5469d..00000000000 |
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--- a/sci-biology/allpathslg/files/allpathslg-52488_fix-buildsystem.patch |
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+++ /dev/null |
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@@ -1,33 +0,0 @@ |
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-Fix build system to remove hardcoded debugging flags. |
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- |
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---- allpathslg-52488/configure.ac |
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-+++ allpathslg-52488/configure.ac |
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-@@ -12,7 +12,7 @@ |
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- AC_OPENMP |
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- AC_OPENMP_CHECK |
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- |
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--CXXFLAGS="$CXXFLAGS -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote . -ggdb -DNDEBUG" |
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-+CXXFLAGS="$CXXFLAGS -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -mieee-fp -fno-strict-aliasing -iquote . -DNDEBUG" |
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- |
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- OS_RELEASE="`uname -r`" |
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- AC_SUBST(CXXFLAGS) |
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---- allpathslg-52488/m4/broad.m4 |
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-+++ allpathslg-52488/m4/broad.m4 |
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-@@ -35,12 +35,14 @@ |
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- OLD_CFLAGS=$CFLAGS |
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- CFLAGS="$OPENMP_CFLAGS $CFLAGS" |
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- AC_MSG_CHECKING([validity of OpenMP configuation.]) |
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-- AC_LINK_IFELSE([#ifndef _OPENMP |
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-+ AC_LINK_IFELSE([ |
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-+ AC_LANG_SOURCE([[ |
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-+ #ifndef _OPENMP |
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- choke me |
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- #endif |
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- #include <omp.h> |
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-- int main () { return omp_get_num_threads (); }], |
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-- [], |
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-+ int main () { return omp_get_num_threads (); } |
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-+ ]])],[], |
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- [AC_MSG_BROAD_FAIL([Your compiler must support OpenMP.])]) |
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- CXXFLAGS=$OLD_CXXFLAGS |
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- CFLAGS=$OLD_CFLAGS |
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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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deleted file mode 100644 |
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index 56d04069435..00000000000 |
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--- a/sci-biology/allpathslg/files/allpathslg-52488_remove-namespace-std.patch |
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+++ /dev/null |
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@@ -1,1770 +0,0 @@ |
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-Remove 'using namespace std' causing massive havoc with newly |
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-introduced std::align in GCC-5. Fix bug |
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-https://bugs.gentoo.org/show_bug.cgi?id=568440 |
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- |
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---- allpathslg-52488/src/agp/AgpFile.cc |
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-+++ allpathslg-52488/src/agp/AgpFile.cc |
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-@@ -4,6 +4,8 @@ |
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- #include "agp/AgpFile.h" |
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- #include "TokenizeString.h" |
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- |
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-+using std::cerr; |
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-+ |
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- char agp_contig::TypeChar_() const |
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- { |
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- switch ( type_ ) |
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---- allpathslg-52488/src/agp/AgpFile.h |
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-+++ allpathslg-52488/src/agp/AgpFile.h |
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-@@ -9,6 +9,8 @@ |
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- |
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- #include "agp/AgpMods.h" |
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- |
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-+using std::max; |
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-+ |
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- class agp_entry |
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- { |
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- public: |
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---- allpathslg-52488/src/agp/AgpMods.cc |
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-+++ allpathslg-52488/src/agp/AgpMods.cc |
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-@@ -7,6 +7,8 @@ |
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- |
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- #include "system/System.h" |
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- |
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-+using std::istrstream; |
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-+ |
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- bool |
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- agp_mods::SuperShouldBeRemoved( int super_id ) const |
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- { |
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---- allpathslg-52488/src/agp/AgpMods.h |
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-+++ allpathslg-52488/src/agp/AgpMods.h |
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-@@ -7,6 +7,8 @@ |
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- #include "String.h" |
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- #include "Vec.h" |
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- |
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-+using std::swap; |
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-+ |
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- // The class contig_range provides begin and end positions on a |
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- // contig. If the end position is before the begin position, the |
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- // range is considered reversed. If a length is provided, the range |
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---- allpathslg-52488/src/allpaths_cache/CacheReadsMerge.cc |
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-+++ allpathslg-52488/src/allpaths_cache/CacheReadsMerge.cc |
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-@@ -56,6 +56,8 @@ |
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- #include "feudal/VirtualMasterVec.h" |
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- #include "random/Shuffle.h" |
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- |
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-+using std::map; |
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-+ |
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- typedef VirtualMasterVec<BaseVec> VBaseVecVec; |
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- typedef VirtualMasterVec<QualVec> VQualVecVec; |
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- |
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---- allpathslg-52488/src/AnAssemblyClass.h |
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-+++ allpathslg-52488/src/AnAssemblyClass.h |
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-@@ -19,6 +19,8 @@ |
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- #include "ReadLocation.h" |
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- #include "ReadPairing.h" |
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- |
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-+using std::map; |
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-+ |
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- class assembly; |
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- |
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- class super { |
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---- allpathslg-52488/src/efasta/EfastaTools.cc |
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-+++ allpathslg-52488/src/efasta/EfastaTools.cc |
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-@@ -19,6 +19,8 @@ |
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- #include "math/Array.h" |
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- #include <iostream> |
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- |
181 |
-+using std::set; |
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-+ |
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- #define Err(message) \ |
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- { cout << message << endl << "\nInvalid.\n" << endl; \ |
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- TracebackThisProcess( ); } |
186 |
---- allpathslg-52488/src/Equiv.cc |
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-+++ allpathslg-52488/src/Equiv.cc |
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-@@ -9,6 +9,8 @@ |
189 |
- #include "Equiv.h" |
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- #include "Vec.h" |
191 |
- |
192 |
-+using std::swap; |
193 |
-+ |
194 |
- bool equivalence_relation::equiv(int a, int b) const |
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- { if ( a == b ) return true; |
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- int c = a; |
197 |
---- allpathslg-52488/src/FastaFilestream.cc |
198 |
-+++ allpathslg-52488/src/FastaFilestream.cc |
199 |
-@@ -13,6 +13,8 @@ |
200 |
- |
201 |
- #include <strstream> |
202 |
- |
203 |
-+using std::string; |
204 |
-+ |
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- template <typename vecT, typename seqT, typename convT, typename verifT> |
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- FastaFilestream<vecT,seqT,convT,verifT>::FastaFilestream( const String& filename, |
207 |
- FastaNameParser* name_parser ) |
208 |
---- allpathslg-52488/src/FastaFilestreamPreview.cc |
209 |
-+++ allpathslg-52488/src/FastaFilestreamPreview.cc |
210 |
-@@ -11,6 +11,8 @@ |
211 |
- |
212 |
- #include <algorithm> |
213 |
- |
214 |
-+using std::streamoff; |
215 |
-+ |
216 |
- FastaFilestreamPreview::FastaFilestreamPreview(istream& filestream) |
217 |
- : max_sequence_size_(0), start_offset_(0) |
218 |
- { |
219 |
---- allpathslg-52488/src/FastaFilestreamPreview.h |
220 |
-+++ allpathslg-52488/src/FastaFilestreamPreview.h |
221 |
-@@ -12,6 +12,8 @@ |
222 |
- |
223 |
- #include "Vec.h" |
224 |
- |
225 |
-+using std::streampos; |
226 |
-+ |
227 |
- // FastaFilestreamPreview understands just enough about the fasta |
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- // format to be able to count the number of sequences in the specified |
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- // filestream and to know where each sequence starts in that filestream. |
230 |
---- allpathslg-52488/src/Fastavector.cc |
231 |
-+++ allpathslg-52488/src/Fastavector.cc |
232 |
-@@ -14,6 +14,8 @@ |
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- #include <istream> |
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- #include <string> |
235 |
- |
236 |
-+using std::max; |
237 |
-+ |
238 |
- // Split this into chunks, separated by gaps ('n'), and return each chunk as a |
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- // gapless fastavector. |
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- // TODO: generalize this into a templatized STL algorithm. |
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---- allpathslg-52488/src/Fastavector.h |
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-+++ allpathslg-52488/src/Fastavector.h |
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-@@ -24,6 +24,9 @@ |
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- #include <iostream> |
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- #include <unistd.h> |
246 |
- |
247 |
-+using std::string; |
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-+using std::istringstream; |
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-+ |
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- typedef std::tuple<String, int, int> FastaRegion; |
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- |
252 |
- class fastaindex { |
253 |
---- allpathslg-52488/src/FetchReads.cc |
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-+++ allpathslg-52488/src/FetchReads.cc |
255 |
-@@ -36,6 +36,8 @@ |
256 |
- #include "Qualvector.h" |
257 |
- #include "random/Random.h" |
258 |
- |
259 |
-+using std::istringstream; |
260 |
-+ |
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- // Heuristic constants: |
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- |
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- namespace |
264 |
---- allpathslg-52488/src/feudal/BaseVec.cc |
265 |
-+++ allpathslg-52488/src/feudal/BaseVec.cc |
266 |
-@@ -21,6 +21,7 @@ |
267 |
- using std::ostream; |
268 |
- using std::cout; |
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- using std::endl; |
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-+using std::max_element; |
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- |
272 |
- // Cap: in a given basevector, replace any sequence of N > n identical |
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- // bases by n of the same base. |
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---- allpathslg-52488/src/graph/Digraph.cc |
275 |
-+++ allpathslg-52488/src/graph/Digraph.cc |
276 |
-@@ -17,6 +17,9 @@ |
277 |
- #include "graph/Digraph.h" |
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- #include "math/Functions.h" |
279 |
- |
280 |
-+using std::make_pair; |
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-+using std::priority_queue; |
282 |
-+ |
283 |
- void digraph::TransferEdges( int v, int w, const Bool enter_only ) |
284 |
- { ForceAssert( v != w ); |
285 |
- |
286 |
---- allpathslg-52488/src/graph/Digraph.h |
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-+++ allpathslg-52488/src/graph/Digraph.h |
288 |
-@@ -52,6 +52,8 @@ |
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- #include "system/TraceVal.h" |
290 |
- #include <cstddef> |
291 |
- |
292 |
-+using std::function; |
293 |
-+ |
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- typedef pair<int, int> VertexPair; |
295 |
- |
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- typedef int vrtx_t; |
297 |
---- allpathslg-52488/src/graph/DigraphTemplate.h |
298 |
-+++ allpathslg-52488/src/graph/DigraphTemplate.h |
299 |
-@@ -34,6 +34,8 @@ |
300 |
- #include "graph/Digraph.h" |
301 |
- #include <cstddef> |
302 |
- |
303 |
-+using std::make_pair; |
304 |
-+ |
305 |
- template<class E> vec<int> digraphE<E>:: EdgesBoundedBy( const int e1, const int e2, |
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- const vec<int>& to_left, const vec<int>& to_right ) const |
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- { int v = to_right[e1], w = to_left[e2]; |
308 |
---- allpathslg-52488/src/graph/GraphAlgorithms.h |
309 |
-+++ allpathslg-52488/src/graph/GraphAlgorithms.h |
310 |
-@@ -9,7 +9,7 @@ |
311 |
- #ifndef GRAPH__GRAPH_ALGORITHMS__H_ |
312 |
- #define GRAPH__GRAPH_ALGORITHMS__H_ |
313 |
- |
314 |
-- |
315 |
-+using std::map; |
316 |
- |
317 |
- // -------------- Union Find --------------- |
318 |
- // |
319 |
---- allpathslg-52488/src/IndexedAlignmentPlusVector.h |
320 |
-+++ allpathslg-52488/src/IndexedAlignmentPlusVector.h |
321 |
-@@ -15,6 +15,8 @@ |
322 |
- |
323 |
- #include "Alignment.h" |
324 |
- |
325 |
-+using std::streampos; |
326 |
-+using std::streamoff; |
327 |
- |
328 |
- // This class encapsulates the header information for both vectors and indices. |
329 |
- |
330 |
---- allpathslg-52488/src/kmers/kmer_parcels/KmerParcelsClasses.h |
331 |
-+++ allpathslg-52488/src/kmers/kmer_parcels/KmerParcelsClasses.h |
332 |
-@@ -6,6 +6,9 @@ |
333 |
- // Institute is not responsible for its use, misuse, or functionality. // |
334 |
- /////////////////////////////////////////////////////////////////////////////// |
335 |
- |
336 |
-+using std::hex; |
337 |
-+using std::dec; |
338 |
-+ |
339 |
- // --------------------------------- |
340 |
- // NaifTimer |
341 |
- // --------------------------------- |
342 |
---- allpathslg-52488/src/kmers/naif_kmer/KernelErrorFinder.h |
343 |
-+++ allpathslg-52488/src/kmers/naif_kmer/KernelErrorFinder.h |
344 |
-@@ -13,8 +13,8 @@ |
345 |
- #include "kmers/naif_kmer/LockedBlocks.h" |
346 |
- #include "kmers/naif_kmer/Kmers.h" |
347 |
- |
348 |
-- |
349 |
-- |
350 |
-+using std::make_pair; |
351 |
-+using std::stringstream; |
352 |
- |
353 |
- |
354 |
- |
355 |
---- allpathslg-52488/src/kmers/naif_kmer/Kmers.h |
356 |
-+++ allpathslg-52488/src/kmers/naif_kmer/Kmers.h |
357 |
-@@ -14,7 +14,7 @@ |
358 |
- |
359 |
- #include "kmers/naif_kmer/KmerFunctions.h" |
360 |
- |
361 |
-- |
362 |
-+using std::string; |
363 |
- |
364 |
- // ---- 256 random 64bit numbers to compute hash key |
365 |
- |
366 |
---- allpathslg-52488/src/layout/ContigActualloc.h |
367 |
-+++ allpathslg-52488/src/layout/ContigActualloc.h |
368 |
-@@ -17,6 +17,8 @@ |
369 |
- #include "system/Crash.h" |
370 |
- #include "Misc.h" |
371 |
- |
372 |
-+using std::set; |
373 |
-+using std::map; |
374 |
- |
375 |
- // |
376 |
- // Class contig_actualloc |
377 |
---- allpathslg-52488/src/lookup/ImperfectLookup.h |
378 |
-+++ allpathslg-52488/src/lookup/ImperfectLookup.h |
379 |
-@@ -51,6 +51,8 @@ |
380 |
- #include "lookup/LookupTools.h" |
381 |
- #include "lookup/AlignCollector.h" |
382 |
- |
383 |
-+using std::auto_ptr; |
384 |
-+ |
385 |
- class TaskTimer; |
386 |
- |
387 |
- |
388 |
---- allpathslg-52488/src/lookup/LookAlign.cc |
389 |
-+++ allpathslg-52488/src/lookup/LookAlign.cc |
390 |
-@@ -29,6 +29,8 @@ |
391 |
- #include "random/Random.h" |
392 |
- #include "system/ParsedArgs.h" |
393 |
- |
394 |
-+using std::istrstream; |
395 |
-+ |
396 |
- String QUERY("QUERY"); |
397 |
- |
398 |
- void look_align::ResetFromAlign(const align & al, const basevector & b1, |
399 |
---- allpathslg-52488/src/lookup/LookupTable.h |
400 |
-+++ allpathslg-52488/src/lookup/LookupTable.h |
401 |
-@@ -18,6 +18,8 @@ |
402 |
- |
403 |
- #include <set> |
404 |
- |
405 |
-+using std::set; |
406 |
-+ |
407 |
- typedef pair<unsigned int, unsigned int> LocSeq; |
408 |
- |
409 |
- /// |
410 |
---- allpathslg-52488/src/lookup/QueryLookupTableCore.cc |
411 |
-+++ allpathslg-52488/src/lookup/QueryLookupTableCore.cc |
412 |
-@@ -465,6 +465,9 @@ |
413 |
- #include "system/ParsedArgs.h" |
414 |
- #include "system/file/FileReader.h" |
415 |
- |
416 |
-+using std::istrstream; |
417 |
-+using std::less_equal; |
418 |
-+ |
419 |
- #define ABORT(MSG) \ |
420 |
- { out << MSG << " Abort." << endl << endl; \ |
421 |
- exit(1); } |
422 |
---- allpathslg-52488/src/lookup/ShortQueryLookup.cc |
423 |
-+++ allpathslg-52488/src/lookup/ShortQueryLookup.cc |
424 |
-@@ -32,6 +32,8 @@ |
425 |
- #include "lookup/AlignCollector.h" |
426 |
- #include "lookup/ImperfectLookup.h" |
427 |
- |
428 |
-+using std::ios_base; |
429 |
-+ |
430 |
- // Run an alignment processing chain: seqs -> look -> receiver -> aligns |
431 |
- // That is, look turns seqs into hits, which receiver accepts |
432 |
- // and turns into alignments which are passed to aligns. The |
433 |
---- allpathslg-52488/src/Map.h |
434 |
-+++ allpathslg-52488/src/Map.h |
435 |
-@@ -23,7 +23,7 @@ |
436 |
- #include <unordered_map> |
437 |
- #include <ext/hash_map> |
438 |
- using namespace __gnu_cxx; |
439 |
-- |
440 |
-+using std::map; |
441 |
- |
442 |
- template <class K, class V, class C=std::less<K>> |
443 |
- using StdMap = std::map<K,V,C,typename DefaultAllocator<std::pair<K const,V>>::type>; |
444 |
---- allpathslg-52488/src/math/Array.h |
445 |
-+++ allpathslg-52488/src/math/Array.h |
446 |
-@@ -13,6 +13,8 @@ |
447 |
- #include "Vec.h" |
448 |
- #include "Map.h" |
449 |
- |
450 |
-+using std::fill; |
451 |
-+ |
452 |
- // ============================================================================== |
453 |
- // A fixed-size simple c-style 2D array that allocates faster than vec< vec<T> > |
454 |
- // The elements are uninitialized. |
455 |
---- allpathslg-52488/src/math/Functions.cc |
456 |
-+++ allpathslg-52488/src/math/Functions.cc |
457 |
-@@ -10,7 +10,7 @@ |
458 |
- #include "STLExtensions.h" |
459 |
- #include "math/Functions.h" |
460 |
- |
461 |
-- |
462 |
-+using std::make_pair; |
463 |
- |
464 |
- |
465 |
- /* CombineNormalDistribution Filipe Ribeiro 2009-06-22 |
466 |
---- allpathslg-52488/src/math/Functions.h |
467 |
-+++ allpathslg-52488/src/math/Functions.h |
468 |
-@@ -15,6 +15,10 @@ |
469 |
- #include <cmath> |
470 |
- #include <numeric> |
471 |
- |
472 |
-+using std::min; |
473 |
-+using std::cerr; |
474 |
-+using std::swap; |
475 |
-+ |
476 |
- // =========================================================================== |
477 |
- // |
478 |
- // Min functions |
479 |
---- allpathslg-52488/src/math/HoInterval.cc |
480 |
-+++ allpathslg-52488/src/math/HoInterval.cc |
481 |
-@@ -10,6 +10,8 @@ |
482 |
- #include "math/HoInterval.h" |
483 |
- #include "STLExtensions.h" |
484 |
- |
485 |
-+using std::make_pair; |
486 |
-+ |
487 |
- bool ho_interval::Merge(const ho_interval & o) { |
488 |
- if (!Meets(*this,o)) return false; |
489 |
- *this = Span(*this, o); |
490 |
---- allpathslg-52488/src/math/HoInterval.h |
491 |
-+++ allpathslg-52488/src/math/HoInterval.h |
492 |
-@@ -14,6 +14,8 @@ |
493 |
- #include "feudal/MasterVec.h" |
494 |
- #include "feudal/SerfVec.h" |
495 |
- |
496 |
-+using std::max; |
497 |
-+ |
498 |
- /// Class: ho_interval |
499 |
- /// A half-open interval [a, b). |
500 |
- class ho_interval { |
501 |
---- allpathslg-52488/src/math/IntFunction.h |
502 |
-+++ allpathslg-52488/src/math/IntFunction.h |
503 |
-@@ -21,6 +21,8 @@ |
504 |
- |
505 |
- #include "MainTools.h" |
506 |
- |
507 |
-+using std::deque; |
508 |
-+using std::fixed; |
509 |
- |
510 |
- #define __INT_FUNCTION_BINARY_VERSION__ 2 |
511 |
- |
512 |
---- allpathslg-52488/src/PackAlign.h |
513 |
-+++ allpathslg-52488/src/PackAlign.h |
514 |
-@@ -133,6 +133,8 @@ |
515 |
- #include "pairwise_aligners/Mutmer.h" |
516 |
- #include "feudal/BinaryStream.h" |
517 |
- |
518 |
-+using std::make_pair; |
519 |
-+ |
520 |
- const int Bits2 = 3, Bits3 = 7, Bits4 = 15, Bits10 = 1023, Bits12 = 4095, |
521 |
- Bits16 = 65535; |
522 |
- |
523 |
---- allpathslg-52488/src/PairsManager.h |
524 |
-+++ allpathslg-52488/src/PairsManager.h |
525 |
-@@ -61,6 +61,7 @@ |
526 |
- #include "feudal/BinaryStream.h" |
527 |
- #include <cstddef> |
528 |
- |
529 |
-+using std::make_pair; |
530 |
- |
531 |
- class PairsManager; // forward declaration |
532 |
- |
533 |
---- allpathslg-52488/src/pairwise_aligners/MakeAlignsMethod.cc |
534 |
-+++ allpathslg-52488/src/pairwise_aligners/MakeAlignsMethod.cc |
535 |
-@@ -19,6 +19,9 @@ |
536 |
- #include "pairwise_aligners/AlignFromMutmers.h" |
537 |
- #include "pairwise_aligners/SmithWatBandedA.h" |
538 |
- |
539 |
-+using std::map; |
540 |
-+using std::set; |
541 |
-+ |
542 |
- // If there's a perfect match of length at least perf but we produced no proper |
543 |
- // alignment, use banded Smith-Waterman to create one. |
544 |
- |
545 |
---- allpathslg-52488/src/pairwise_aligners/MatchList.cc |
546 |
-+++ allpathslg-52488/src/pairwise_aligners/MatchList.cc |
547 |
-@@ -9,6 +9,8 @@ |
548 |
- |
549 |
- #include "pairwise_aligners/MatchList.h" |
550 |
- |
551 |
-+using std::max; |
552 |
-+ |
553 |
- bool MatchList::FindMatchInSorted( const int id1, const Match& newMatch ) const |
554 |
- { |
555 |
- const vec<Match>& sortedMatches = m_sortedMatches[id1]; |
556 |
---- allpathslg-52488/src/paths/AlignHyperKmerPath.cc |
557 |
-+++ allpathslg-52488/src/paths/AlignHyperKmerPath.cc |
558 |
-@@ -23,6 +23,9 @@ |
559 |
- #include "paths/KmerBaseBroker.h" |
560 |
- #include "paths/KmerPath.h" |
561 |
- |
562 |
-+using std::ostringstream; |
563 |
-+using std::set; |
564 |
-+ |
565 |
- // Function: AlignHyperKmerPath |
566 |
- // |
567 |
- // AlignHyperKmerPath takes a HyperKmerPath h, whose KmerPath edges are assumed |
568 |
---- allpathslg-52488/src/paths/CAltFasta.cc |
569 |
-+++ allpathslg-52488/src/paths/CAltFasta.cc |
570 |
-@@ -11,7 +11,7 @@ |
571 |
- #include "paths/FixSomeIndelsUtils.h" |
572 |
- #include "efasta/EfastaTools.h" |
573 |
- |
574 |
-- |
575 |
-+using std::set; |
576 |
- |
577 |
- /** |
578 |
- * CAltFasta |
579 |
---- allpathslg-52488/src/paths/ChangeLibraryStats.cc |
580 |
-+++ allpathslg-52488/src/paths/ChangeLibraryStats.cc |
581 |
-@@ -47,8 +47,10 @@ |
582 |
- |
583 |
- int libID = pairs.libraryID( libName ); |
584 |
- ForceAssertLt( libID, nLibraries); ForceAssertGe( libID, 0 ); |
585 |
-- cout << "old: " << PRINT4( libName, libID, pairs.getLibrarySep(libID), pairs.getLibrarySD(libID) ); |
586 |
-- cout << "new: " << PRINT4( libName, libID, sep, dev ); |
587 |
-+ cout << "old: "; |
588 |
-+ PRINT4( libName, libID, pairs.getLibrarySep(libID), pairs.getLibrarySD(libID) ); |
589 |
-+ cout << "new: "; |
590 |
-+ PRINT4( libName, libID, sep, dev ); |
591 |
- pairs.changeLibrarySepSd( libID, sep, dev ); |
592 |
- } |
593 |
- in.close(); |
594 |
---- allpathslg-52488/src/paths/CorrectLongReadsTools.h |
595 |
-+++ allpathslg-52488/src/paths/CorrectLongReadsTools.h |
596 |
-@@ -16,6 +16,8 @@ |
597 |
- #include "paths/LongReadTools.h" |
598 |
- #include "paths/Uniseq.h" |
599 |
- |
600 |
-+using std::map; |
601 |
-+ |
602 |
- class heuristics { |
603 |
- |
604 |
- public: |
605 |
---- allpathslg-52488/src/paths/ExtendUnipathSeqs.cc |
606 |
-+++ allpathslg-52488/src/paths/ExtendUnipathSeqs.cc |
607 |
-@@ -13,6 +13,9 @@ |
608 |
- |
609 |
- #include <set> |
610 |
- |
611 |
-+using std::set; |
612 |
-+using std::back_inserter; |
613 |
-+ |
614 |
- void ExtendUnipathSeqs( const vecKmerPath& unipaths, |
615 |
- const vecUnipathSeq& unipathSeqs, |
616 |
- vecUnipathSeq& extendedUnipathSeqs, |
617 |
---- allpathslg-52488/src/paths/FindErrorsCore.cc |
618 |
-+++ allpathslg-52488/src/paths/FindErrorsCore.cc |
619 |
-@@ -20,6 +20,8 @@ |
620 |
- #include "kmers/naif_kmer/KernelPreCorrector.h" |
621 |
- #include "system/WorklistN.h" |
622 |
- |
623 |
-+using std::map; |
624 |
-+ |
625 |
- static inline |
626 |
- String Tag(String S = "FEC") { return Date() + " (" + S + "): "; } |
627 |
- |
628 |
---- allpathslg-52488/src/paths/FindErrorsCore.h |
629 |
-+++ allpathslg-52488/src/paths/FindErrorsCore.h |
630 |
-@@ -14,7 +14,7 @@ |
631 |
- |
632 |
- #include "kmers/KmerSpectra.h" |
633 |
- |
634 |
-- |
635 |
-+using std::set; |
636 |
- |
637 |
- class PC_Params |
638 |
- { |
639 |
---- allpathslg-52488/src/paths/FindUnipathSeedsLG.cc |
640 |
-+++ allpathslg-52488/src/paths/FindUnipathSeedsLG.cc |
641 |
-@@ -16,6 +16,8 @@ |
642 |
- #include "paths/simulation/Placement.h" |
643 |
- #include <thread> |
644 |
- |
645 |
-+using std::ostringstream; |
646 |
-+ |
647 |
- // A whole bunch of variables that are shared by parallel threads. |
648 |
- |
649 |
- static const digraphE<fsepdev>* FG_ptr; |
650 |
---- allpathslg-52488/src/paths/FindUnipathSeedsLG.h |
651 |
-+++ allpathslg-52488/src/paths/FindUnipathSeedsLG.h |
652 |
-@@ -19,7 +19,7 @@ |
653 |
- #include "paths/simulation/Placement.h" // placement |
654 |
- #include "paths/UnipathNhoodLG.h" // sepdev, fsepdev |
655 |
- |
656 |
-- |
657 |
-+using std::string; |
658 |
- |
659 |
- enum SeedStatus |
660 |
- { SEED_GOOD, SEED_ISOLATED, SEED_SHORT, SEED_HIGH_CN, SEED_ZERO_CN, SEED_RC_ON_REF, SEED_REDUNDANT, SEED_RC_OF_SEED }; |
661 |
---- allpathslg-52488/src/paths/FixLocal.cc |
662 |
-+++ allpathslg-52488/src/paths/FixLocal.cc |
663 |
-@@ -88,6 +88,8 @@ |
664 |
- #include "paths/Unipath.h" |
665 |
- #include "paths/FindErrorsCore.h" |
666 |
- |
667 |
-+using std::ostringstream; |
668 |
-+ |
669 |
- void AddToPileup( const read_loc& rl, const basevector& b, const qualvector& q, |
670 |
- const basevector& tig, vec<dumbcall>& calls ) |
671 |
- { align a; |
672 |
---- allpathslg-52488/src/paths/FragmentFillerDefs.h |
673 |
-+++ allpathslg-52488/src/paths/FragmentFillerDefs.h |
674 |
-@@ -28,6 +28,8 @@ |
675 |
- #include <set> |
676 |
- #include <time.h> |
677 |
- |
678 |
-+using std::map; |
679 |
-+ |
680 |
- namespace |
681 |
- { |
682 |
- |
683 |
---- allpathslg-52488/src/paths/GetHomes.cc |
684 |
-+++ allpathslg-52488/src/paths/GetHomes.cc |
685 |
-@@ -17,6 +17,8 @@ |
686 |
- #include "paths/Uniseq.h" |
687 |
- #include "util/SearchFastb2Core.h" |
688 |
- |
689 |
-+using std::ostringstream; |
690 |
-+ |
691 |
- class vepath { |
692 |
- |
693 |
- public: |
694 |
---- allpathslg-52488/src/paths/HyperFastavector.cc |
695 |
-+++ allpathslg-52488/src/paths/HyperFastavector.cc |
696 |
-@@ -14,6 +14,8 @@ |
697 |
- #include "feudal/BinaryStream.h" |
698 |
- #include <thread> |
699 |
- |
700 |
-+using std::ostringstream; |
701 |
-+ |
702 |
- // Order a pair of vec<int>s lexicographically using subset relation. |
703 |
- |
704 |
- struct order_vecint_binsubset_pair |
705 |
---- allpathslg-52488/src/paths/HyperKmerPathCleaner.cc |
706 |
-+++ allpathslg-52488/src/paths/HyperKmerPathCleaner.cc |
707 |
-@@ -11,6 +11,7 @@ |
708 |
- #include "paths/HyperKmerPathCleaner.h" |
709 |
- #include <set> |
710 |
- |
711 |
-+using std::set; |
712 |
- |
713 |
- void HyperKmerPathCleaner::CleanUpGraph( HyperKmerPath& ans ) const { |
714 |
- |
715 |
---- allpathslg-52488/src/paths/InsertWalker.h |
716 |
-+++ allpathslg-52488/src/paths/InsertWalker.h |
717 |
-@@ -34,7 +34,7 @@ |
718 |
- #include "paths/KmerPath.h" |
719 |
- #include "TaskTimer.h" // TaskTimer |
720 |
- |
721 |
-- |
722 |
-+using std::set; |
723 |
- |
724 |
- |
725 |
- |
726 |
---- allpathslg-52488/src/paths/InternalMergeImpl.cc |
727 |
-+++ allpathslg-52488/src/paths/InternalMergeImpl.cc |
728 |
-@@ -17,7 +17,7 @@ |
729 |
- #include "paths/InternalMergeImpl.h" |
730 |
- #include "graph/Digraph.h" |
731 |
- |
732 |
-- |
733 |
-+using std::set; |
734 |
- |
735 |
- |
736 |
- /******************************************************************************* |
737 |
---- allpathslg-52488/src/paths/KmerAlignSet.h |
738 |
-+++ allpathslg-52488/src/paths/KmerAlignSet.h |
739 |
-@@ -12,6 +12,8 @@ |
740 |
- #include "Basevector.h" |
741 |
- #include "CoreTools.h" |
742 |
- |
743 |
-+using std::make_pair; |
744 |
-+ |
745 |
- // KmerAlignSet. It represents a set of alignments of a read to unibases, although |
746 |
- // in principle the 'read' could be any sequence and the 'unibases' could be any set |
747 |
- // of sequences. |
748 |
---- allpathslg-52488/src/paths/KmerBaseBroker.h |
749 |
-+++ allpathslg-52488/src/paths/KmerBaseBroker.h |
750 |
-@@ -20,6 +20,8 @@ |
751 |
- #include <algorithm> // for set_union |
752 |
- #include <map> |
753 |
- |
754 |
-+using std::map; |
755 |
-+ |
756 |
- /** |
757 |
- Class: KmerBaseBrokerTemplate |
758 |
- |
759 |
---- allpathslg-52488/src/paths/KmerPathDatabase.cc |
760 |
-+++ allpathslg-52488/src/paths/KmerPathDatabase.cc |
761 |
-@@ -4,6 +4,8 @@ |
762 |
- #include "feudal/BinaryStream.h" |
763 |
- #include <map> |
764 |
- |
765 |
-+using std::map; |
766 |
-+ |
767 |
- // Methods of class KmerPathDatabaseTemplate. |
768 |
- |
769 |
- template <class TAG> |
770 |
---- allpathslg-52488/src/paths/KmerPath.h |
771 |
-+++ allpathslg-52488/src/paths/KmerPath.h |
772 |
-@@ -22,6 +22,8 @@ |
773 |
- #include "HashSimple.h" |
774 |
- #include "graph/Digraph.h" |
775 |
- |
776 |
-+using std::make_pair; |
777 |
-+ |
778 |
- class KmerPathLoc; // forward declaration |
779 |
- |
780 |
- /** |
781 |
---- allpathslg-52488/src/paths/KmerPathInterval.cc |
782 |
-+++ allpathslg-52488/src/paths/KmerPathInterval.cc |
783 |
-@@ -128,11 +128,11 @@ |
784 |
- } |
785 |
- |
786 |
- template void Contains( const vec<tagged_rpint>& segs, kmer_id_t index, |
787 |
-- vec<longlong>& answer, bool append, int cap ); |
788 |
-+ vec<longlong>& answer, bool append = false, int cap = -1 ); |
789 |
- template void Contains( const vec<big_tagged_rpint>& segs, kmer_id_t index, |
790 |
-- vec<longlong>& answer, bool append, int cap ); |
791 |
-+ vec<longlong>& answer, bool append = false, int cap = -1 ); |
792 |
- template void Contains( const vec<new_tagged_rpint>& segs, kmer_id_t index, |
793 |
-- vec<longlong>& answer, bool append, int cap ); |
794 |
-+ vec<longlong>& answer, bool append = false, int cap = -1 ); |
795 |
- |
796 |
- // Overload Contains() with a second version that looks for all intervals overlapping |
797 |
- // a given KmerPathInterval, instead of a single kmer. |
798 |
-@@ -203,11 +203,11 @@ |
799 |
- } |
800 |
- |
801 |
- template void Contains( const vec<tagged_rpint>& segs, KmerPathInterval rpi, |
802 |
-- vec<longlong>& answer, bool append, int cap ); |
803 |
-+ vec<longlong>& answer, bool append = false, int cap = -1 ); |
804 |
- template void Contains( const vec<big_tagged_rpint>& segs, KmerPathInterval rpi, |
805 |
-- vec<longlong>& answer, bool append, int cap ); |
806 |
-+ vec<longlong>& answer, bool append = false, int cap = -1 ); |
807 |
- template void Contains( const vec<new_tagged_rpint>& segs, KmerPathInterval rpi, |
808 |
-- vec<longlong>& answer, bool append, int cap ); |
809 |
-+ vec<longlong>& answer, bool append = false, int cap = -1 ); |
810 |
- |
811 |
- // This will efficiently find a single instance of the requested kmer. |
812 |
- // Intended for base lookup, where you don't need to find all of them. |
813 |
---- allpathslg-52488/src/paths/KmerPathInterval.h |
814 |
-+++ allpathslg-52488/src/paths/KmerPathInterval.h |
815 |
-@@ -8,6 +8,8 @@ |
816 |
- #include "CommonSemanticTypes.h" |
817 |
- #include "feudal/BinaryStreamTraits.h" |
818 |
- |
819 |
-+using std::max; |
820 |
-+ |
821 |
- // Portability note: endianness |
822 |
- // The implementations here would need to be changed for big endian architectures. |
823 |
- |
824 |
-@@ -116,6 +118,15 @@ |
825 |
- To do: check that "gaps in kmer paths are not used for assembly from short reads" |
826 |
- is true. |
827 |
- */ |
828 |
-+ |
829 |
-+class KmerPathInterval; |
830 |
-+ |
831 |
-+template<class TAG> |
832 |
-+void Contains( const vec<TAG>& segs, kmer_id_t index, vec<longlong>& answer, bool append = false, int cap = -1 ); |
833 |
-+ |
834 |
-+template<class TAG> |
835 |
-+void Contains( const vec<TAG>& segs, KmerPathInterval rpi, vec<longlong>& answer, bool append = false, int cap = -1 ); |
836 |
-+ |
837 |
- class KmerPathInterval { |
838 |
- public: |
839 |
- KmerPathInterval( ) { } |
840 |
-@@ -364,11 +375,11 @@ |
841 |
- |
842 |
- template<class TAG> |
843 |
- friend void Contains( const vec<TAG>& segs, kmer_id_t index, |
844 |
-- vec<longlong>& answer, bool append = false, int cap = -1 ); |
845 |
-+ vec<longlong>& answer, bool append, int cap ); |
846 |
- |
847 |
- template<class TAG> |
848 |
- friend void Contains( const vec<TAG>& segs, KmerPathInterval rpi, |
849 |
-- vec<longlong>& answer, bool append = false, int cap = -1 ); |
850 |
-+ vec<longlong>& answer, bool append, int cap ); |
851 |
- |
852 |
- template<class TAG> |
853 |
- friend longlong Instance( const vec<TAG>& segs, kmer_id_t k ); |
854 |
-@@ -491,11 +502,11 @@ |
855 |
- |
856 |
- template<class TAG> |
857 |
- friend void Contains( const vec<TAG>& segs, kmer_id_t index, |
858 |
-- vec<longlong>& answer, bool append = false, int cap = -1 ); |
859 |
-+ vec<longlong>& answer, bool append, int cap ); |
860 |
- |
861 |
- template<class TAG> |
862 |
- friend void Contains( const vec<TAG>& segs, KmerPathInterval rpi, |
863 |
-- vec<longlong>& answer, bool append = false, int cap = -1 ); |
864 |
-+ vec<longlong>& answer, bool append, int cap ); |
865 |
- |
866 |
- template<class TAG> |
867 |
- friend longlong Instance( const vec<TAG>& segs, kmer_id_t k ); |
868 |
-@@ -622,11 +633,11 @@ |
869 |
- |
870 |
- template<class TAG> |
871 |
- friend void Contains( const vec<TAG>& segs, kmer_id_t index, |
872 |
-- vec<longlong>& answer, bool append = false, int cap = -1 ); |
873 |
-+ vec<longlong>& answer, bool append, int cap ); |
874 |
- |
875 |
- template<class TAG> |
876 |
- friend void Contains( const vec<TAG>& segs, KmerPathInterval rpi, |
877 |
-- vec<longlong>& answer, bool append = false, int cap = -1 ); |
878 |
-+ vec<longlong>& answer, bool append, int cap ); |
879 |
- |
880 |
- template<class TAG> |
881 |
- friend kmer_id_t Instance( const vec<TAG>& segs, kmer_id_t k ); |
882 |
---- allpathslg-52488/src/paths/KPatch.cc |
883 |
-+++ allpathslg-52488/src/paths/KPatch.cc |
884 |
-@@ -32,6 +32,8 @@ |
885 |
- #include "paths/AssemblyEdit.h" |
886 |
- #include "paths/GetNexts.h" |
887 |
- |
888 |
-+using std::ostringstream; |
889 |
-+ |
890 |
- template<int K> void PatchMe( const vec<basevector>& jbases_sorted, |
891 |
- const vec<int64_t>& jbases_sorted_id, const PairsManager& jpairs, |
892 |
- const vec< triple<int64_t,int,int> >& jaligns, const vec<superb>& scaffolds, |
893 |
---- allpathslg-52488/src/paths/LinkingPairs.cc |
894 |
-+++ allpathslg-52488/src/paths/LinkingPairs.cc |
895 |
-@@ -9,6 +9,8 @@ |
896 |
- #include "paths/LinkingPairs.h" |
897 |
- #include "math/Array.h" |
898 |
- |
899 |
-+using std::multiset; |
900 |
-+ |
901 |
- void LinkingPairs::Init(int nlibs_, const vec<int>& lens ) |
902 |
- { |
903 |
- nlibs = nlibs_; |
904 |
---- allpathslg-52488/src/paths/long/EvalByReads.cc |
905 |
-+++ allpathslg-52488/src/paths/long/EvalByReads.cc |
906 |
-@@ -19,6 +19,8 @@ |
907 |
- #include <queue> |
908 |
- #include <omp.h> |
909 |
- |
910 |
-+using std::priority_queue; |
911 |
-+ |
912 |
- namespace { |
913 |
- struct CompareReadPlaceByQsum { |
914 |
- bool operator() (const read_place& a, const read_place& b) |
915 |
---- allpathslg-52488/src/paths/long/EvalCorrected.cc |
916 |
-+++ allpathslg-52488/src/paths/long/EvalCorrected.cc |
917 |
-@@ -25,6 +25,8 @@ |
918 |
- #include "paths/long/MakeKmerStuff.h" |
919 |
- #include "random/Random.h" |
920 |
- |
921 |
-+using std::set; |
922 |
-+ |
923 |
- void EvalCorrected( |
924 |
- const VecEFasta& corrected0, // corrected reads |
925 |
- const vec<int>& cid, // ids of corrected reads |
926 |
---- allpathslg-52488/src/paths/long/fosmid/Fosmids.cc |
927 |
-+++ allpathslg-52488/src/paths/long/fosmid/Fosmids.cc |
928 |
-@@ -15,6 +15,9 @@ |
929 |
- #include "paths/long/fosmid/Fosmids.h" |
930 |
- #include "math/HoInterval.h" |
931 |
- |
932 |
-+using std::istringstream; |
933 |
-+using std::ostringstream; |
934 |
-+ |
935 |
- vec<int> ChrSizes(void) |
936 |
- { |
937 |
- return {249250621,243199373,198022430,191154276,180915260,171115067, |
938 |
---- allpathslg-52488/src/paths/long/KmerAlign.cc |
939 |
-+++ allpathslg-52488/src/paths/long/KmerAlign.cc |
940 |
-@@ -12,6 +12,8 @@ |
941 |
- #include "Equiv.h" |
942 |
- #include "VecUtilities.h" |
943 |
- |
944 |
-+using std::map; |
945 |
-+ |
946 |
- void KmerAlign( |
947 |
- const vec< pair<int,int> > & offset, |
948 |
- vec< pair<int,int> > & aligns, |
949 |
---- allpathslg-52488/src/paths/long/OverlapReads.cc |
950 |
-+++ allpathslg-52488/src/paths/long/OverlapReads.cc |
951 |
-@@ -10,6 +10,10 @@ |
952 |
- #include "FeudalMimic.h" |
953 |
- #include <queue> |
954 |
- |
955 |
-+using std::max; |
956 |
-+using std::queue; |
957 |
-+using std::make_pair; |
958 |
-+ |
959 |
- // ================================ static methods ============================= |
960 |
- |
961 |
- // If tail b1[len1-overlap:len1) is the same as head b2[0: overlap) |
962 |
---- allpathslg-52488/src/paths/long/RefTraceTools.cc |
963 |
-+++ allpathslg-52488/src/paths/long/RefTraceTools.cc |
964 |
-@@ -10,6 +10,8 @@ |
965 |
- #include "VecUtilities.h" |
966 |
- #include "math/HoInterval.h" |
967 |
- |
968 |
-+using std::get; |
969 |
-+ |
970 |
- void CreateHBPlus(const HyperBasevector& hb, const vec<int>& inv, |
971 |
- HyperBasevector& hbp, vec<pair<int,Bool>>& hbp_to_hb) |
972 |
- { |
973 |
---- allpathslg-52488/src/paths/long/ultra/ConsensusScoreModel.cc |
974 |
-+++ allpathslg-52488/src/paths/long/ultra/ConsensusScoreModel.cc |
975 |
-@@ -12,6 +12,8 @@ |
976 |
- #include "VecUtilities.h" |
977 |
- #include <map> |
978 |
- |
979 |
-+using std::map; |
980 |
-+ |
981 |
- ConsensusScoreModel::ConsensusScoreModel( double del_rate, double ins_rate, double sub_rate, |
982 |
- bool ignore_matching_score, bool score_fast ) |
983 |
- { |
984 |
---- allpathslg-52488/src/paths/long/VariantCallTools.cc |
985 |
-+++ allpathslg-52488/src/paths/long/VariantCallTools.cc |
986 |
-@@ -27,6 +27,8 @@ |
987 |
- #include "paths/long/VariantReadSupport.h" |
988 |
- #include "kmers/KMer.h" |
989 |
- |
990 |
-+using std::stack; |
991 |
-+ |
992 |
- namespace { |
993 |
- |
994 |
- bool IsBubbleEdge(int eid, const HyperBasevector& hb, const vec<int>& to_left, |
995 |
---- allpathslg-52488/src/paths/long/VariantReadSupport.cc |
996 |
-+++ allpathslg-52488/src/paths/long/VariantReadSupport.cc |
997 |
-@@ -23,6 +23,13 @@ |
998 |
- #include "paths/long/ReadOriginTracker.h" |
999 |
- #include "paths/long/EvalByReads.h" |
1000 |
- |
1001 |
-+#include <cmath> |
1002 |
-+ |
1003 |
-+using std::get; |
1004 |
-+using std::make_tuple; |
1005 |
-+using std::ignore; |
1006 |
-+using std::tie; |
1007 |
-+ |
1008 |
- namespace { |
1009 |
- void CalcLengthProbSimple(vec<double>&vOut,const double dProbIns_len, const double dProbDel_len, const uint64_t org_length){ |
1010 |
- const double dProbIns=dProbIns_len; |
1011 |
-@@ -158,7 +165,7 @@ |
1012 |
- for(uint64_t ff=1;ff<nFlavors;++ff){ |
1013 |
- for( size_t ll = 2 ; ll <= get<0>(n_q_len[ff]) ; ++ll){ dFactor /= (long double)(ll); } |
1014 |
- } |
1015 |
-- if( dFactor==std::numeric_limits<long double>::infinity() || isnan(dFactor) ){ dFactor=1.0; } |
1016 |
-+ if( dFactor==std::numeric_limits<long double>::infinity() || std::isnan(dFactor) ){ dFactor=1.0; } |
1017 |
- if(verbosity>0) std::cout << "dFactor " << dFactor << std::endl; |
1018 |
- |
1019 |
- long double dDenom=0.0; |
1020 |
-@@ -193,7 +200,7 @@ |
1021 |
- } |
1022 |
- } |
1023 |
- if(verbosity>0) std::cout <<"denom: " << dDenom<< std::endl; |
1024 |
-- if( dDenom < std::numeric_limits<long double>::epsilon() * 100 || isnan(dDenom)) return; |
1025 |
-+ if( dDenom < std::numeric_limits<long double>::epsilon() * 100 || std::isnan(dDenom)) return; |
1026 |
- ForceAssert(dDenom>0); |
1027 |
- if(verbosity>0){ |
1028 |
- for( uint64_t row=0;row<nFlavors;++row){ |
1029 |
---- allpathslg-52488/src/paths/long/VariantReadSupport.h |
1030 |
-+++ allpathslg-52488/src/paths/long/VariantReadSupport.h |
1031 |
-@@ -5,6 +5,8 @@ |
1032 |
- #include "Qualvector.h" |
1033 |
- #include "paths/HyperBasevector.h" |
1034 |
- |
1035 |
-+using std::tuple; |
1036 |
-+ |
1037 |
- // forward declaration |
1038 |
- class read_place; |
1039 |
- class ReadOriginTracker; |
1040 |
---- allpathslg-52488/src/paths/long/Variants.cc |
1041 |
-+++ allpathslg-52488/src/paths/long/Variants.cc |
1042 |
-@@ -22,6 +22,8 @@ |
1043 |
- #include "paths/long/VariantFilters.h" |
1044 |
- #include "paths/long/VariantPostProcess.h" |
1045 |
- |
1046 |
-+using std::set; |
1047 |
-+ |
1048 |
- int MarkVariants( HyperEfasta& he, const vec<VariantSignature>& v_signatures, |
1049 |
- const long_logging& logc ) |
1050 |
- { double clock = WallClockTime( ); |
1051 |
---- allpathslg-52488/src/paths/LongReadTools.h |
1052 |
-+++ allpathslg-52488/src/paths/LongReadTools.h |
1053 |
-@@ -17,6 +17,8 @@ |
1054 |
- #include "kmers/KmerRecord.h" |
1055 |
- #include "paths/AssemblyEdit.h" |
1056 |
- |
1057 |
-+using std::ostringstream; |
1058 |
-+ |
1059 |
- // A gap patcher is defined by left and right ints u1 and u2, and a BaseVec r, |
1060 |
- // whose left end aligns to u1 starting at tpos1 and whose right end aligns to u2 |
1061 |
- // ending at tpos2, where the positions are in terms of the BaseVecs associated |
1062 |
---- allpathslg-52488/src/paths/MakeScaffoldsCloseBest.cc |
1063 |
-+++ allpathslg-52488/src/paths/MakeScaffoldsCloseBest.cc |
1064 |
-@@ -29,6 +29,8 @@ |
1065 |
- #include "paths/reporting/CLinkBundle.h" |
1066 |
- #include <sstream> |
1067 |
- |
1068 |
-+using std::ostringstream; |
1069 |
-+ |
1070 |
- // An slink is a link between scaffolds. The first scaffold is not represented |
1071 |
- // in the object. |
1072 |
- |
1073 |
---- allpathslg-52488/src/paths/Mixmer.cc |
1074 |
-+++ allpathslg-52488/src/paths/Mixmer.cc |
1075 |
-@@ -73,6 +73,9 @@ |
1076 |
- #include "util/ReadTracker.h" |
1077 |
- #include "util/SearchFastb2Core.h" |
1078 |
- |
1079 |
-+using std::ostringstream; |
1080 |
-+using std::istrstream; |
1081 |
-+ |
1082 |
- // CorrectErrors. |
1083 |
- |
1084 |
- void CorrectErrors( vecbasevector& bases, vecqualvector& quals, |
1085 |
---- allpathslg-52488/src/paths/MuxGraph.cc |
1086 |
-+++ allpathslg-52488/src/paths/MuxGraph.cc |
1087 |
-@@ -6,6 +6,7 @@ |
1088 |
- |
1089 |
- #include <set> |
1090 |
- |
1091 |
-+using std::set; |
1092 |
- |
1093 |
- // Functions to translate pathIds to nodeIds and back. |
1094 |
- |
1095 |
---- allpathslg-52488/src/paths/MuxSearchAgent.h |
1096 |
-+++ allpathslg-52488/src/paths/MuxSearchAgent.h |
1097 |
-@@ -15,6 +15,10 @@ |
1098 |
- #include "paths/MuxSearchState.h" |
1099 |
- #include "paths/MuxSearchPolicy.h" |
1100 |
- |
1101 |
-+using std::hex; |
1102 |
-+using std::dec; |
1103 |
-+using std::mem_fun; |
1104 |
-+ |
1105 |
- /// The search agent directed by the SearchDirector of a |
1106 |
- /// KmerPathMuxSearcher. |
1107 |
- /// |
1108 |
---- allpathslg-52488/src/paths/MuxSearchPolicy.h |
1109 |
-+++ allpathslg-52488/src/paths/MuxSearchPolicy.h |
1110 |
-@@ -29,6 +29,7 @@ |
1111 |
- #include <hash_set> |
1112 |
- #endif |
1113 |
- |
1114 |
-+using std::map; |
1115 |
- |
1116 |
- //////////////////////////////////////////////////////////////////////////// |
1117 |
- /// |
1118 |
---- allpathslg-52488/src/paths/OffsetTracker.cc |
1119 |
-+++ allpathslg-52488/src/paths/OffsetTracker.cc |
1120 |
-@@ -10,6 +10,8 @@ |
1121 |
- #include "paths/OffsetTracker.h" |
1122 |
- #include <queue> |
1123 |
- |
1124 |
-+using std::priority_queue; |
1125 |
-+ |
1126 |
- MutableOffsetTracker::MutableOffsetTracker( const vecUnipathSeq& unipathSeqs, |
1127 |
- const MuxGraph& inverseMuxGraph, |
1128 |
- const int firstSuperSeq, |
1129 |
---- allpathslg-52488/src/paths/PairDistFitting.h |
1130 |
-+++ allpathslg-52488/src/paths/PairDistFitting.h |
1131 |
-@@ -38,7 +38,7 @@ |
1132 |
- // |
1133 |
- template <class T> |
1134 |
- void MostProbableGap( const T& distr, const int len1, const int len2, const vec< pair< int, int > >& links, |
1135 |
-- int& gap, int& std, bool verbose=false ) |
1136 |
-+ int& gap, int& std, bool verbose ) |
1137 |
- { |
1138 |
- ForceAssertGt( links.isize(), 0 ); |
1139 |
- // find the averge of x1 + x2 ( <x1+x2> = <L> - g in the ideal case ) |
1140 |
---- allpathslg-52488/src/paths/PairDistModels.h |
1141 |
-+++ allpathslg-52488/src/paths/PairDistModels.h |
1142 |
-@@ -23,6 +23,8 @@ |
1143 |
- #include <map> |
1144 |
- #include "math/IntDistribution.h" |
1145 |
- |
1146 |
-+using std::map; |
1147 |
-+ |
1148 |
- // ===================================================== |
1149 |
- // Class ProbFuncInterface |
1150 |
- // |
1151 |
---- allpathslg-52488/src/paths/PatcherCottageCore.cc |
1152 |
-+++ allpathslg-52488/src/paths/PatcherCottageCore.cc |
1153 |
-@@ -22,6 +22,8 @@ |
1154 |
- #include "system/AllOfOutput.h" |
1155 |
- #include "system/SharedMem.h" |
1156 |
- |
1157 |
-+using std::ostringstream; |
1158 |
-+ |
1159 |
- void PatcherCottageCore( basevector L, basevector R, const int sep, |
1160 |
- const int dev, vecbasevector& reads, vecqualvector& quals, |
1161 |
- vec< pair<int,int> >& pairs, String& report, |
1162 |
---- allpathslg-52488/src/paths/PolymorphismRemoveCore.h |
1163 |
-+++ allpathslg-52488/src/paths/PolymorphismRemoveCore.h |
1164 |
-@@ -19,7 +19,7 @@ |
1165 |
- |
1166 |
- #include "kmers/naif_kmer/KmerFreqAffixesMap.h" |
1167 |
- |
1168 |
-- |
1169 |
-+using std::map; |
1170 |
- |
1171 |
- typedef Kmer29 Kmer_t; |
1172 |
- typedef KmerFreqAffixes<Kmer_t> KmerRec_t; |
1173 |
---- allpathslg-52488/src/paths/ReadsToPathsCoreX.cc |
1174 |
-+++ allpathslg-52488/src/paths/ReadsToPathsCoreX.cc |
1175 |
-@@ -20,6 +20,8 @@ |
1176 |
- #include "paths/MakeAlignsPathsParallelX.h" |
1177 |
- #include "paths/ReadsToPathsCoreX.h" |
1178 |
- |
1179 |
-+using std::map; |
1180 |
-+ |
1181 |
- static inline |
1182 |
- String Tag(String S = "RTPCX") { return Date() + " (" + S + "): "; } |
1183 |
- |
1184 |
---- allpathslg-52488/src/paths/RemodelGapTools.cc |
1185 |
-+++ allpathslg-52488/src/paths/RemodelGapTools.cc |
1186 |
-@@ -18,6 +18,9 @@ |
1187 |
- #include "paths/RemodelGapTools.h" |
1188 |
- #include "random/NormalDistribution.h" |
1189 |
- |
1190 |
-+using std::istringstream; |
1191 |
-+using std::ostringstream; |
1192 |
-+ |
1193 |
- // GapComp |
1194 |
- // |
1195 |
- // d = possible gap |
1196 |
---- allpathslg-52488/src/paths/reporting/CLinkBundle.cc |
1197 |
-+++ allpathslg-52488/src/paths/reporting/CLinkBundle.cc |
1198 |
-@@ -8,6 +8,8 @@ |
1199 |
- |
1200 |
- #include "paths/reporting/CLinkBundle.h" |
1201 |
- |
1202 |
-+using std::make_pair; |
1203 |
-+ |
1204 |
- /** |
1205 |
- * CLinkBundle |
1206 |
- * Constructor |
1207 |
---- allpathslg-52488/src/paths/reporting/CSuperLinks.cc |
1208 |
-+++ allpathslg-52488/src/paths/reporting/CSuperLinks.cc |
1209 |
-@@ -15,6 +15,8 @@ |
1210 |
- #include "paths/reporting/COffset.h" |
1211 |
- #include "paths/reporting/CSuperLinks.h" |
1212 |
- |
1213 |
-+using std::set; |
1214 |
-+ |
1215 |
- /** |
1216 |
- * class CSuperLinks |
1217 |
- * Constructor |
1218 |
---- allpathslg-52488/src/paths/reporting/MapSeeds.cc |
1219 |
-+++ allpathslg-52488/src/paths/reporting/MapSeeds.cc |
1220 |
-@@ -24,7 +24,7 @@ |
1221 |
- #include "paths/simulation/Placement.h" |
1222 |
- #include "feudal/BinaryStream.h" |
1223 |
- |
1224 |
-- |
1225 |
-+using std::ostringstream; |
1226 |
- |
1227 |
- // MakeDepend: dependency QueryLookupTable |
1228 |
- |
1229 |
---- allpathslg-52488/src/paths/SamplePairedReadDistributions.cc |
1230 |
-+++ allpathslg-52488/src/paths/SamplePairedReadDistributions.cc |
1231 |
-@@ -68,6 +68,8 @@ |
1232 |
- #include "math/IntDistribution.h" |
1233 |
- #include "math/IntFrequencies.h" |
1234 |
- |
1235 |
-+using std::list; |
1236 |
-+ |
1237 |
- static inline |
1238 |
- String Tag(String S = "SPRD") { return Date() + " (" + S + "): "; } |
1239 |
- |
1240 |
---- allpathslg-52488/src/paths/SamplePairedReadStats.cc |
1241 |
-+++ allpathslg-52488/src/paths/SamplePairedReadStats.cc |
1242 |
-@@ -46,6 +46,8 @@ |
1243 |
- #include "paths/HyperBasevector.h" |
1244 |
- #include "paths/ReadsToPathsCoreX.h" |
1245 |
- |
1246 |
-+using std::list; |
1247 |
-+ |
1248 |
- // auxiliary routines ------------------------------- |
1249 |
- void pair_alignment_data( const PairsManager& pairs, const vecbasevector& reads, const VecQualNibbleVec &quals, |
1250 |
- FirstLookupFinderECJ& lfinder, FirstLookupFilterECJ& lfilter, |
1251 |
---- allpathslg-52488/src/paths/SimpleGapCloser.cc |
1252 |
-+++ allpathslg-52488/src/paths/SimpleGapCloser.cc |
1253 |
-@@ -44,6 +44,8 @@ |
1254 |
- #include "paths/Unipath.h" |
1255 |
- #include "system/AllOfOutput.h" |
1256 |
- |
1257 |
-+using std::ostringstream; |
1258 |
-+ |
1259 |
- class bridge { |
1260 |
- |
1261 |
- public: |
1262 |
---- allpathslg-52488/src/paths/SimpleWalk.cc |
1263 |
-+++ allpathslg-52488/src/paths/SimpleWalk.cc |
1264 |
-@@ -15,6 +15,9 @@ |
1265 |
- #include "paths/PairedPair.h" |
1266 |
- #include "paths/SimpleWalk.h" |
1267 |
- |
1268 |
-+using std::make_pair; |
1269 |
-+using std::priority_queue; |
1270 |
-+ |
1271 |
- namespace |
1272 |
- { |
1273 |
- |
1274 |
---- allpathslg-52488/src/paths/simulation/VCF.cc |
1275 |
-+++ allpathslg-52488/src/paths/simulation/VCF.cc |
1276 |
-@@ -16,6 +16,8 @@ |
1277 |
- #include "system/Assert.h" |
1278 |
- #include <utility> |
1279 |
- |
1280 |
-+using std::istringstream; |
1281 |
-+ |
1282 |
- namespace { |
1283 |
- |
1284 |
- // split - tokenize a string based on a separator and return a vector of strings representing the |
1285 |
---- allpathslg-52488/src/paths/simulation/VCF.h |
1286 |
-+++ allpathslg-52488/src/paths/simulation/VCF.h |
1287 |
-@@ -21,7 +21,8 @@ |
1288 |
- |
1289 |
- using std::string; |
1290 |
- using std::vector; |
1291 |
-- |
1292 |
-+using std::ostringstream; |
1293 |
-+using std::map; |
1294 |
- |
1295 |
- // VCFWriter use a streamlined data structure compared to VCF, which was hard coded to use VCFChromosome |
1296 |
- class VCFWriter |
1297 |
---- allpathslg-52488/src/paths/SubmissionPrep.cc |
1298 |
-+++ allpathslg-52488/src/paths/SubmissionPrep.cc |
1299 |
-@@ -21,6 +21,8 @@ |
1300 |
- #include "paths/AssemblyCleanupTools.h" |
1301 |
- #include "math/HoInterval.h" |
1302 |
- |
1303 |
-+using std::ostringstream; |
1304 |
-+ |
1305 |
- /** |
1306 |
- * SubmissionPrep |
1307 |
- * |
1308 |
---- allpathslg-52488/src/paths/SubsumptionList.cc |
1309 |
-+++ allpathslg-52488/src/paths/SubsumptionList.cc |
1310 |
-@@ -2,6 +2,8 @@ |
1311 |
- |
1312 |
- #include "paths/SubsumptionList.h" |
1313 |
- |
1314 |
-+using std::back_inserter; |
1315 |
-+ |
1316 |
- // Functions to translate pathIds to indexes and back. |
1317 |
- |
1318 |
- OrientedKmerPathId PathIdFromIndex( int index ) |
1319 |
---- allpathslg-52488/src/paths/SuperBaseVector.h |
1320 |
-+++ allpathslg-52488/src/paths/SuperBaseVector.h |
1321 |
-@@ -10,6 +10,8 @@ |
1322 |
- #include <numeric> |
1323 |
- #include <functional> |
1324 |
- |
1325 |
-+using std::mem_fun_ref; |
1326 |
-+ |
1327 |
- /// A simple class which holds a series of basevectors with |
1328 |
- /// (possibly negative) gaps between them. This is what a |
1329 |
- /// KmerPath logically maps to in sequence space. The function |
1330 |
---- allpathslg-52488/src/paths/UnibaseCopyNumber3.cc |
1331 |
-+++ allpathslg-52488/src/paths/UnibaseCopyNumber3.cc |
1332 |
-@@ -43,7 +43,7 @@ |
1333 |
- #include <omp.h> |
1334 |
- // MakeDepend: library OMP |
1335 |
- |
1336 |
-- |
1337 |
-+using std::istrstream; |
1338 |
- |
1339 |
- // Check if the gap size from u1 to u2 is the same as from u2* to u1*. |
1340 |
- void CheckGaps( |
1341 |
---- allpathslg-52488/src/paths/UnipathEval.cc |
1342 |
-+++ allpathslg-52488/src/paths/UnipathEval.cc |
1343 |
-@@ -35,6 +35,9 @@ |
1344 |
- #include <omp.h> |
1345 |
- // MakeDepend: library OMP |
1346 |
- |
1347 |
-+using std::ostringstream; |
1348 |
-+using std::list; |
1349 |
-+ |
1350 |
- typedef double gc_t; |
1351 |
- typedef int unipath_size_t; |
1352 |
- typedef BinsVec2 < unipath_size_t, gc_t, PredictionStats > bin2PredStat; |
1353 |
---- allpathslg-52488/src/paths/UnipathFixerTools.cc |
1354 |
-+++ allpathslg-52488/src/paths/UnipathFixerTools.cc |
1355 |
-@@ -33,6 +33,8 @@ |
1356 |
- #include "util/SearchFastb2Core.h" |
1357 |
- #include <vector> |
1358 |
- |
1359 |
-+using std::ostringstream; |
1360 |
-+ |
1361 |
- size_t const PCottageJoinData::HEADER; |
1362 |
- |
1363 |
- void AlignReadsToUnipaths( const String& run_dir, const String& jump_reads, |
1364 |
---- allpathslg-52488/src/paths/UnipathNhoodCommon.cc |
1365 |
-+++ allpathslg-52488/src/paths/UnipathNhoodCommon.cc |
1366 |
-@@ -12,6 +12,8 @@ |
1367 |
- #include "paths/simulation/Placement.h" |
1368 |
- #include <sstream> |
1369 |
- |
1370 |
-+using std::ostringstream; |
1371 |
-+ |
1372 |
- /** |
1373 |
- Function: PrintNhood |
1374 |
- |
1375 |
---- allpathslg-52488/src/paths/UnipathPatcher.cc |
1376 |
-+++ allpathslg-52488/src/paths/UnipathPatcher.cc |
1377 |
-@@ -47,6 +47,8 @@ |
1378 |
- #include "paths/UnipathFixerTools.h" |
1379 |
- #include "system/SharedMem.h" |
1380 |
- |
1381 |
-+using std::istrstream; |
1382 |
-+ |
1383 |
- void GapStatsAlt( vec<int> gap, vec<int> gapdev, int& gap_ave, int& gapdev_ave ) |
1384 |
- { |
1385 |
- // If there are less than six gaps, we directly compute their mean. |
1386 |
---- allpathslg-52488/src/paths/Uniseq.cc |
1387 |
-+++ allpathslg-52488/src/paths/Uniseq.cc |
1388 |
-@@ -498,7 +498,7 @@ |
1389 |
- const gapster& gx = G( ).EdgeObjectByIndexFrom( x, 0 ); |
1390 |
- uniseq p = Vert(x); |
1391 |
- int y = From(x)[0]; |
1392 |
-- if ( !To(y).size( ) == 2 ) continue; |
1393 |
-+ if ( !(To(y).size( ) == 2) ) continue; |
1394 |
- int e = -1; |
1395 |
- for ( int j = 0; j < To(y).isize( ); j++ ) |
1396 |
- if ( To(y)[j] != x ) e = j; |
1397 |
-@@ -518,7 +518,7 @@ |
1398 |
- const gapster& gx = G( ).EdgeObjectByIndexTo( x, 0 ); |
1399 |
- uniseq p = Vert(x); |
1400 |
- int y = To(x)[0]; |
1401 |
-- if ( !From(y).size( ) == 2 ) continue; |
1402 |
-+ if ( !(From(y).size( ) == 2) ) continue; |
1403 |
- int e = -1; |
1404 |
- for ( int j = 0; j < From(y).isize( ); j++ ) |
1405 |
- if ( From(y)[j] != x ) e = j; |
1406 |
---- allpathslg-52488/src/paths/Useq.cc |
1407 |
-+++ allpathslg-52488/src/paths/Useq.cc |
1408 |
-@@ -10,6 +10,8 @@ |
1409 |
- #include "CoreTools.h" |
1410 |
- #include "paths/Useq.h" |
1411 |
- |
1412 |
-+using std::make_pair; |
1413 |
-+ |
1414 |
- int useq::Kmers( ) const |
1415 |
- { Assert( unibases_ != 0 ); |
1416 |
- int kmers = 0; |
1417 |
---- allpathslg-52488/src/PrintAlignment.h |
1418 |
-+++ allpathslg-52488/src/PrintAlignment.h |
1419 |
-@@ -14,6 +14,8 @@ |
1420 |
- #include "CoreTools.h" |
1421 |
- #include "Qualvector.h" |
1422 |
- |
1423 |
-+using std::ostringstream; |
1424 |
-+ |
1425 |
- void PrintBlanks( ostream& out, int n ); |
1426 |
- |
1427 |
- template<class BASEVEC> |
1428 |
---- allpathslg-52488/src/Qualvector.cc |
1429 |
-+++ allpathslg-52488/src/Qualvector.cc |
1430 |
-@@ -10,6 +10,8 @@ |
1431 |
- #include "FastIfstream.h" |
1432 |
- #include "Qualvector.h" |
1433 |
- |
1434 |
-+using std::istrstream; |
1435 |
-+ |
1436 |
- /// \file |
1437 |
- /// \ingroup grp_quals |
1438 |
- /// \copydoc Qualvector.h |
1439 |
---- allpathslg-52488/src/ReadLocation.cc |
1440 |
-+++ allpathslg-52488/src/ReadLocation.cc |
1441 |
-@@ -16,6 +16,9 @@ |
1442 |
- #include "Vec.h" |
1443 |
- #include "system/file/FileReader.h" |
1444 |
- |
1445 |
-+using std::streampos; |
1446 |
-+using std::map; |
1447 |
-+ |
1448 |
- void read_location::ForceInBounds( ostream * out_ptr ) |
1449 |
- { if ( (int) LengthOfRead( ) > LengthOfContig( ) ) |
1450 |
- { if ( out_ptr ) |
1451 |
---- allpathslg-52488/src/ReadLocationUtil.cc |
1452 |
-+++ allpathslg-52488/src/ReadLocationUtil.cc |
1453 |
-@@ -9,7 +9,7 @@ |
1454 |
- #include "STLExtensions.h" |
1455 |
- #include "VecAlignmentPlus.h" |
1456 |
- |
1457 |
-- |
1458 |
-+using std::map; |
1459 |
- |
1460 |
- int AlignsCount( const vec<read_location> &locs, |
1461 |
- int loc_id, |
1462 |
---- allpathslg-52488/src/reporting/ScaffoldLayout.cc |
1463 |
-+++ allpathslg-52488/src/reporting/ScaffoldLayout.cc |
1464 |
-@@ -21,6 +21,8 @@ |
1465 |
- #include <omp.h> |
1466 |
- // MakeDepend: library OMP |
1467 |
- |
1468 |
-+using std::ostringstream; |
1469 |
-+ |
1470 |
- int main(int argc, char **argv) |
1471 |
- { |
1472 |
- RunTime( ); |
1473 |
---- allpathslg-52488/src/SeqInterval.cc |
1474 |
-+++ allpathslg-52488/src/SeqInterval.cc |
1475 |
-@@ -9,6 +9,7 @@ |
1476 |
- #include "SeqInterval.h" |
1477 |
- #include "Vec.h" |
1478 |
- |
1479 |
-+using std::min; |
1480 |
- |
1481 |
- /* |
1482 |
- * seq_interval |
1483 |
---- allpathslg-52488/src/SeqInterval.h |
1484 |
-+++ allpathslg-52488/src/SeqInterval.h |
1485 |
-@@ -14,7 +14,10 @@ |
1486 |
- #include <algorithm> |
1487 |
- #include <iostream> |
1488 |
- |
1489 |
--using namespace std; |
1490 |
-+using std::binary_function; |
1491 |
-+using std::ostream; |
1492 |
-+using std::istream; |
1493 |
-+using std::max; |
1494 |
- |
1495 |
- /* |
1496 |
- * class seq_interval |
1497 |
---- allpathslg-52488/src/Set.h |
1498 |
-+++ allpathslg-52488/src/Set.h |
1499 |
-@@ -16,6 +16,8 @@ |
1500 |
- #include <iostream> |
1501 |
- #include <set> |
1502 |
- |
1503 |
-+using std::set; |
1504 |
-+ |
1505 |
- template <class T, class C=std::less<T>> |
1506 |
- using StdSet = std::set<T,C,typename DefaultAllocator<T>::type>; |
1507 |
- |
1508 |
---- allpathslg-52488/src/ShortVector.h |
1509 |
-+++ allpathslg-52488/src/ShortVector.h |
1510 |
-@@ -14,6 +14,8 @@ |
1511 |
- #include "system/Types.h" |
1512 |
- #include "feudal/BinaryStream.h" |
1513 |
- |
1514 |
-+using std::uninitialized_fill_n; |
1515 |
-+ |
1516 |
- // ================================================================================ |
1517 |
- // |
1518 |
- // A shortvector holds a list of up to 255 things of any type T. |
1519 |
---- allpathslg-52488/src/STLExtensions.h |
1520 |
-+++ allpathslg-52488/src/STLExtensions.h |
1521 |
-@@ -9,8 +9,6 @@ |
1522 |
- #ifndef STLEXTENSIONS_H |
1523 |
- #define STLEXTENSIONS_H |
1524 |
- |
1525 |
--using namespace std; |
1526 |
-- |
1527 |
- #include <functional> |
1528 |
- #include <vector> |
1529 |
- #include <bitset> |
1530 |
-@@ -21,6 +19,14 @@ |
1531 |
- #include "feudal/BinaryStream.h" |
1532 |
- #include "system/StaticAssert.h" |
1533 |
- |
1534 |
-+using std::binary_function; |
1535 |
-+using std::unary_function; |
1536 |
-+using std::pair; |
1537 |
-+using std::bitset; |
1538 |
-+using std::initializer_list; |
1539 |
-+using std::vector; |
1540 |
-+using std::ostream; |
1541 |
-+ |
1542 |
- /// minimum<T> is a function object. |
1543 |
- /// |
1544 |
- /// If f is an object of class minimum<T> and x and y are objects of |
1545 |
---- allpathslg-52488/src/system/MiscUtil.cc |
1546 |
-+++ allpathslg-52488/src/system/MiscUtil.cc |
1547 |
-@@ -21,6 +21,8 @@ |
1548 |
- #include "system/HTMLUtils.h" |
1549 |
- #include "system/Utils.h" |
1550 |
- |
1551 |
-+using std::list; |
1552 |
-+ |
1553 |
- static Bool makeOnlyIfNeeded = True; |
1554 |
- |
1555 |
- void SetMakeOnlyIfNeeded( Bool newMakeOnlyIfNeeded ) { |
1556 |
---- allpathslg-52488/src/system/MiscUtil.h |
1557 |
-+++ allpathslg-52488/src/system/MiscUtil.h |
1558 |
-@@ -27,6 +27,9 @@ |
1559 |
- #include "CommonSemanticTypes.h" |
1560 |
- #include "graph/Digraph.h" |
1561 |
- |
1562 |
-+using std::map; |
1563 |
-+using std::set; |
1564 |
-+ |
1565 |
- // Semantic type: shellcmd_t |
1566 |
- // The name of a shell command. |
1567 |
- SemanticType( String, shellcmd_t ); |
1568 |
---- allpathslg-52488/src/system/ParsedArgs.cc |
1569 |
-+++ allpathslg-52488/src/system/ParsedArgs.cc |
1570 |
-@@ -26,6 +26,9 @@ |
1571 |
- #include "system/HostName.h" |
1572 |
- #include "system/UseGDB.h" |
1573 |
- |
1574 |
-+using std::istrstream; |
1575 |
-+using std::mem_fun_ref; |
1576 |
-+ |
1577 |
- #ifndef FatalErr |
1578 |
- #define FatalErr(message) { cout << message << endl << endl; exit(-1); } |
1579 |
- #endif |
1580 |
---- allpathslg-52488/src/system/ParsedArgs.h |
1581 |
-+++ allpathslg-52488/src/system/ParsedArgs.h |
1582 |
-@@ -97,6 +97,8 @@ |
1583 |
- #include "TokenizeString.h" |
1584 |
- #include "ParseSet.h" |
1585 |
- |
1586 |
-+using std::stringstream; |
1587 |
-+ |
1588 |
- class parsed_arg_help { |
1589 |
- |
1590 |
- public: |
1591 |
---- allpathslg-52488/src/system/ProcBuf.cc |
1592 |
-+++ allpathslg-52488/src/system/ProcBuf.cc |
1593 |
-@@ -15,6 +15,8 @@ |
1594 |
- #include <sys/wait.h> |
1595 |
- #include <unistd.h> |
1596 |
- |
1597 |
-+using std::ios_base; |
1598 |
-+ |
1599 |
- namespace |
1600 |
- { |
1601 |
- size_t const BUFFER_SIZE = 8192; |
1602 |
---- allpathslg-52488/src/system/RunTime.cc |
1603 |
-+++ allpathslg-52488/src/system/RunTime.cc |
1604 |
-@@ -41,6 +41,10 @@ |
1605 |
- #include <unwind.h> |
1606 |
- #endif |
1607 |
- |
1608 |
-+using std::strstream; |
1609 |
-+using std::hex; |
1610 |
-+using std::setw; |
1611 |
-+ |
1612 |
- /// =========================================================================== |
1613 |
- /// |
1614 |
- /// ReturnAddress(i), where 0 <= i <= 100: get the return address. The |
1615 |
---- allpathslg-52488/src/system/RunTime.h |
1616 |
-+++ allpathslg-52488/src/system/RunTime.h |
1617 |
-@@ -14,6 +14,8 @@ |
1618 |
- #include "system/Exit.h" |
1619 |
- #include "system/Types.h" |
1620 |
- |
1621 |
-+using std::ostream; |
1622 |
-+ |
1623 |
- typedef void ArachneSignalHandler(int, siginfo_t*, void*); |
1624 |
- |
1625 |
- void arachne_signal_handler( int signal_number, siginfo_t* info, void* context, |
1626 |
---- allpathslg-52488/src/system/System.cc |
1627 |
-+++ allpathslg-52488/src/system/System.cc |
1628 |
-@@ -36,6 +36,10 @@ |
1629 |
- |
1630 |
- #include <dirent.h> |
1631 |
- |
1632 |
-+using std::istringstream; |
1633 |
-+using std::istream_iterator; |
1634 |
-+using std::ostringstream; |
1635 |
-+ |
1636 |
- int SystemInternal( String command, const char *shell, |
1637 |
- int* pStatus, int* pErrNo ) |
1638 |
- { |
1639 |
-@@ -1088,7 +1092,7 @@ |
1640 |
- |
1641 |
- bool isReadable( String const& filename ) |
1642 |
- { ifstream ifs(filename.c_str()); |
1643 |
-- return ifs; } |
1644 |
-+ return static_cast<bool>(ifs); } |
1645 |
- |
1646 |
- int Glob( const String& x, vector<String>& xs ) |
1647 |
- { glob_t globbuf; |
1648 |
---- allpathslg-52488/src/system/System.h |
1649 |
-+++ allpathslg-52488/src/system/System.h |
1650 |
-@@ -21,6 +21,18 @@ |
1651 |
- #include "system/Exit.h" |
1652 |
- #include "system/file/TempFile.h" |
1653 |
- |
1654 |
-+using std::vector; |
1655 |
-+using std::ostream; |
1656 |
-+using std::ofstream; |
1657 |
-+using std::ifstream; |
1658 |
-+using std::istream; |
1659 |
-+using std::ios; |
1660 |
-+using std::cout; |
1661 |
-+using std::flush; |
1662 |
-+using std::endl; |
1663 |
-+using std::setprecision; |
1664 |
-+using std::fixed; |
1665 |
-+ |
1666 |
- #ifndef InputErr |
1667 |
- #define InputErr(message) \ |
1668 |
- cout << "\nFatal error at " << Date() << ": " << message \ |
1669 |
---- allpathslg-52488/src/system/TraceVal.h |
1670 |
-+++ allpathslg-52488/src/system/TraceVal.h |
1671 |
-@@ -25,6 +25,9 @@ |
1672 |
- #include "system/Assert.h" |
1673 |
- #include "system/Exit.h" |
1674 |
- |
1675 |
-+using std::cout; |
1676 |
-+using std::endl; |
1677 |
-+ |
1678 |
- // Macros: Tracing macros |
1679 |
- // TRACEVAL_ON - undefine if you're not doing tracing |
1680 |
- // TRACEVAL_STOP_TRACING_COPIES -- call before an operation that shuffles |
1681 |
---- allpathslg-52488/src/system/Types.h |
1682 |
-+++ allpathslg-52488/src/system/Types.h |
1683 |
-@@ -14,7 +14,7 @@ |
1684 |
- #include <cstdlib> |
1685 |
- #include <netinet/in.h> |
1686 |
- |
1687 |
--using namespace std; |
1688 |
-+ |
1689 |
- |
1690 |
- // This assumes that all suns run Solaris... |
1691 |
- #if __sun == 1 |
1692 |
---- allpathslg-52488/src/system/WorklistUtils.cc |
1693 |
-+++ allpathslg-52488/src/system/WorklistUtils.cc |
1694 |
-@@ -32,6 +32,10 @@ |
1695 |
- #include <sys/resource.h> |
1696 |
- #include <unistd.h> |
1697 |
- |
1698 |
-+using std::istringstream; |
1699 |
-+using std::istream_iterator; |
1700 |
-+using std::min; |
1701 |
-+ |
1702 |
- namespace |
1703 |
- { |
1704 |
- pthread_t gMainThread; |
1705 |
---- allpathslg-52488/src/util/FastaParser.cc |
1706 |
-+++ allpathslg-52488/src/util/FastaParser.cc |
1707 |
-@@ -22,6 +22,7 @@ |
1708 |
- |
1709 |
- using std::string; |
1710 |
- using std::vector; |
1711 |
-+using std::istringstream; |
1712 |
- |
1713 |
- char* FastaParser::readLine() |
1714 |
- { |
1715 |
---- allpathslg-52488/src/util/FastaParser.h |
1716 |
-+++ allpathslg-52488/src/util/FastaParser.h |
1717 |
-@@ -24,6 +24,8 @@ |
1718 |
- #include <fstream> |
1719 |
- #include <vector> |
1720 |
- |
1721 |
-+using std::max; |
1722 |
-+ |
1723 |
- /// Base class for the parsers for sequence, quality, and bits which follow. |
1724 |
- class FastaParser |
1725 |
- { |
1726 |
---- allpathslg-52488/src/util/FastbStats.cc |
1727 |
-+++ allpathslg-52488/src/util/FastbStats.cc |
1728 |
-@@ -18,6 +18,8 @@ |
1729 |
- |
1730 |
- #include "random/Random.h" |
1731 |
- |
1732 |
-+using std::map; |
1733 |
-+ |
1734 |
- typedef VirtualMasterVec<BaseVec> VBaseVecVec; |
1735 |
- |
1736 |
- |
1737 |
---- allpathslg-52488/src/util/Happening.cc |
1738 |
-+++ allpathslg-52488/src/util/Happening.cc |
1739 |
-@@ -25,6 +25,8 @@ |
1740 |
- #include "FastIfstream.h" |
1741 |
- #include "MainTools.h" |
1742 |
- |
1743 |
-+using std::istringstream; |
1744 |
-+ |
1745 |
- vec<String> tracebacks; |
1746 |
- Bool TALLYG; |
1747 |
- |
1748 |
---- allpathslg-52488/src/util/MemMonitor.cc |
1749 |
-+++ allpathslg-52488/src/util/MemMonitor.cc |
1750 |
-@@ -21,7 +21,7 @@ |
1751 |
- #include <signal.h> |
1752 |
- #include <time.h> |
1753 |
- |
1754 |
--using namespace std; |
1755 |
-+using std::string; |
1756 |
- |
1757 |
- // convertion factors between jiffies and seconds (check your system!!!) |
1758 |
- const double sec_jif = 100.0; |
1759 |
---- allpathslg-52488/src/util/Quala2Qualb.cc |
1760 |
-+++ allpathslg-52488/src/util/Quala2Qualb.cc |
1761 |
-@@ -11,6 +11,8 @@ |
1762 |
- #include "FastIfstream.h" |
1763 |
- #include "Qualvector.h" |
1764 |
- |
1765 |
-+using std::istrstream; |
1766 |
-+ |
1767 |
- int main(int argc, char *argv[]) |
1768 |
- { |
1769 |
- RunTime(); |
1770 |
---- allpathslg-52488/src/util/QualbStats.cc |
1771 |
-+++ allpathslg-52488/src/util/QualbStats.cc |
1772 |
-@@ -20,6 +20,7 @@ |
1773 |
- #include "Qualvector.h" |
1774 |
- #include "Basevector.h" |
1775 |
- |
1776 |
-+using std::scientific; |
1777 |
- |
1778 |
- #define NQ 256 |
1779 |
- |
1780 |
---- allpathslg-52488/src/util/ReadTrack.cc |
1781 |
-+++ allpathslg-52488/src/util/ReadTrack.cc |
1782 |
-@@ -33,6 +33,9 @@ |
1783 |
- #include "util/ReadTracker.h" |
1784 |
- #include "util/RunCommand.h" |
1785 |
- |
1786 |
-+using std::map; |
1787 |
-+using std::set; |
1788 |
-+ |
1789 |
- // Return filename portion of path (after last slash) |
1790 |
- String basename(const String path) |
1791 |
- { |
1792 |
---- allpathslg-52488/src/util/ReadTracker.cc |
1793 |
-+++ allpathslg-52488/src/util/ReadTracker.cc |
1794 |
-@@ -11,6 +11,9 @@ |
1795 |
- #include "VecUtilities.h" |
1796 |
- #include "util/ReadTracker.h" |
1797 |
- |
1798 |
-+using std::string; |
1799 |
-+using std::istringstream; |
1800 |
-+ |
1801 |
- unsigned int |
1802 |
- ReadTracker::AddSource(String s) |
1803 |
- { |
1804 |
---- allpathslg-52488/src/util/RunCommand.cc |
1805 |
-+++ allpathslg-52488/src/util/RunCommand.cc |
1806 |
-@@ -14,6 +14,8 @@ |
1807 |
- #include <unistd.h> |
1808 |
- #include <sstream> |
1809 |
- |
1810 |
-+using std::ostringstream; |
1811 |
-+ |
1812 |
- /** |
1813 |
- * RunCommand |
1814 |
- */ |
1815 |
---- allpathslg-52488/src/util/TextTable.cc |
1816 |
-+++ allpathslg-52488/src/util/TextTable.cc |
1817 |
-@@ -13,6 +13,8 @@ |
1818 |
- #include <sstream> |
1819 |
- #include <iterator> |
1820 |
- |
1821 |
-+using std::max; |
1822 |
-+ |
1823 |
- vec<vec<String> > TextTable::GetTable( ) const { |
1824 |
- vec<vec<String> > table; |
1825 |
- for ( size_t i = 0; i < lines.size(); ++i ) { |
1826 |
---- allpathslg-52488/src/util/TextTable.h |
1827 |
-+++ allpathslg-52488/src/util/TextTable.h |
1828 |
-@@ -33,6 +33,8 @@ |
1829 |
- #include "Vec.h" |
1830 |
- #include "feudal/TrackingAllocator.h" |
1831 |
- |
1832 |
-+using std::string; |
1833 |
-+ |
1834 |
- class TextTable { |
1835 |
- public: |
1836 |
- // == Special types to draw line and manipulate tables == |
1837 |
---- allpathslg-52488/src/Vec.h |
1838 |
-+++ allpathslg-52488/src/Vec.h |
1839 |
-@@ -50,6 +50,11 @@ |
1840 |
- #include "Compare.h" |
1841 |
- #include "system/file/FileReader.h" |
1842 |
- |
1843 |
-+using std::numeric_limits; |
1844 |
-+using std::ostream_iterator; |
1845 |
-+using std::setfill; |
1846 |
-+using std::setw; |
1847 |
-+ |
1848 |
- ///////////////////////////////////////////////////////////////////////////// |
1849 |
- // |
1850 |
- // vec Class Declaration and Template Definitions |
1851 |
---- allpathslg-52488/src/VecOverlap.cc |
1852 |
-+++ allpathslg-52488/src/VecOverlap.cc |
1853 |
-@@ -12,6 +12,9 @@ |
1854 |
- #include "STLExtensions.h" |
1855 |
- #include <numeric> |
1856 |
- |
1857 |
-+using std::max; |
1858 |
-+using std::make_pair; |
1859 |
-+ |
1860 |
- // Represents the suffix of the index'th word starting at the pos'th |
1861 |
- // character. |
1862 |
- template <class T> |
1863 |
---- allpathslg-52488/src/VecUtilities.h |
1864 |
-+++ allpathslg-52488/src/VecUtilities.h |
1865 |
-@@ -37,6 +37,9 @@ |
1866 |
- #include "Vec.h" |
1867 |
- #include <cstddef> |
1868 |
- |
1869 |
-+using std::less; |
1870 |
-+using std::equal_to; |
1871 |
-+using std::greater; |
1872 |
- |
1873 |
- ///////////////////////////////////////////////////////////////////////////// |
1874 |
- // |