diff options
| author | V3n3RiX <venerix@redcorelinux.org> | 2017-12-25 17:37:52 +0000 |
|---|---|---|
| committer | V3n3RiX <venerix@redcorelinux.org> | 2017-12-25 17:37:52 +0000 |
| commit | 2f51c9978dda4c6e8debca43e4235ecc86914032 (patch) | |
| tree | bc41e1c4383040034174c327504f702c8517a123 /sci-biology/allpathslg | |
| parent | 51536d2fe4697ba9114d611178bb9e20d3d5b729 (diff) | |
gentoo resync : 25.12.2017
Diffstat (limited to 'sci-biology/allpathslg')
| -rw-r--r-- | sci-biology/allpathslg/Manifest | 3 | ||||
| -rw-r--r-- | sci-biology/allpathslg/allpathslg-52488-r2.ebuild | 24 | ||||
| -rw-r--r-- | sci-biology/allpathslg/files/allpathslg-52488-gcc7.patch | 13 |
3 files changed, 20 insertions, 20 deletions
diff --git a/sci-biology/allpathslg/Manifest b/sci-biology/allpathslg/Manifest index 49f0d85cb203..dab34c2f1993 100644 --- a/sci-biology/allpathslg/Manifest +++ b/sci-biology/allpathslg/Manifest @@ -1,4 +1,5 @@ +AUX allpathslg-52488-gcc7.patch 790 BLAKE2B d3993e840b7b53791b0830fc993553c45c00d5d81881750066327106ad45f13bd0f4dba48c8cc0bdf3655d20ff3cefa659b8d41f582a73376188109860e5f2eb SHA512 bde085541f74278aba8edd1c41dd3a2541a7ce7f3a6647b5f3ed19613545bbfff287463e90e785b4476c677d2456d4c87818730b95941b27744549fcdd62d935 DIST allpathslg-52488-patchset.tar.bz2 11405 BLAKE2B 7a4c36884ac95a4eb23291720e422ce1ec41d0bea3a0b10582aa1d8154234971eb8d06979a969e65c1ec1eab031d2500a1ec40809019c8b4aa1d1d2e81427dbe SHA512 a1d58c131afeef04a9d7a2520fcd28a853317323fdcab1a253cb2548546bbc559993c74a68a8032a5d0e865ac2c2d53ff6b4c149aade2d1f87a2ab4116ebe4cc DIST allpathslg-52488.tar.gz 3121949 BLAKE2B b75904f9e8256a14c97abae45a0cb41718f95d27a4a072b6144bd125abb57682faa180de6a18399ab4fa43988344c436ca1eab8412433353fcc746c432c33031 SHA512 c44ef1a3ed5b343bf096663309cc399e79d65e83175232743cf330fd0d426633bd0d388922fd0c73ac0927d85ea9005549c8e4f7711c79fea7107068510ef30d -EBUILD allpathslg-52488-r2.ebuild 1547 BLAKE2B 0ff97cce907b769446002e704f04524450e5370aba0a5f5fcf66313851fa3708e4c204e1dcde637537ebffaa1baf549b7aa1bc097bc293ee9d43488aa952f205 SHA512 39958550cd4ba2d2e17843860a0354f383fe15850b393aa8a48edc76e59307899afedc878ea68f8c2077f720d6e6f631d32ca1b1c11256e5800cb40d6b9027a6 +EBUILD allpathslg-52488-r2.ebuild 1016 BLAKE2B e707f2cebafd829c0ccf712a5b72eb10c39663ccfa3f2a8f279200286f609905b3be756d64c42748667e4171aef36435bb9386f8d807db29584bdc74ceee92ab SHA512 106002b58ebd2616d216e61d164102f5eed7204a19d470a30d2f0e6ef685009fa737866c563fccc1980a6577b1f2e30af01756f291701914a67101a96a60bd87 MISC metadata.xml 267 BLAKE2B 7cf386952842945148119de3263231db4d1046d5f54811f7e303ed8ec4d27cbc1960b99c92daf6f32e5b981c2fb9f50ec666be6193865d6e18541b7427a152a9 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403 diff --git a/sci-biology/allpathslg/allpathslg-52488-r2.ebuild b/sci-biology/allpathslg/allpathslg-52488-r2.ebuild index e68430e2462d..964904d66551 100644 --- a/sci-biology/allpathslg/allpathslg-52488-r2.ebuild +++ b/sci-biology/allpathslg/allpathslg-52488-r2.ebuild @@ -23,31 +23,17 @@ DEPEND=" dev-libs/boost:=" PATCHES=( - "${WORKDIR}/${P}-patchset/${P}_fix-buildsystem.patch" - "${WORKDIR}/${P}-patchset/${P}_remove-namespace-std.patch" + "${WORKDIR}"/${P}-patchset/${P}_fix-buildsystem.patch + "${WORKDIR}"/${P}-patchset/${P}_remove-namespace-std.patch + "${FILESDIR}"/${P}-gcc7.patch ) pkg_pretend() { - # as of release 44849, GCC 4.7.0 (or higher) is required - # seems pre gcc-4.7 users must stay with: - # ftp://ftp.broadinstitute.org/pub/crd/ALLPATHS/Release-LG/latest_source_code/2013/2013-01/allpathslg-44837.tar.gz - if [[ ${MERGE_TYPE} != binary ]]; then - tc-is-gcc && [[ $(gcc-version) < 4.7 ]] && \ - die "You need to use gcc >4.7" - fi + [[ ${MERGE_TYPE} != binary ]] && tc-check-openmp } pkg_setup() { - if ! tc-has-openmp; then - ewarn "OpenMP is not available in your current selected compiler" - - if tc-is-clang; then - ewarn "OpenMP support in sys-devel/clang is provided by sys-libs/libomp," - ewarn "which you will need to build ${CATEGORY}/${PN} with USE=\"openmp\"" - fi - - die "need openmp capable compiler" - fi + [[ ${MERGE_TYPE} != binary ]] && tc-check-openmp } src_prepare() { diff --git a/sci-biology/allpathslg/files/allpathslg-52488-gcc7.patch b/sci-biology/allpathslg/files/allpathslg-52488-gcc7.patch new file mode 100644 index 000000000000..7c5e1267e4e9 --- /dev/null +++ b/sci-biology/allpathslg/files/allpathslg-52488-gcc7.patch @@ -0,0 +1,13 @@ +--- a/src/paths/long/VariantCallTools.cc ++++ b/src/paths/long/VariantCallTools.cc +@@ -1870,8 +1870,8 @@ + bool i_is_indel = (change[i].first.size() != change[i].second.size()); + if (i_is_indel) inserted_base += change[i].second.size()-1; + size_t j = i + 1; +- while (j < edits.size() && abs(edits[j].second - edits[j-1].second +- - change[j-1].first.size()) < MinClumpSep) { ++ while (j < edits.size() && std::abs(edits[j].second - edits[j-1].second ++ - static_cast<int>(change[j-1].first.size())) < MinClumpSep) { + nmatch += edits[j].second - edits[j-1].second - change[j-1].first.size(); + bool j_is_indel = (change[j].first.size() != change[j].second.size()); + if (j_is_indel) |