This is an automated email from the git hooks/post-receive script. misterc-guest pushed a commit to branch master in repository spades.
commit 87072be729eedc6f095bb96d203a03319e5c840c Author: Michael R. Crusoe <[email protected]> Date: Wed Apr 19 05:49:16 2017 -0700 spelling fixes --- debian/patches/0112_spelling.patch | 78 ------------------------ debian/patches/series | 1 + debian/patches/spelling | 118 +++++++++++++++++++++++++++++++++++++ 3 files changed, 119 insertions(+), 78 deletions(-) diff --git a/debian/patches/0112_spelling.patch b/debian/patches/0112_spelling.patch deleted file mode 100644 index eca75b3..0000000 --- a/debian/patches/0112_spelling.patch +++ /dev/null @@ -1,78 +0,0 @@ -Description: minor spelling fixes -Author: Sascha Steinbiss <[email protected]> ---- spades.orig/src/dipspades/polymorphic_bulge_remover/bulge_splitter.hpp -+++ spades/src/dipspades/polymorphic_bulge_remover/bulge_splitter.hpp -@@ -260,7 +260,7 @@ - SplitOppositeEdge(split_res, split_paths.second, split_partlens.second); - - // update non splitted path -- TRACE("Update non splitted path"); -+ TRACE("Update non-split path"); - if(num_splits.second != 0){ - size_t edge_ind = vertices_to_split_[indexes.first].edge_ind_ + 1; - split_paths.first.push_back(default_paths.first[edge_ind]); -@@ -298,7 +298,7 @@ - - set<size_t> processed_indices; - while(num_done_splits < num_splits_.first + num_splits_.second){ -- TRACE("Splitted index - " << split_index << " , owner - " << -+ TRACE("Split index - " << split_index << " , owner - " << - vertices_to_split_[split_index].owner_path_); - - size_t opposite_index = IndexFirstOppositeEdge(split_index, processed_indices); -@@ -418,8 +418,8 @@ - if(!PerformSplitting(range1, range2)) - return SplitResult(graph_); - -- TRACE("Splitted spath1 - " << SimplePathWithVerticesToString(graph_, split_paths_.first)); -- TRACE("Splitted spath2 - " << SimplePathWithVerticesToString(graph_, split_paths_.second)); -+ TRACE("Split spath1 - " << SimplePathWithVerticesToString(graph_, split_paths_.first)); -+ TRACE("Split spath2 - " << SimplePathWithVerticesToString(graph_, split_paths_.second)); - return SplitResult(graph_, split_paths_.first, split_paths_.second); - } - -@@ -445,7 +445,7 @@ - auto split_res = spaths_splitter.SplitSubpaths( - subpath_range(0, bulge->path1().size() - 1), - subpath_range(0, bulge->path2().size() - 1)); -- TRACE("bulge was splitted"); -+ TRACE("bulge was split"); - TRACE("1st new bulge side - " << SimplePathWithVerticesToString(graph_, split_res.path1())); - TRACE("2nd new bulge side - " << SimplePathWithVerticesToString(graph_, split_res.path2())); - return shared_ptr<BaseBulge>(new Bulge(graph_, graph_.k(), split_res.path1(), split_res.path2())); ---- spades.orig/src/dipspades/polymorphic_bulge_remover/bulge_gluer.hpp -+++ spades/src/dipspades/polymorphic_bulge_remover/bulge_gluer.hpp -@@ -74,7 +74,7 @@ - auto splitted_bulge = splitter_.SplitBulge(directed_bulge, glue_def_res); - - if(IsSplittedBulgeCorrect(splitted_bulge)){ -- TRACE("Splitted bulge correct"); -+ TRACE("Split bulge correct"); - GlueSplittedBulge(splitted_bulge); - return true; - } ---- spades.orig/src/debruijn/pacbio/pac_index.hpp -+++ spades/src/debruijn/pacbio/pac_index.hpp -@@ -534,7 +534,7 @@ - || !IsConsistent(s, *(iter->second), - *(next_iter->second))) { - if (next_iter != cur_cluster.end()) { -- DEBUG("clusters splitted:"); -+ DEBUG("clusters split:"); - DEBUG("on "<< iter->second->str(g_)); - DEBUG("and " << next_iter->second->str(g_)); - } ---- spades.orig/src/dipspades/kmer_gluing/equal_sequence_gluer.hpp -+++ spades/src/dipspades/kmer_gluing/equal_sequence_gluer.hpp -@@ -74,9 +74,9 @@ - pos2 = graph_.length(edge1) - tmp - 1; - } - INFO(pos1 << " " << pos2 << " " << graph_.length(edge1)) -- TRACE("Edge1 " << graph_.int_id(edge1) << " will be splitted"); -+ TRACE("Edge1 " << graph_.int_id(edge1) << " will be split"); - pair<EdgeId, EdgeId> split_edges = graph_.SplitEdge(edge1, pos1 + 1); -- TRACE("Splitted pair was created"); -+ TRACE("Split pair was created"); - TRACE("New edge1: " << graph_.int_id(split_edges.first) << ", length: " << graph_.length(split_edges.first)); - TRACE("New edge2: " << graph_.int_id(split_edges.second) << ", length: " << graph_.length(split_edges.second)); - edge1 = split_edges.first; diff --git a/debian/patches/series b/debian/patches/series index 4705406..0d3a95c 100644 --- a/debian/patches/series +++ b/debian/patches/series @@ -17,3 +17,4 @@ 0116_stable_link_order.patch 0117_build_with_debug.patch fix-bool-cast +spelling diff --git a/debian/patches/spelling b/debian/patches/spelling new file mode 100644 index 0000000..3ab5d50 --- /dev/null +++ b/debian/patches/spelling @@ -0,0 +1,118 @@ +From: Michael R. Crusoe <[email protected]> +Subject: Spelling fixes +--- spades.orig/manual.html ++++ spades/manual.html +@@ -760,7 +760,7 @@ + Make sure that files with right reads are given in the same order as corresponding files with left reads. + + <p> +- For example, if you have one paired-end library splitted into two pairs of files: ++ For example, if you have one paired-end library split into two pairs of files: + <pre class="code"> + <code> + lib_pe1_left_1.fastq +@@ -989,7 +989,7 @@ + </pre> + + <p> +- If a single-read library is splitted into several files: ++ If a single-read library is split into several files: + + <pre class="code"> + <code> +@@ -1138,7 +1138,7 @@ + </pre> + + <p> +-Since the current version of Bandage does not accept paths with gaps, paths corresponding contigs/scaffolds jumping over a gap in the assembly graph are splitted by semicolon at the gap positions. For example, the following record ++Since the current version of Bandage does not accept paths with gaps, paths corresponding contigs/scaffolds jumping over a gap in the assembly graph are split by semicolon at the gap positions. For example, the following record + <pre> + <code> + NODE_3_length_237403_cov_243.207_ID_45 +--- spades.orig/src/common/assembly_graph/stats/picture_dump.hpp ++++ spades/src/common/assembly_graph/stats/picture_dump.hpp +@@ -123,7 +123,7 @@ + INFO("Genome mapping results:"); + INFO("Covered k+1-mers:" << covered_kp1mers << " of " << (genome_.size() - k_) << " which is " + << (100.0 * (double) covered_kp1mers / (double) (genome_.size() - k_)) << "%"); +- INFO("Covered k+1-mers form " << break_number + 1 << " contigious parts"); ++ INFO("Covered k+1-mers form " << break_number + 1 << " contiguous parts"); + INFO("Continuity failtures " << fail); + } + }; +--- spades.orig/src/common/modules/alignment/pacbio/pac_index.hpp ++++ spades/src/common/modules/alignment/pacbio/pac_index.hpp +@@ -581,7 +581,7 @@ + || !IsConsistent(*(iter->second), + *(next_iter->second))) { + if (next_iter != cur_cluster.end()) { +- DEBUG("clusters splitted:"); ++ DEBUG("clusters split:"); + DEBUG("on "<< iter->second->str(g_)); + DEBUG("and " << next_iter->second->str(g_)); + } +--- spades.orig/src/projects/dipspades/kmer_gluing/equal_sequence_gluer.hpp ++++ spades/src/projects/dipspades/kmer_gluing/equal_sequence_gluer.hpp +@@ -74,9 +74,9 @@ + pos2 = graph_.length(edge1) - tmp - 1; + } + INFO(pos1 << " " << pos2 << " " << graph_.length(edge1)) +- TRACE("Edge1 " << graph_.int_id(edge1) << " will be splitted"); ++ TRACE("Edge1 " << graph_.int_id(edge1) << " will be split"); + pair<EdgeId, EdgeId> split_edges = graph_.SplitEdge(edge1, pos1 + 1); +- TRACE("Splitted pair was created"); ++ TRACE("Split pair was created"); + TRACE("New edge1: " << graph_.int_id(split_edges.first) << ", length: " << graph_.length(split_edges.first)); + TRACE("New edge2: " << graph_.int_id(split_edges.second) << ", length: " << graph_.length(split_edges.second)); + edge1 = split_edges.first; +--- spades.orig/src/projects/dipspades/polymorphic_bulge_remover/bulge_gluer.hpp ++++ spades/src/projects/dipspades/polymorphic_bulge_remover/bulge_gluer.hpp +@@ -74,7 +74,7 @@ + auto splitted_bulge = splitter_.SplitBulge(directed_bulge, glue_def_res); + + if(IsSplittedBulgeCorrect(splitted_bulge)){ +- TRACE("Splitted bulge correct"); ++ TRACE("Split bulge correct"); + GlueSplittedBulge(splitted_bulge); + return true; + } +--- spades.orig/src/projects/dipspades/polymorphic_bulge_remover/bulge_splitter.hpp ++++ spades/src/projects/dipspades/polymorphic_bulge_remover/bulge_splitter.hpp +@@ -260,7 +260,7 @@ + SplitOppositeEdge(split_res, split_paths.second, split_partlens.second); + + // update non splitted path +- TRACE("Update non splitted path"); ++ TRACE("Update non split path"); + if(num_splits.second != 0){ + size_t edge_ind = vertices_to_split_[indexes.first].edge_ind_ + 1; + split_paths.first.push_back(default_paths.first[edge_ind]); +@@ -298,7 +298,7 @@ + + set<size_t> processed_indices; + while(num_done_splits < num_splits_.first + num_splits_.second){ +- TRACE("Splitted index - " << split_index << " , owner - " << ++ TRACE("Split index - " << split_index << " , owner - " << + vertices_to_split_[split_index].owner_path_); + + size_t opposite_index = IndexFirstOppositeEdge(split_index, processed_indices); +@@ -418,8 +418,8 @@ + if(!PerformSplitting(range1, range2)) + return SplitResult(graph_); + +- TRACE("Splitted spath1 - " << SimplePathWithVerticesToString(graph_, split_paths_.first)); +- TRACE("Splitted spath2 - " << SimplePathWithVerticesToString(graph_, split_paths_.second)); ++ TRACE("Split spath1 - " << SimplePathWithVerticesToString(graph_, split_paths_.first)); ++ TRACE("Split spath2 - " << SimplePathWithVerticesToString(graph_, split_paths_.second)); + return SplitResult(graph_, split_paths_.first, split_paths_.second); + } + +@@ -445,7 +445,7 @@ + auto split_res = spaths_splitter.SplitSubpaths( + subpath_range(0, bulge->path1().size() - 1), + subpath_range(0, bulge->path2().size() - 1)); +- TRACE("bulge was splitted"); ++ TRACE("bulge was split"); + TRACE("1st new bulge side - " << SimplePathWithVerticesToString(graph_, split_res.path1())); + TRACE("2nd new bulge side - " << SimplePathWithVerticesToString(graph_, split_res.path2())); + return shared_ptr<BaseBulge>(new Bulge(graph_, graph_.k(), split_res.path1(), split_res.path2())); -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/spades.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
