[med-svn] [spades] 05/05: spelling fixes
Michael Crusoe
misterc-guest at moszumanska.debian.org
Wed Apr 19 13:24:38 UTC 2017
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 <michael.crusoe at gmail.com>
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 <satta at debian.org>
---- 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 <michael.crusoe at gmail.com>
+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()));
--
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