Merge remote-tracking branch 'upstream/master'

lbcb-sci · Oct 9, 2019 · 2c5672e · 2c5672e
2 parents 9df1ce8 + ededb83
commit 2c5672e
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Showing 5 changed files with 14 additions and 10 deletions.
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -1,6 +1,6 @@
 cmake_minimum_required(VERSION 3.2)
 project(racon)
-set(racon_version 1.4.7)
+set(racon_version 1.4.9)
 
 set(CMAKE_ARCHIVE_OUTPUT_DIRECTORY ${PROJECT_BINARY_DIR}/lib)
 set(CMAKE_LIBRARY_OUTPUT_DIRECTORY ${PROJECT_BINARY_DIR}/lib)

diff --git a/README.md b/README.md
@@ -102,13 +102,13 @@ Usage of `racon` is as following:
         --no-trimming
             disables consensus trimming at window ends
         -m, --match <int>
-            default: 5
+            default: 3
             score for matching bases
         -x, --mismatch <int>
-            default: -4
+            default: -5
             score for mismatching bases
         -g, --gap <int>
-            default: -8
+            default: -4
             gap penalty (must be negative)
         -t, --threads <int>
             default: 1

diff --git a/src/window.cpp b/src/window.cpp
@@ -42,6 +42,10 @@ Window::~Window() {
 void Window::add_layer(const char* sequence, uint32_t sequence_length,
     const char* quality, uint32_t quality_length, uint32_t begin, uint32_t end) {
 
+    if (sequence_length == 0 || begin == end) {
+        return;
+    }
+
     if (quality != nullptr && sequence_length != quality_length) {
         fprintf(stderr, "[racon::Window::add_layer] error: "
             "unequal quality size!\n");
@@ -87,14 +91,14 @@ bool Window::generate_consensus(std::shared_ptr<spoa::AlignmentEngine> alignment
         spoa::Alignment alignment;
         if (positions_[i].first < offset && positions_[i].second >
             sequences_.front().second - offset) {
-            alignment = alignment_engine->align_sequence_with_graph(
-                sequences_[i].first, sequences_[i].second, graph);
+            alignment = alignment_engine->align(sequences_[i].first,
+                sequences_[i].second, graph);
         } else {
             std::vector<int32_t> mapping;
             auto subgraph = graph->subgraph(positions_[i].first,
                 positions_[i].second, mapping);
-            alignment = alignment_engine->align_sequence_with_graph(
-                sequences_[i].first, sequences_[i].second, subgraph);
+            alignment = alignment_engine->align( sequences_[i].first,
+                sequences_[i].second, subgraph);
             subgraph->update_alignment(alignment, mapping);
         }
 

diff --git a/vendor/bioparser b/vendor/bioparser
diff --git a/vendor/spoa b/vendor/spoa
+2 −0		.travis.yml
+12 −5		CMakeLists.txt
+59 −36		README.md
+34 −14		include/spoa/alignment_engine.hpp
+65 −54		include/spoa/graph.hpp
+47 −23		src/alignment_engine.cpp
+144 −123		src/graph.cpp
+105 −71		src/main.cpp
+5 −4		src/sequence.cpp
+6 −7		src/sequence.hpp
+1,328 −232		src/simd_alignment_engine.cpp
+28 −15		src/simd_alignment_engine.hpp
+727 −127		src/sisd_alignment_engine.cpp
+25 −14		src/sisd_alignment_engine.hpp
+579 −29		test/spoa_test.cpp
+1 −1		vendor/bioparser
+1 −1		vendor/googletest