From fd6ec33da04d34eba544864bea63ab3e2e5183bd Mon Sep 17 00:00:00 2001
From: "Overduin, Sam" <sam.overduin@wur.nl>
Date: Fri, 22 Nov 2019 15:34:53 +0100
Subject: [PATCH] Changed scope of static const MAGIC_LOOP_CONSTANT due to
CLion build process complaining. Shouldn't break anything. Also uploaded
aa_todo_notes. In future will not mention this file.
---
aa_todo_notes | 22 +++++++++++++++++++
.../scaffolder2015/path_polisher.hpp | 7 +++---
2 files changed, 26 insertions(+), 3 deletions(-)
create mode 100644 aa_todo_notes
diff --git a/aa_todo_notes b/aa_todo_notes
new file mode 100644
index 00000000..34733621
--- /dev/null
+++ b/aa_todo_notes
@@ -0,0 +1,22 @@
+##append_taxa_tree_to_reads.py
+from kraken to read header -> done!!
+
+To test:
+/mnt/LTR_userdata/overd008/tools/spades_install/bin/spades-core /home/overd008/mnt/lustre/output/spades/test/K55/configs/config.info /home/overd008/mnt/lustre/output/spades/test/K55/configs/mda_mode.info /home/overd008/mnt/lustre/output/spades/test/K55/configs/meta_mode.info
+
+---------here-----------
+
+## Parse taxonomy from reads
+Barcode mapping parser
+common\barcode_index\barcode_index_builder.hpp @105 FillMapFrom10XReads
+@118 add string tax_string = GetTaxaTreeFromRead(read)
+ # Encode as vector of pointers to ints?
+@150 copy similar parser
+
+
+## Settle taxonomy of edges
+New function (implement where? Just before transition taxa filter? Seperately?)
+
+## Add transition taxonomy filter here:
+M:\aa_Thesis_code\SPAdes-3.13.0-dev\src\common\modules\path_extend\read_cloud_path_extend\scaffold_graph_construction\
+scaffold_graph_construction_pipeline.cpp@209
diff --git a/src/common/modules/path_extend/scaffolder2015/path_polisher.hpp b/src/common/modules/path_extend/scaffolder2015/path_polisher.hpp
index 7d8cc183..b36ee78e 100644
--- a/src/common/modules/path_extend/scaffolder2015/path_polisher.hpp
+++ b/src/common/modules/path_extend/scaffolder2015/path_polisher.hpp
@@ -18,6 +18,7 @@
#include "assembly_graph/dijkstra/dijkstra_helper.hpp"
namespace path_extend {
+ static const size_t MAGIC_LOOP_CONSTANT = 1000;
class PathGapCloser {
protected:
@@ -150,7 +151,6 @@ class SimpleExtenderFactory : public GapExtenderFactory {
const GraphCoverageMap &cover_map_;
UsedUniqueStorage& unique_;
const std::shared_ptr<GapExtensionChooserFactory> chooser_factory_;
- static const size_t MAGIC_LOOP_CONSTANT = 1000;
public:
SimpleExtenderFactory(const conj_graph_pack &gp,
const GraphCoverageMap &cover_map,
@@ -167,8 +167,9 @@ public:
auto chooser = chooser_factory_->CreateChooser(original_path, position);
DEBUG("Created chooser");
auto extender = std::make_shared<SimpleExtender>(gp_, cover_map_, unique_,
- chooser_factory_->CreateChooser(original_path, position),
- MAGIC_LOOP_CONSTANT,
+ chooser,
+ path_extend::MAGIC_LOOP_CONSTANT,
+ //changed location of MAGIC_LOOP_CONSTANT because CLion compilation threw errors
false,
false);
DEBUG("Returning extender");
--
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