Commit fd6ec33d authored by Overduin, Sam's avatar Overduin, Sam
Browse files

Changed scope of static const MAGIC_LOOP_CONSTANT due to CLion build process...

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.
parent 8c9c2508
##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
......@@ -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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