Adding submodules

medvedevgroup · Jan 15, 2019 · d57a491 · d57a491
1 parent 12f4d77
commit d57a491
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Showing 44 changed files with 11 additions and 1,191 deletions.
diff --git a/.gitmodules b/.gitmodules
@@ -0,0 +1,6 @@
+[submodule "TwoPaCo"]
+	path = TwoPaCo
+	url = https://github.com/medvedevgroup/TwoPaCo
+[submodule "spoa"]
+	path = spoa
+	url = https://github.com/rvaser/spoa
diff --git a/TwoPaCo b/TwoPaCo
diff --git a/spoa b/spoa
diff --git a/src/blocksfinder.h b/src/blocksfinder.h
@@ -209,7 +209,7 @@ namespace Sibelia
 					if (finder.count_++ % finder.progressPortion_ == 0)
 					{
 						finder.progressMutex_.lock();
-						std::cout << '.';
+						std::cout << '.' << std::flush;
 						finder.progressMutex_.unlock();
 					}
 
@@ -565,7 +565,7 @@ namespace Sibelia
 			}
 
 			using namespace std::placeholders;
-			std::sort(shuffle.begin(), shuffle.end(), std::bind(DegreeCompare, std::cref(storage_), _1, _2));
+			std::random_shuffle(shuffle.begin(), shuffle.end());
 #ifdef _DEBUG_OUT_
 			//OutputMissing("test/test7/segment.txt", "missing");
 			OutputSubgraph("alignment.maf", "subgraph.txt", "pair.txt");
@@ -574,7 +574,7 @@ namespace Sibelia
 			srand(time(0));
 			time_t mark = time(0);
 			count_ = 0;
-			std::cout << '[';
+			std::cout << '[' << std::flush;
 			progressPortion_ = shuffle.size() / progressCount_;
 			tbb::task_scheduler_init init(threads);
 			tbb::parallel_for(tbb::blocked_range<size_t>(0, shuffle.size()), ProcessVertex(*this, shuffle));

diff --git a/src/util/compare_annotation.py b/src/util/compare_annotation.py
diff --git a/src/util/maskn.py b/src/util/maskn.py
diff --git a/src/util/micerun/run.sh b/src/util/micerun/run.sh
diff --git a/src/util/mousemart/align_lagan.sh b/src/util/mousemart/align_lagan.sh
diff --git a/src/util/mousemart/collect_lagan_bin.py b/src/util/mousemart/collect_lagan_bin.py
diff --git a/src/util/mousemart/download_genome.sh b/src/util/mousemart/download_genome.sh
diff --git a/src/util/mousemart/gene_xml.py b/src/util/mousemart/gene_xml.py
diff --git a/src/util/mousemart/generate_blocks_pwise.py b/src/util/mousemart/generate_blocks_pwise.py
diff --git a/src/util/mousemart/generate_genes.py b/src/util/mousemart/generate_genes.py
diff --git a/src/util/mousemart/get.sh b/src/util/mousemart/get.sh
diff --git a/src/util/mousemart/get_all.sh b/src/util/mousemart/get_all.sh
diff --git a/src/util/mousemart/mice.txt b/src/util/mousemart/mice.txt