auto-update to UShER commit 771ecb71a02fd208b1b395438d9c3501896637c7

amkram · Aug 27, 2021 · dfd5c3c · dfd5c3c
1 parent d950ea3
commit dfd5c3c
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Showing 3 changed files with 15 additions and 16 deletions.
diff --git a/README.md b/README.md
@@ -10,7 +10,7 @@
 
   [![License: AGPL v3](https://img.shields.io/badge/License-AGPL%20v3-blue.svg)](LICENSE)
   [![Integration Tests](https://github.com/amkram/shusher/actions/workflows/build_and_test.yml/badge.svg)](https://github.com/amkram/shusher/actions/workflows/build_and_test.yml)<!---BEGIN_USHER_BADGE-->
-<a target="_blank" href="https://github.com/yatisht/usher/tree/0555be77c91ce3b798ae59b4ba2bd3d42a02cf11"><img src="https://img.shields.io/badge/UShER%20Version-commit%200555be77-%235e0000"/></a>
+<a target="_blank" href="https://github.com/yatisht/usher/tree/771ecb71a02fd208b1b395438d9c3501896637c7"><img src="https://img.shields.io/badge/UShER%20Version-commit%20771ecb71-%235e0000"/></a>
 <!---END_USHER_BADGE-->
 
   | :computer_mouse:	Access ShUShER <a target="_blank" href="https://shusher.gi.ucsc.edu">here</a>! |

diff --git a/usher-port/src/mutation_annotated_tree.cpp b/usher-port/src/mutation_annotated_tree.cpp
@@ -5,6 +5,7 @@
 #include <google/protobuf/io/coded_stream.h>
 #include <iomanip>
 #include <iostream>
+#include <random>
 #include <sys/mman.h>
 #include <sys/stat.h>
 #include <unistd.h>
@@ -1513,7 +1514,7 @@ void Mutation_Annotated_Tree::get_random_sample_subtrees (Mutation_Annotated_Tre
     //size_t random_subtree_size = print_subtrees_size/2;
     //size_t nearest_subtree_size = print_subtrees_size - random_subtree_size;
 
-    size_t random_subtree_size = 0;
+    size_t random_subtree_size = subtree_size/5;
     size_t nearest_subtree_size = subtree_size - random_subtree_size;
 
     //Set a constant random seed
@@ -1606,22 +1607,20 @@ void Mutation_Annotated_Tree::get_random_sample_subtrees (Mutation_Annotated_Tre
                     }
                     leaves_to_keep.emplace_back(n.node->identifier); 
                 }
-            } else {
-                for (auto l: T->get_leaves(anc->identifier)) {
-                    leaves_to_keep.emplace_back(l->identifier);
-                }
-            }
 
-            // Add non-overlapping random subtree samples
-            for (auto l: random_ordered_leaves) {
-                if (leaves_to_keep.size() < subtree_size) {
-                    if (std::find(leaves_to_keep.begin(), leaves_to_keep.end(), l->identifier) == leaves_to_keep.end()) {
-                        leaves_to_keep.emplace_back(l->identifier);
+                std::random_device rd;
+                std::mt19937 g(rd());
+                std::shuffle(node_distances.begin()+nearest_subtree_size, node_distances.end(), g);
+
+                for (auto n = node_distances.begin()+nearest_subtree_size; n != node_distances.end(); n++) {
+                    if (leaves_to_keep.size() == subtree_size) {
+                        break;
                     }
+                    leaves_to_keep.emplace_back(n->node->identifier); 
                 }
-
-                if (leaves_to_keep.size() >= subtree_size) {
-                    break;
+            } else {
+                for (auto l: T->get_leaves(anc->identifier)) {
+                    leaves_to_keep.emplace_back(l->identifier);
                 }
             }
 

diff --git a/usher_version.txt b/usher_version.txt
@@ -1 +1 @@
-0555be77c91ce3b798ae59b4ba2bd3d42a02cf11
+771ecb71a02fd208b1b395438d9c3501896637c7