sam2lca: Lowest Common Ancestor for SAM/BAM/CRAM alignment files
نویسندگان
چکیده
منابع مشابه
Lowest Common Ancestor(LCA)
Before embarking into the technicalities of the different algorithms for LCA, let us first agree on the terminology that we will be using throughout this article. Let there be a rooted tree T(E,V). A node x ∈ T is called an ancestor of a node y ∈ T if the path from the root of T to y goes through x. Also, a node v ∈ T is called to be a common ancestor of x and y if it is an ancestor of both x a...
متن کاملFast Lowest Common Ancestor Computations in Dags
This work studies lowest common ancestor problems in directed acyclic graphs. We present fast algorithms for solving the All-Pairs Representative LCA and AllPairs All LCA problems with expected running time of O(n2 log n) and O(n3 log log n) respectively. The speed-ups over recently developed methods are achieved by applying transitive reduction on the input dags. The algorithms are experimenta...
متن کامل.1 Range Minimum Query (rmq) 1.2 Lowest Common Ancestor (lca)
We care not only about the value of the minimum element, but also about the index k of the minimum element between A[i] and A[j]; given the index, it is easy to look up the actual value of the minimum element, so it is a more interesting problem to find the index of the minimum element between A[i] and A[j]. The range minimum query problem is not a tree problem, but it closely related to a tree...
متن کاملImproved Algorithms for the All-pairs Lowest Common Ancestor Problem in Directed Acyclic Graphs
We present a new algorithm for solving the all-pairs lowest common ancestor problem in directed acyclic graphs (dags). Our algorithm runs in time O(n), where λ satisfies the equation ω(1, λ, 1) = 1 + 2λ and ω(1, λ, 1) is the exponent of the multiplication of an n × n matrix by an n × n matrix. By the currently best bounds on ω(1, λ, 1), the running time of our algorithm is O(n). Our algorithm i...
متن کاملA scalable approach to computing representative lowest common ancestor in directed acyclic graphs
LCA computation for vertex pairs in trees can be achieved in constant time after linear-time preprocessing. However, extension of these techniques to compute LCA for vertex-pairs in DAGs has been not possible due to the non-tree edges in a DAG. In this paper, we present an algorithm for computing the LCA for vertex pairs in a DAG which treats the DAG’s spanning tree and its non-tree edges separ...
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ژورنال
عنوان ژورنال: Journal of open source software
سال: 2022
ISSN: ['2475-9066']
DOI: https://doi.org/10.21105/joss.04360