From 7e231cfd3a320f5ca8d8f5dbb31e7caf56753423 Mon Sep 17 00:00:00 2001 From: Heng Li Date: Thu, 3 Aug 2017 21:28:01 -0400 Subject: [PATCH] minor wording improvement --- tex/minimap2.tex | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/tex/minimap2.tex b/tex/minimap2.tex index 4f987ce..41dba31 100644 --- a/tex/minimap2.tex +++ b/tex/minimap2.tex @@ -68,7 +68,7 @@ and the ability to produce detailed alignment. %\subsubsection{Chaining} An \emph{anchor} is a 3-tuple $(x,y,w)$, indicating interval $[x-w+1,x]$ on the reference matching interval $[y-w+1,y]$ on the query. Given a list of anchors -sorted by the ending reference position $x$, let $f(i)$ be the maximal chaining +sorted by ending reference position $x$, let $f(i)$ be the maximal chaining score up to the $i$-th anchor in the list. $f(i)$ can be calculated with dynamic programming (DP): \begin{equation}\label{eq:chain} @@ -186,7 +186,7 @@ GraphMap~\citep{Sovic:2016aa}, minialign~\citep{Suzuki:2016} and NGMLR~\citep{Sedlazeck169557}. We excluded rHAT~\citep{Liu:2016ab}, LAMSA~\citep{Liu:2017aa} and Kart~\citep{Lin:2017aa} because they either -crashed or produced malformatted output. In this evaluation, Minimap2 has a +crashed or produced malformatted output. In this evaluation, Minimap2 has higher power to distinguish unique and repetitive hits, and achieves overall higher mapping accuracy (Fig.~\ref{fig:eval}a). It is still the most accurate even if we skip DP-based alignment (data not shown), suggesting chaining alone @@ -219,9 +219,9 @@ banding~\citep{Suzuki130633} or incremental banding. In addition to reference-based read mapping, minimap2 inherits minimap's ability to search against huge multi-species databases and to find read overlaps. On a few test data sets, minimap2 appears to yield slightly better -miniasm assembly. Minimap2 can also align long assemblies or closely related -genomes, though more thorough evaluations are needed. Genome alignment is an -intricate topic. +miniasm assembly. Minimap2 can also align closely related genomes, though it +would benefit from more thorough evaluations. Genome alignment is an intricate +topic. \section*{Acknowledgements} We owe a debt of gratitude to Hajime Suzuki for releasing his masterpiece and @@ -315,9 +315,9 @@ y_{rt}&=&\max\{0,y_{r-1,t}+u_{r-1,t}-z_{rt}+q\}-q-e\\ \tilde{y}_{rt}&=&\max\{0,\tilde{y}_{r-1,t}+u_{r-1,t}-z_{rt}+\tilde{q}\}-\tilde{q}-\tilde{e} \end{array}\right. \end{equation*} -In this formulation, cells with the same row index $r$ are independent of each -other. This allows us to fully vectorize the computation of all cells on the -same anti-diagonal in one inner loop. +In this formulation, cells with the same diagonal index $r$ are independent of +each other. This allows us to fully vectorize the computation of all cells on +the same anti-diagonal in one inner loop. On the condition that $q+e<\tilde{q}+\tilde{e}$ and $e>\tilde{e}$, the boundary condition of this equation in the diagonal-anti-diagonal coordinate is