diff --git a/tex/minimap2.tex b/tex/minimap2.tex index 798a94d..3828f26 100644 --- a/tex/minimap2.tex +++ b/tex/minimap2.tex @@ -97,12 +97,12 @@ $O(h\cdot m)$. In practice, we can almost always find the optimal chain with $h=50$; even if the heuristic fails, the optimal chain is often close. %\subsubsection{Backtracking} -Let $P(i)$ be the index of the best predecessor of anchor $i$. It equals 0 if -$f(i)=w_i$ or $\argmax_j\{f(j)+\eta(j,i)-\gamma(j,i)\}$ otherwise. For each -anchor $i$ in the descending order of $f(i)$, we apply $P(\cdot)$ repeatedly to -find its predecessor and mark each visited $i$ as `used', until $P(i)=0$ or we -reach an already `used' $i$. This way we find all chains with no anchors used -in more than one chains. +For backtracking, let $P(i)$ be the index of the best predecessor of anchor +$i$. It equals 0 if $f(i)=w_i$ or $\argmax_j\{f(j)+\eta(j,i)-\gamma(j,i)\}$ +otherwise. For each anchor $i$ in the descending order of $f(i)$, we apply +$P(\cdot)$ repeatedly to find its predecessor and mark each visited $i$ as +`used', until $P(i)=0$ or we reach an already `used' $i$. This way we find all +chains with no anchors used in more than one chains. %\subsubsection{Identifying primary chains} In the absence of copy number changes, each query segment should not be mapped