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added one transition phrase 

as there are no subsubsections now
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Heng Li 2017-08-03 18:01:48 -04:00
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tex/minimap2.tex
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@ -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