From 7a63b46876f4bebcf7615db683b6593ac99e271e Mon Sep 17 00:00:00 2001
From: Heng Li <lh3@me.com>
Date: Fri, 18 Oct 2024 11:11:13 -0400
Subject: [PATCH] Release ropebwt3-3.8 (r248)

---
 NEWS.md          | 19 ++++++++++++++++++
 main.c           |  2 +-
 tex/ropebwt3.tex | 52 ++++++++++++++++++++++++------------------------
 3 files changed, 46 insertions(+), 27 deletions(-)

diff --git a/NEWS.md b/NEWS.md
index 1097197..5170964 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,3 +1,22 @@
+Release 3.8-r248 (18 October 2024)
+----------------------------------
+
+Notable changes:
+
+ * Improvement: a faster algorithm to locate a subset of positions in a suffix
+   array interval. Given m highly similar genomes, the expected time is O(s/m)
+   where s is the suffix array sample rate.
+
+ * New feature: added option `mem -p` to optionally output a semi-random subset
+   of SMEM positions.
+
+ * New feature: added auxiliary script `rb3tools.js` for generating mappability
+   filter and for simple SNP calling.
+
+(3.8: 18 October 2024, r248)
+
+
+
 Release 3.7-r226 (17 September 2024)
 ------------------------------------
 
diff --git a/main.c b/main.c
index c6b3e1f..3ff5ba9 100644
--- a/main.c
+++ b/main.c
@@ -5,7 +5,7 @@
 #include "io.h"
 #include "ketopt.h"
 
-#define RB3_VERSION "3.7-r247-dirty"
+#define RB3_VERSION "3.7-r248"
 
 int main_build(int argc, char *argv[]);
 int main_merge(int argc, char *argv[]);
diff --git a/tex/ropebwt3.tex b/tex/ropebwt3.tex
index 3286dae..16960c6 100644
--- a/tex/ropebwt3.tex
+++ b/tex/ropebwt3.tex
@@ -210,32 +210,32 @@ \subsection{Basic concepts}
 {\bf (c)} The prefix directed acyclic word graph (DAWG) of $T$ by merging nodes with identical suffix array intervals.}\label{fig:1}
 \end{figure}
 
-\begin{algorithm}[tb]
-	\caption{A naive bwa-aln algorithm with PSSM}\label{algo:bwa-aln}
-	\begin{algorithmic}[1]
-		\Procedure{BwaAlnPSSM}{$B,P,s,g$}\Comment{$g$ is gap penalty}
-			\State $H\gets\mbox{empty heap prioritized on the 1st value}$
-			\State $H.{\rm push}(0,|P|,0,|T|)$
-			\While{$H$ is not empty}
-				\State $(p,i,l,h)\gets H.{\rm pop}()$\Comment{element with the smallest $p$}
-				\If{$i=0$}
-					\State \Return $[l,h)$\Comment{this is the best match}
-				\EndIf
-				\State $H.{\rm push}(p+g_{i-1},i-1,l,h)$\Comment{insertion}
-				\State $a\gets P[i-1]$
-				\For{$c\in\Sigma$}\Comment{match, mismatch or deletion}
-					\State $l'\gets C_B(c)+{\rm rank}_B(c,l)$\Comment{backward search}
-					\State $h'\gets C_B(c)+{\rm rank}_B(c,h)$
-					\If{$l'<h'$}\Comment{$[l',h')$ is a child of $[l,h)$}
-						\State $H.{\rm push}(p+s_i(a|c),i-1,l',h')$\Comment{(mis)match}
-						\State $H.{\rm push}(p+g_i,i,l',h')$\Comment{deletion}
-					\EndIf
-				\EndFor
-			\EndWhile
-			\State \Return $\emptyset$\Comment{no match}
-		\EndProcedure
-	\end{algorithmic}
-\end{algorithm}
+%\begin{algorithm}[tb]
+%	\caption{A naive bwa-aln algorithm with PSSM}\label{algo:bwa-aln}
+%	\begin{algorithmic}[1]
+%		\Procedure{BwaAlnPSSM}{$B,P,s,g$}\Comment{$g$ is gap penalty}
+%			\State $H\gets\mbox{empty heap prioritized on the 1st value}$
+%			\State $H.{\rm push}(0,|P|,0,|T|)$
+%			\While{$H$ is not empty}
+%				\State $(p,i,l,h)\gets H.{\rm pop}()$\Comment{element with the smallest $p$}
+%				\If{$i=0$}
+%					\State \Return $[l,h)$\Comment{this is the best match}
+%				\EndIf
+%				\State $H.{\rm push}(p+g_{i-1},i-1,l,h)$\Comment{insertion}
+%				\State $a\gets P[i-1]$
+%				\For{$c\in\Sigma$}\Comment{match, mismatch or deletion}
+%					\State $l'\gets C_B(c)+{\rm rank}_B(c,l)$\Comment{backward search}
+%					\State $h'\gets C_B(c)+{\rm rank}_B(c,h)$
+%					\If{$l'<h'$}\Comment{$[l',h')$ is a child of $[l,h)$}
+%						\State $H.{\rm push}(p+s_i(a|c),i-1,l',h')$\Comment{(mis)match}
+%						\State $H.{\rm push}(p+g_i,i,l',h')$\Comment{deletion}
+%					\EndIf
+%				\EndFor
+%			\EndWhile
+%			\State \Return $\emptyset$\Comment{no match}
+%		\EndProcedure
+%	\end{algorithmic}
+%\end{algorithm}
 
 %\begin{algorithm}[!b]
 %	\caption{Retrieve the $i$-th sequence, $0\le i<m$}\label{algo:get}