Release ropebwt3-3.3 (r149)

lh3 · Aug 7, 2024 · de32b65 · de32b65
1 parent ed06021
commit de32b65
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Showing 4 changed files with 36 additions and 7 deletions.
diff --git a/Makefile b/Makefile
@@ -59,3 +59,4 @@ search.o: fm-index.h rb3priv.h rld0.h mrope.h rope.h io.h align.h ketopt.h
 search.o: kthread.h kalloc.h
 ssa.o: rb3priv.h fm-index.h rld0.h mrope.h rope.h io.h kalloc.h kthread.h
 ssa.o: ketopt.h
+test.o: rld0.h
diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,31 @@
+Release 3.3-r149 (6 August 2024)
+--------------------------------
+
+Notable changes in the `sw` command:
+
+ * New feature: option to try SW only when there is a long MEM. This is not
+   enabled by default.
+
+ * New feature: option to output unmapped reads in PAF
+
+ * Bugfix: backtracking the F state could be wrong in corner cases
+
+ * Bugfix: coordinates on the reverse strand were not flipped in PAF
+
+ * Breaking: don't output the reference sequence in the rs tag by default
+
+Other new features:
+
+ * New feature: added the stat command to report the number of runs. Only
+   working for the FMD format for now.
+
+ * New feature: added `--min-gap` to the `mem` command to output regions not
+   covered by long MEMs.
+
+(3.3: 6 August 2024, r149)
+
+
+
 Release 3.2-r137 (23 July 2024)
 -------------------------------
 

diff --git a/README.md b/README.md
@@ -269,12 +269,12 @@ number of input bases.
 
 |Dataset        |Algorithm |Elapsed|CPU time|Peak RAM|
 |:--------------|:---------|------:|-------:|-------:|
-|human100       |rb3 build |  33.7h|  803.6h|  82.3GB|
-|               |rb3 merge |  24.2h|  757.2h|  70.7GB|
-|               |grlBWT    |   8.3h|   29.6h|  84.8GB|
-|               |pfp-thres |  51.7h|   51.5h| 788.1GB|
-|ecoli315k      |rb3 build | 128.7h| 3826.8h|  20.5GB|
-|CommonBacteria |rb3 build |  26.5d|  830.3d|  67.3GB|
+|human100       |rb3 build | 33.7 h| 803.6 h|  82.3 G|
+|               |rb3 merge | 24.2 h| 757.2 h|  70.7 G|
+|               |grlBWT    |  8.3 h|  29.6 h|  84.8 G|
+|               |pfp-thres | 51.7 h|  51.5 h| 788.1 G|
+|ecoli315k      |rb3 build |128.7 h|3826.8 h|  20.5 G|
+|CommonBacteria |rb3 build | 26.5 d| 830.3 d|  67.3 G|
 
 For human100, the following methods were evaluated:
 

diff --git a/main.c b/main.c
@@ -5,7 +5,7 @@
 #include "io.h"
 #include "ketopt.h"
 
-#define RB3_VERSION "3.2-r147-dirty"
+#define RB3_VERSION "3.3-r149"
 
 int main_build(int argc, char *argv[]);
 int main_merge(int argc, char *argv[]);