diff --git a/Makefile b/Makefile index e0e8170..4d56050 100644 --- 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 index 7bb37ac..c3ba408 100644 --- 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 index 808d030..7f542e6 100644 --- 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 index 766c397..57ca3ba 100644 --- 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[]);