drafted the release notes

NEWS.md

@@ -1,3 +1,28 @@
+Release 2.29-r1283 (18 April 2025)
+----------------------------------
+
+Notable changes:
+
+ * New feature: added the `splice:sr` preset for short RNA-seq read alignment.
+   Users may use `-j` to specify known gene annotation to improve spliced
+   alignment close to the ends of reads. Also added `--write-junc` and
+   `--pass1` for 2-pass short-read RNA-seq alignment.
+
+ * Experimental feature: read splice scores from a file specified by `--spsc`
+   and consider the scores during base alignment. The feature makes it possible
+   to apply advanced splice models and to improve spliced alignment.
+
+ * Change: adjusted the mapping quality calculation for spliced alignment.
+
+This release produces identical genomic long-read alignment to v2.27. Short
+genomic read alignment and the mapping quality of long RNA-seq read alignment
+may slightly differ in very rare cases. Minimap2 now supports short/long
+genomic/RNA-seq read alignment.
+
+(2.29: 18 April 2025, r1283)
+
+
+
 Release 2.28-r1209 (27 March 2024)
 ----------------------------------
 

minimap2.1

@@ -1,4 +1,4 @@
-.TH minimap2 1 "13 April 2025" "minimap2-2.28-dirty (r1274)" "Bioinformatics tools"
+.TH minimap2 1 "18 April 2025" "minimap2-2.29 (r1283)" "Bioinformatics tools"
 .SH NAME
 .PP
 minimap2 - mapping and alignment between collections of DNA sequences

python/cmappy.pxd

@@ -52,6 +52,8 @@ cdef extern from "minimap.h":
 
 		int pe_ori, pe_bonus
 
+		int jump_min_match;
+
 		float mid_occ_frac
 		float q_occ_frac
 		int32_t min_mid_occ