Release miniprot-0.7 (r207)

NEWS.md

@@ -1,3 +1,30 @@
+Release 0.7-r207 (25 December 2022)
+-----------------------------------
+
+Notable changes:
+
+ * Improvement: replaced open syncmers with modimers. This simplifies the code
+   and slightly reduces the memory.
+
+ * Improvement: fine tune parameters for higher sensitivity at a minor cost of
+   junction accuracy: a) only index ORFs >= 30bp; b) reduced max k-mer
+   occurrences from 50k to 20k; c) sample k-mers at a rate of 50%; d) reduced
+   min number of k-mers from 5 to 3; e) add a bonus chaining score for anchors
+   on the same reference block.
+
+ * Improvement: adjust the max k-mer occurrence dynamically per protein.
+
+ * Improvement: implemented 2-level chaining like minimap2 and minigraph. This
+   reduces chaining time.
+
+ * Bugfix: fixed a rare off-by-1 memory violation
+
+ * Bugfix: fixed a memory leak
+
+(0.7: 25 December 2022, r207)
+
+
+
 Release 0.6-r185 (12 December 2022)
 -----------------------------------
 

miniprot.1

@@ -1,4 +1,4 @@
-.TH miniprot 1 "12 December 2022" "miniprot-0.6 (r185)" "Bioinformatics tools"
+.TH miniprot 1 "25 December 2022" "miniprot-0.7 (r207)" "Bioinformatics tools"
 .SH NAME
 .PP
 miniprot - protein-to-genome alignment with splicing and frameshifts
@@ -39,8 +39,13 @@ Miniprot aligns protein sequences to a genome allowing potential frameshifts and
 .BI -k \ INT
 K-mer size for genome-wide indexing [6]
 .TP
-.BI -s \ INT
-Syncmer submer size [4]. In average, miniprot selects a k-mer every 2*(k-s)+1 residues.
+.BI -M \ INT
+Sample k-mers at a rate
+.RI 1/2** INT
+[1]. Increasing this option reduces peak memory but decreases sensitivity.
+.TP
+.BI -L \ INT
+Minimum ORF length to index [30]
 .TP
 .BI -b \ INT
 Number of bits per bin [8]. Miniprot splits the genome into non-overlapping bins of 2^8 bp in size.
@@ -140,6 +145,9 @@ Change the ID field in GFF3 to
 .RI QueryName CHAR HitIndex
 []. If not specified, the default ID looks like `MP000012'.
 .TP
+.B --gtf
+Output in the GTF format
+.TP
 .B -u
 Print unmapped query proteins
 .TP
@@ -149,6 +157,11 @@ Output up to
 .BR -N }
 alignments per query [1000].
 .TP
+.BI --outs \ FLOAT
+Output an alignment only if its score is at least
+.IR FLOAT *bestScore,
+where bestScore is the best alignment score of the protein [0.99]
+.TP
 .BI -K \ NUM
 Query batch size [2M]
 .SH OUTPUT FORMAT

miniprot.h

@@ -3,7 +3,7 @@
 
 #include <stdint.h>
 
-#define MP_VERSION "0.6-r204-dirty"
+#define MP_VERSION "0.7-r207"
 
 #define MP_F_NO_SPLICE    0x1
 #define MP_F_NO_ALIGN     0x2