Release minigraph-0.14 (r415)

NEWS.md

@@ -1,3 +1,17 @@
+Release 0.14-r415 (19 December 2020)
+------------------------------------
+
+Notable changes:
+
+ * Added the `--call` option to find the allele/walk in each bubble.
+
+ * Reduced the default minimum variant length (option `-L`) from 100 to 50 for
+   the consistency with the SV community.
+
+(19 December 2020, r415)
+
+
+
 Release 0.13-r397 (3 December 2020)
 -----------------------------------
 

main.c

@@ -225,13 +225,13 @@ int main(int argc, char *argv[])
 		fprintf(fp_help, "    -p FLOAT     min secondary-to-primary score ratio [%g]\n", opt.pri_ratio);
 		fprintf(fp_help, "    -N INT       retain at most INT secondary mappings [%d]\n", opt.best_n);
 		fprintf(fp_help, "    -D           skip self diagonal matches\n");
-		fprintf(fp_help, "    --cov        remap and generate segment and link use frequencies; output GFA\n");
 		fprintf(fp_help, "  Graph generation:\n");
 		fprintf(fp_help, "    --ggen       perform incremental graph generation\n");
 		fprintf(fp_help, "    -q INT       min mapping quality [%d]\n", gpt.min_mapq);
 		fprintf(fp_help, "    -l NUM       min alignment length [%d]\n", gpt.min_map_len);
 		fprintf(fp_help, "    -d NUM       min alignment length for depth calculation [%d]\n", gpt.min_depth_len);
 		fprintf(fp_help, "    -L INT       min variant length [%d]\n", gpt.min_var_len);
+		fprintf(fp_help, "    --call       call the graph path in each bubble and output BED\n");
 		fprintf(fp_help, "  Input/output:\n");
 		fprintf(fp_help, "    -t INT       number of threads [%d]\n", n_threads);
 		fprintf(fp_help, "    -o FILE      output mappings to FILE [stdout]\n");

minigraph.1

@@ -1,4 +1,4 @@
-.TH minigraph 1 "3 December 2020" "minigraph-0.13 (r397)" "Bioinformatics tools"
+.TH minigraph 1 "19 December 2020" "minigraph-0.14 (r415)" "Bioinformatics tools"
 
 .SH NAME
 .PP
@@ -151,19 +151,11 @@ Graph generation algorithm. So far only a
 algorithm is implemented [simple]. With this option, all query sequences are
 loaded into memory.
 .TP
-.B --cov
-Remap and generate segment and link use frequencies. This option triggers GFA
-output. When used with
-.BR --ggen ,
-minigraph writes the frequency of link uses and the average breadth of coverage
-of each segment to the
-.B cf
-tag. When used without
-.BR --ggen ,
-minigraph writes the count of link uses and the average depth of coverage of
-each segment to the
-.B dc
-tag.
+.B --call
+Call the graph path in each bubble and output in a BED-based format:
+.RS
+  ctg  start  end  sourceNode  sinkNode  walk:strand:queryName:qStart:qEnd
+.RE
 .TP
 .BI -q \ INT
 Minimum mapping quality [5]
@@ -185,6 +177,23 @@ Forcefully resolve query overlaps [no]
 .TP
 .BR --inv = yes | no
 Generate graphs with inversions or not [yes]
+.TP
+.B --cov
+Remap and generate segment and link use frequencies. This option triggers GFA
+output. When used with
+.BR --ggen ,
+minigraph writes the frequency of link uses and the average breadth of coverage
+of each segment to the
+.B cf
+tag. When used without
+.BR --ggen ,
+minigraph writes the count of link uses and the average depth of coverage of
+each segment to the
+.B dc
+tag.
+.B
+WARNING:
+THIS OPTION IS DEPRECATED AND MAY BE REMOVED IN FUTURE.
 .SS Input/output options
 .TP 10
 .BI -o \ FILE

minigraph.h

@@ -4,7 +4,7 @@
 #include <stdint.h>
 #include "gfa.h"
 
-#define MG_VERSION "0.13-r414-dirty"
+#define MG_VERSION "0.14-r415"
 
 #define MG_M_SPLICE       0x10
 #define MG_M_SR           0x20