r1163: increased the default -I to 8G

To reduce accidental errors when mapping against diploid human assemblies.
eskutkaan · Apr 7, 2023 · a026c69 · a026c69
1 parent ea2042a
commit a026c69
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Showing 4 changed files with 4 additions and 4 deletions.
diff --git a/main.c b/main.c
@@ -325,7 +325,7 @@ int main(int argc, char *argv[])
 		fprintf(fp_help, "    -k INT       k-mer size (no larger than 28) [%d]\n", ipt.k);
 		fprintf(fp_help, "    -w INT       minimizer window size [%d]\n", ipt.w);
 //		fprintf(fp_help, "    -j INT       syncmer submer size (overriding -w) []\n");
-		fprintf(fp_help, "    -I NUM       split index for every ~NUM input bases [4G]\n");
+		fprintf(fp_help, "    -I NUM       split index for every ~NUM input bases [8G]\n");
 		fprintf(fp_help, "    -d FILE      dump index to FILE []\n");
 		fprintf(fp_help, "  Mapping:\n");
 		fprintf(fp_help, "    -f FLOAT     filter out top FLOAT fraction of repetitive minimizers [%g]\n", opt.mid_occ_frac);

diff --git a/minimap.h b/minimap.h
@@ -5,7 +5,7 @@
 #include <stdio.h>
 #include <sys/types.h>
 
-#define MM_VERSION "2.24-r1162-dirty"
+#define MM_VERSION "2.24-r1163-dirty"
 
 #define MM_F_NO_DIAG       0x001 // no exact diagonal hit
 #define MM_F_NO_DUAL       0x002 // skip pairs where query name is lexicographically larger than target name

diff --git a/minimap2.1 b/minimap2.1
@@ -101,7 +101,7 @@ on the HPC sequence.
 .BI -I \ NUM
 Load at most
 .I NUM
-target bases into RAM for indexing [4G]. If there are more than
+target bases into RAM for indexing [8G]. If there are more than
 .I NUM
 bases in
 .IR target.fa ,

diff --git a/options.c b/options.c
@@ -8,7 +8,7 @@ void mm_idxopt_init(mm_idxopt_t *opt)
 	opt->k = 15, opt->w = 10, opt->flag = 0;
 	opt->bucket_bits = 14;
 	opt->mini_batch_size = 50000000;
-	opt->batch_size = 4000000000ULL;
+	opt->batch_size = 8000000000ULL;
 }
 
 void mm_mapopt_init(mm_mapopt_t *opt)