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r141: replaced -b with -a (for SAM output) 

-b sounds like BAM. I like -a better.
This commit is contained in:
Heng Li 2017-07-01 16:54:59 -04:00
parent 67cad9dff3
commit da90b614db
2 changed files with 8 additions and 8 deletions
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10
main.c
View File

@ -10,7 +10,7 @@
#include "minimap.h"
#include "mmpriv.h"
#define MM_VERSION "2.0-r131-pre"
#define MM_VERSION "2.0-r141-pre"
void liftrlimit()
{
@ -50,7 +50,7 @@ static struct option long_options[] = {
{ "min-chain-score",required_argument, 0, 'm' },
{ "mask-level", required_argument, 0, 'M' },
{ "min-dp-score", required_argument, 0, 's' },
{ "sam", no_argument, 0, 'b' },
{ "sam", no_argument, 0, 'a' },
{ 0, 0, 0, 0}
};
@ -68,7 +68,7 @@ int main(int argc, char *argv[])
mm_realtime0 = realtime();
mm_mapopt_init(&opt);
while ((c = getopt_long(argc, argv, "bw:k:t:r:f:Vv:g:I:d:ST:s:x:Hcp:M:n:z:A:B:O:E:m:D:", long_options, &long_idx)) >= 0) {
while ((c = getopt_long(argc, argv, "aw:k:t:r:f:Vv:g:I:d:ST:s:x:Hcp:M:n:z:A:B:O:E:m:D:", long_options, &long_idx)) >= 0) {
if (c == 'w') w = atoi(optarg);
else if (c == 'k') k = atoi(optarg);
else if (c == 'H') is_hpc = 1;
@ -83,7 +83,7 @@ int main(int argc, char *argv[])
else if (c == 'M') opt.mask_level = atof(optarg);
else if (c == 'c') opt.flag |= MM_F_CIGAR;
else if (c == 'S') opt.flag |= MM_F_AVA | MM_F_NO_SELF;
else if (c == 'b') opt.flag |= MM_F_OUT_SAM | MM_F_CIGAR;
else if (c == 'a') opt.flag |= MM_F_OUT_SAM | MM_F_CIGAR;
else if (c == 'T') opt.sdust_thres = atoi(optarg);
else if (c == 'n') opt.min_cnt = atoi(optarg);
else if (c == 'm') opt.min_chain_score = atoi(optarg);
@ -155,7 +155,7 @@ int main(int argc, char *argv[])
fprintf(stderr, " -z INT Z-drop score [%d]\n", opt.zdrop);
fprintf(stderr, " -s INT minimal peak DP alignment score [%d]\n", opt.min_dp_max);
fprintf(stderr, " Input/Output:\n");
fprintf(stderr, " -b output in the SAM format (PAF by default)\n");
fprintf(stderr, " -a output in the SAM format (PAF by default)\n");
fprintf(stderr, " -c output CIGAR in PAF\n");
fprintf(stderr, " -t INT number of threads [%d]\n", n_threads);
// fprintf(stderr, " -v INT verbose level [%d]\n", mm_verbose);

6
minimap2.1
View File

@ -1,4 +1,4 @@
.TH minimap2 1 "30 June 2017" "minimap2-2.0-r126-pre" "Bioinformatics tools"
.TH minimap2 1 "1 July 2017" "minimap2-2.0-r141-pre" "Bioinformatics tools"
.SH NAME
.PP
minimap2 - mapping and alignment between collections of DNA sequences
@ -28,7 +28,7 @@ minimap2
* Long-read alignment with CIGAR:
.RS 4
minimap2
.B -b
.B -a
.RB [ -x
.IR preset ]
.I target.mmi
@ -212,7 +212,7 @@ the final CIGAR. It is the score of the max scoring segment in the alignment
and may be different from the total alignment score.
.SS Input/output options
.TP 10
.B -b
.B -a
Generate CIGAR and output alignments in the SAM format. Minimap2 outputs in PAF
by default.
.TP