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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 "minimap.h"
#include "mmpriv.h" #include "mmpriv.h"
#define MM_VERSION "2.0-r131-pre" #define MM_VERSION "2.0-r141-pre"
void liftrlimit() void liftrlimit()
{ {
@ -50,7 +50,7 @@ static struct option long_options[] = {
{ "min-chain-score",required_argument, 0, 'm' }, { "min-chain-score",required_argument, 0, 'm' },
{ "mask-level", required_argument, 0, 'M' }, { "mask-level", required_argument, 0, 'M' },
{ "min-dp-score", required_argument, 0, 's' }, { "min-dp-score", required_argument, 0, 's' },
{ "sam", no_argument, 0, 'b' }, { "sam", no_argument, 0, 'a' },
{ 0, 0, 0, 0} { 0, 0, 0, 0}
}; };
@ -68,7 +68,7 @@ int main(int argc, char *argv[])
mm_realtime0 = realtime(); mm_realtime0 = realtime();
mm_mapopt_init(&opt); 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); if (c == 'w') w = atoi(optarg);
else if (c == 'k') k = atoi(optarg); else if (c == 'k') k = atoi(optarg);
else if (c == 'H') is_hpc = 1; 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 == 'M') opt.mask_level = atof(optarg);
else if (c == 'c') opt.flag |= MM_F_CIGAR; 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 == '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 == 'T') opt.sdust_thres = atoi(optarg);
else if (c == 'n') opt.min_cnt = atoi(optarg); else if (c == 'n') opt.min_cnt = atoi(optarg);
else if (c == 'm') opt.min_chain_score = 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, " -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, " -s INT minimal peak DP alignment score [%d]\n", opt.min_dp_max);
fprintf(stderr, " Input/Output:\n"); 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, " -c output CIGAR in PAF\n");
fprintf(stderr, " -t INT number of threads [%d]\n", n_threads); fprintf(stderr, " -t INT number of threads [%d]\n", n_threads);
// fprintf(stderr, " -v INT verbose level [%d]\n", mm_verbose); // 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 .SH NAME
.PP .PP
minimap2 - mapping and alignment between collections of DNA sequences minimap2 - mapping and alignment between collections of DNA sequences
@ -28,7 +28,7 @@ minimap2
* Long-read alignment with CIGAR: * Long-read alignment with CIGAR:
.RS 4 .RS 4
minimap2 minimap2
.B -b .B -a
.RB [ -x .RB [ -x
.IR preset ] .IR preset ]
.I target.mmi .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. and may be different from the total alignment score.
.SS Input/output options .SS Input/output options
.TP 10 .TP 10
.B -b .B -a
Generate CIGAR and output alignments in the SAM format. Minimap2 outputs in PAF Generate CIGAR and output alignments in the SAM format. Minimap2 outputs in PAF
by default. by default.
.TP .TP