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r158: optionally ignore base quality

This commit is contained in:
Heng Li 2017-07-05 18:23:50 -04:00
parent d1f518e3ca
commit 9823317e8f
4 changed files with 11 additions and 4 deletions
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6
main.c
View File

@ -10,7 +10,7 @@
#include "minimap.h"
#include "mmpriv.h"
#define MM_VERSION "2.0-r153-pre"
#define MM_VERSION "2.0-r158-pre"
void liftrlimit()
{
@ -70,7 +70,7 @@ int main(int argc, char *argv[])
mm_realtime0 = realtime();
mm_mapopt_init(&opt);
while ((c = getopt_long(argc, argv, "aw:k:t:r:f:Vv:g:I:d:XT:s:x:Hcp:M:n:z:A:B:O:E:m:D:N:", long_options, &long_idx)) >= 0) {
while ((c = getopt_long(argc, argv, "aw:k:t:r:f:Vv:g:I:d:XT:s:x:Hcp:M:n:z:A:B:O:E:m:D:N:Q", 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;
@ -87,6 +87,7 @@ int main(int argc, char *argv[])
else if (c == 'c') opt.flag |= MM_F_CIGAR;
else if (c == 'X') opt.flag |= MM_F_AVA | MM_F_NO_SELF;
else if (c == 'a') opt.flag |= MM_F_OUT_SAM | MM_F_CIGAR;
else if (c == 'Q') opt.flag |= MM_F_NO_QUAL;
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);
@ -161,6 +162,7 @@ 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, " -Q ignore base quality in the input\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);

3
map.c
View File

@ -305,9 +305,10 @@ static void *worker_pipeline(void *shared, int step, void *in)
int i, j;
pipeline_t *p = (pipeline_t*)shared;
if (step == 0) { // step 0: read sequences
int with_qual = (!!(p->opt->flag & MM_F_OUT_SAM) && !(p->opt->flag & MM_F_NO_QUAL));
step_t *s;
s = (step_t*)calloc(1, sizeof(step_t));
s->seq = bseq_read(p->fp, p->mini_batch_size, !!(p->opt->flag & MM_F_OUT_SAM), &s->n_seq);
s->seq = bseq_read(p->fp, p->mini_batch_size, with_qual, &s->n_seq);
if (s->seq) {
s->p = p;
for (i = 0; i < s->n_seq; ++i)

1
minimap.h
View File

@ -11,6 +11,7 @@
#define MM_F_AVA 0x02
#define MM_F_CIGAR 0x04
#define MM_F_OUT_SAM 0x08
#define MM_F_NO_QUAL 0x10
#define MM_IDX_MAGIC "MMI\2"

5
minimap2.1
View File

@ -1,4 +1,4 @@
.TH minimap2 1 "1 July 2017" "minimap2-2.0-r145-pre" "Bioinformatics tools"
.TH minimap2 1 "5 July 2017" "minimap2-2.0-r158-pre" "Bioinformatics tools"
.SH NAME
.PP
minimap2 - mapping and alignment between collections of DNA sequences
@ -218,6 +218,9 @@ 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 -Q
Ignore base quality in the input file.
.TP
.B -a
Generate CIGAR and output alignments in the SAM format. Minimap2 outputs in PAF
by default.