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r911: option -o to output to file (#319)

This commit is contained in:
Heng Li 2019-01-29 10:42:20 -05:00
parent eba237f39d
commit 8b05880f73
3 changed files with 18 additions and 5 deletions
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14
main.c
View File

@ -6,7 +6,7 @@
#include "mmpriv.h"
#include "ketopt.h"
#define MM_VERSION "2.15-r910-dirty"
#define MM_VERSION "2.15-r911-dirty"
#ifdef __linux__
#include <sys/resource.h>
@ -99,7 +99,7 @@ static inline void yes_or_no(mm_mapopt_t *opt, int flag, int long_idx, const cha
int main(int argc, char *argv[])
{
const char *opt_str = "2aSDw:k:K:t:r:f:Vv:g:G:I:d:XT:s:x:Hcp:M:n:z:A:B:O:E:m:N:Qu:R:hF:LC:yYP";
const char *opt_str = "2aSDw:k:K:t:r:f:Vv:g:G:I:d:XT:s:x:Hcp:M:n:z:A:B:O:E:m:N:Qu:R:hF:LC:yYPo:";
ketopt_t o = KETOPT_INIT;
mm_mapopt_t opt;
mm_idxopt_t ipt;
@ -165,6 +165,14 @@ int main(int argc, char *argv[])
else if (c == 'R') rg = o.arg;
else if (c == 'h') fp_help = stdout;
else if (c == '2') opt.flag |= MM_F_2_IO_THREADS;
else if (c == 'o') {
if (strcmp(o.arg, "-") != 0) {
if (freopen(o.arg, "wb", stdout) == NULL) {
fprintf(stderr, "[ERROR]\033[1;31m failed to write the output to file '%s'\033[0m\n", o.arg);
exit(1);
}
}
}
else if (c == 300) ipt.bucket_bits = atoi(o.arg); // --bucket-bits
else if (c == 302) opt.seed = atoi(o.arg); // --seed
else if (c == 303) mm_dbg_flag |= MM_DBG_NO_KALLOC; // --no-kalloc
@ -293,7 +301,7 @@ int main(int argc, char *argv[])
fprintf(fp_help, " -u CHAR how to find GT-AG. f:transcript strand, b:both strands, n:don't match GT-AG [n]\n");
fprintf(fp_help, " Input/Output:\n");
fprintf(fp_help, " -a output in the SAM format (PAF by default)\n");
fprintf(fp_help, " -Q don't output base quality in SAM\n");
fprintf(fp_help, " -o FILE output alignments to FILE [stdout]\n");
fprintf(fp_help, " -L write CIGAR with >65535 ops at the CG tag\n");
fprintf(fp_help, " -R STR SAM read group line in a format like '@RG\\tID:foo\\tSM:bar' []\n");
fprintf(fp_help, " -c output CIGAR in PAF\n");

7
minimap2.1
View File

@ -1,4 +1,4 @@
.TH minimap2 1 "10 January 2019" "minimap2-2.15 (r905)" "Bioinformatics tools"
.TH minimap2 1 "10 January 2019" "minimap2-2.15-dirty (r911)" "Bioinformatics tools"
.SH NAME
.PP
minimap2 - mapping and alignment between collections of DNA sequences
@ -384,6 +384,11 @@ Set 0 to disable [0].
Generate CIGAR and output alignments in the SAM format. Minimap2 outputs in PAF
by default.
.TP
.BI -o \ FILE
Output alignments to
.I FILE
[stdout].
.TP
.B -Q
Ignore base quality in the input file.
.TP

2
splitidx.c
View File

@ -13,7 +13,7 @@ FILE *mm_split_init(const char *prefix, const mm_idx_t *mi)
sprintf(fn, "%s.%.4d.tmp", prefix, mi->index);
if ((fp = fopen(fn, "wb")) == NULL) {
if (mm_verbose >= 1)
fprintf(stderr, "[E::%s] failed to create file '%s'\n", __func__, fn);
fprintf(stderr, "[ERROR]\033[1;31m failed to write to temporary file '%s'\033[0m\n", fn);
exit(1);
}
mm_err_fwrite(&k, 4, 1, fp);