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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 "mmpriv.h"
#include "ketopt.h" #include "ketopt.h"
#define MM_VERSION "2.15-r910-dirty" #define MM_VERSION "2.15-r911-dirty"
#ifdef __linux__ #ifdef __linux__
#include <sys/resource.h> #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[]) 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; ketopt_t o = KETOPT_INIT;
mm_mapopt_t opt; mm_mapopt_t opt;
mm_idxopt_t ipt; mm_idxopt_t ipt;
@ -165,6 +165,14 @@ int main(int argc, char *argv[])
else if (c == 'R') rg = o.arg; else if (c == 'R') rg = o.arg;
else if (c == 'h') fp_help = stdout; else if (c == 'h') fp_help = stdout;
else if (c == '2') opt.flag |= MM_F_2_IO_THREADS; 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 == 300) ipt.bucket_bits = atoi(o.arg); // --bucket-bits
else if (c == 302) opt.seed = atoi(o.arg); // --seed else if (c == 302) opt.seed = atoi(o.arg); // --seed
else if (c == 303) mm_dbg_flag |= MM_DBG_NO_KALLOC; // --no-kalloc 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, " -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, " Input/Output:\n");
fprintf(fp_help, " -a output in the SAM format (PAF by default)\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, " -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, " -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"); 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 .SH NAME
.PP .PP
minimap2 - mapping and alignment between collections of DNA sequences 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 Generate CIGAR and output alignments in the SAM format. Minimap2 outputs in PAF
by default. by default.
.TP .TP
.BI -o \ FILE
Output alignments to
.I FILE
[stdout].
.TP
.B -Q .B -Q
Ignore base quality in the input file. Ignore base quality in the input file.
.TP .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); sprintf(fn, "%s.%.4d.tmp", prefix, mi->index);
if ((fp = fopen(fn, "wb")) == NULL) { if ((fp = fopen(fn, "wb")) == NULL) {
if (mm_verbose >= 1) 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); exit(1);
} }
mm_err_fwrite(&k, 4, 1, fp); mm_err_fwrite(&k, 4, 1, fp);