r474: replaced -S and --cs-no-equal with --cs
This commit is contained in:
Heng Li
parent
3ff6eda3a4
commit
f4a5d3a692
4
format.c
4
format.c
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@ -223,7 +223,7 @@ void mm_write_paf(kstring_t *s, const mm_idx_t *mi, const mm_bseq1_t *t, const m
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mm_sprintf_lite(s, "%d%c", r->p->cigar[k]>>4, "MIDN"[r->p->cigar[k]&0xf]);
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}
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if (r->p && (opt_flag & MM_F_OUT_CS))
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write_cs(km, s, mi, t, r, opt_flag&MM_F_CS_NO_EQUAL);
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write_cs(km, s, mi, t, r, !(opt_flag&MM_F_OUT_CS_LONG));
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}
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static void sam_write_sq(kstring_t *s, char *seq, int l, int rev, int comp)
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@ -391,7 +391,7 @@ void mm_write_sam2(kstring_t *s, const mm_idx_t *mi, const mm_bseq1_t *t, int se
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}
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}
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if (r->p && (opt_flag & MM_F_OUT_CS))
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write_cs(km, s, mi, t, r, MM_F_CS_NO_EQUAL);
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write_cs(km, s, mi, t, r, !(opt_flag&MM_F_OUT_CS_LONG));
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}
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s->s[s->l] = 0; // we always have room for an extra byte (see str_enlarge)
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32
main.c
32
main.c
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@ -6,7 +6,7 @@
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#include "mmpriv.h"
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#include "getopt.h"
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#define MM_VERSION "2.2-r473-dirty"
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#define MM_VERSION "2.2-r474-dirty"
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#ifdef __linux__
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#include <sys/resource.h>
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@ -39,7 +39,7 @@ static struct option long_options[] = {
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{ "sr", no_argument, 0, 0 },
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{ "multi", optional_argument, 0, 0 },
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{ "print-2nd", optional_argument, 0, 0 },
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{ "cs-no-equal", no_argument, 0, 0 },
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{ "cs", optional_argument, 0, 0 },
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{ "help", no_argument, 0, 'h' },
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{ "max-intron-len", required_argument, 0, 'G' },
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{ "version", no_argument, 0, 'V' },
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@ -102,7 +102,6 @@ int main(int argc, char *argv[])
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else if (c == 'p') opt.pri_ratio = atof(optarg);
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else if (c == 'M') opt.mask_level = atof(optarg);
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else if (c == 'c') opt.flag |= MM_F_OUT_CG | MM_F_CIGAR;
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else if (c == 'S') opt.flag |= MM_F_OUT_CS | MM_F_CIGAR;
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else if (c == 'X') opt.flag |= MM_F_AVA | MM_F_NO_SELF;
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else if (c == 'a') opt.flag |= MM_F_OUT_SAM | MM_F_CIGAR;
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else if (c == 'Q') opt.flag |= MM_F_NO_QUAL;
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@ -130,15 +129,27 @@ int main(int argc, char *argv[])
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else if (c == 0 && long_idx ==11) opt.noncan = atoi(optarg); // --cost-non-gt-ag
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else if (c == 0 && long_idx ==12) opt.flag |= MM_F_NO_LJOIN; // --no-long-join
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else if (c == 0 && long_idx ==13) opt.flag |= MM_F_SR; // --sr
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else if (c == 0 && long_idx ==16) opt.flag |= MM_F_CS_NO_EQUAL | MM_F_OUT_CS | MM_F_CIGAR; // --cs-no-equal
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else if (c == 0 && long_idx ==14) { // --multi
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else if (c == 0 && long_idx == 14) { // --multi
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if (optarg == 0 || strcmp(optarg, "yes") == 0 || strcmp(optarg, "y") == 0)
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opt.flag |= MM_F_MULTI_SEG;
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else opt.flag &= ~MM_F_MULTI_SEG;
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} else if (c == 0 && long_idx ==15) { // --print-2nd
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} else if (c == 0 && long_idx == 15) { // --print-2nd
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if (optarg == 0 || strcmp(optarg, "yes") == 0 || strcmp(optarg, "y") == 0)
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opt.flag &= ~MM_F_NO_PRINT_2ND;
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else opt.flag |= MM_F_NO_PRINT_2ND;
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} else if (c == 0 && long_idx == 16) { // --cs
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opt.flag |= MM_F_OUT_CS | MM_F_CIGAR;
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if (optarg == 0 || strcmp(optarg, "short") == 0) {
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opt.flag &= ~MM_F_OUT_CS_LONG;
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} else if (strcmp(optarg, "long") == 0) {
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opt.flag |= MM_F_OUT_CS_LONG;
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} else if (mm_verbose >= 2) {
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fprintf(stderr, "[WARNING]\033[1;31m --cs only takes 'short' or 'long'. Invalid values are assumed to be 'short'.\033[0m\n");
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}
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} else if (c == 'S') {
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opt.flag |= MM_F_OUT_CS | MM_F_CIGAR | MM_F_OUT_CS_LONG;
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if (mm_verbose >= 2)
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fprintf(stderr, "[WARNING]\033[1;31m option -S is deprecated and may be removed in future. Please use --cs=long instead.\033[0m\n");
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} else if (c == 'V') {
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puts(MM_VERSION);
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return 0;
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@ -172,6 +183,11 @@ int main(int argc, char *argv[])
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if (opt.flag & MM_F_SPLICE)
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opt.max_gap_ref = opt.bw = max_gap_ref;
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}
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if ((opt.flag & MM_F_OUT_SAM) && (opt.flag & MM_F_OUT_CS_LONG)) {
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opt.flag &= ~MM_F_OUT_CS_LONG;
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if (mm_verbose >= 2)
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fprintf(stderr, "[WARNING]\033[1;31m in SAM, only the short form of the cs tag is outputted.\033[0m\n");
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}
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if (argc == optind || fp_help == stdout) {
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fprintf(fp_help, "Usage: minimap2 [options] <target.fa>|<target.idx> [query.fa] [...]\n");
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@ -206,7 +222,7 @@ int main(int argc, char *argv[])
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fprintf(fp_help, " -Q don't output base quality in SAM\n");
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fprintf(fp_help, " -R STR SAM read group line in a format like '@RG\\tID:foo\\tSM:bar' []\n");
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fprintf(fp_help, " -c output CIGAR in PAF\n");
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fprintf(fp_help, " -S output the cs tag in PAF (cs encodes both query and ref sequences)\n");
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fprintf(fp_help, " --cs[=STR] output the cs tag; STR is 'short' (if absent) or 'long' [no cs]\n");
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fprintf(fp_help, " -t INT number of threads [%d]\n", n_threads);
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fprintf(fp_help, " -K NUM minibatch size for mapping [200M]\n");
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// fprintf(fp_help, " -v INT verbose level [%d]\n", mm_verbose);
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@ -241,7 +257,7 @@ int main(int argc, char *argv[])
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} else {
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mm_write_sam_hdr(0, rg, MM_VERSION, argc, argv);
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if (mm_verbose >= 2)
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fprintf(stderr, "[WARNING] \033[1;31mFor a multi-part index, no @SQ lines will be outputted.\033[0m\n");
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fprintf(stderr, "[WARNING]\033[1;31m For a multi-part index, no @SQ lines will be outputted.\033[0m\n");
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}
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}
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if (mm_verbose >= 3)
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@ -16,7 +16,7 @@
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#define MM_F_SPLICE_FOR 0x100 // match GT-AG
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#define MM_F_SPLICE_REV 0x200 // match CT-AC, the reverse complement of GT-AG
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#define MM_F_NO_LJOIN 0x400
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#define MM_F_CS_NO_EQUAL 0x800
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#define MM_F_OUT_CS_LONG 0x800
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#define MM_F_SR 0x1000
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#define MM_F_MULTI_SEG 0x2000
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#define MM_F_NO_PRINT_2ND 0x4000
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