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r474: replaced -S and --cs-no-equal with --cs
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@lh3
lh3 committed Oct 5, 2017
1 parent 3ff6eda commit f4a5d3a
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Showing 3 changed files with 27 additions and 11 deletions.
4 changes: 2 additions & 2 deletions format.c
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Original file line number Diff line number Diff line change
Expand Up @@ -223,7 +223,7 @@ void mm_write_paf(kstring_t *s, const mm_idx_t *mi, const mm_bseq1_t *t, const m
mm_sprintf_lite(s, "%d%c", r->p->cigar[k]>>4, "MIDN"[r->p->cigar[k]&0xf]);
}
if (r->p && (opt_flag & MM_F_OUT_CS))
write_cs(km, s, mi, t, r, opt_flag&MM_F_CS_NO_EQUAL);
write_cs(km, s, mi, t, r, !(opt_flag&MM_F_OUT_CS_LONG));
}

static void sam_write_sq(kstring_t *s, char *seq, int l, int rev, int comp)
Expand Down Expand Up @@ -391,7 +391,7 @@ void mm_write_sam2(kstring_t *s, const mm_idx_t *mi, const mm_bseq1_t *t, int se
}
}
if (r->p && (opt_flag & MM_F_OUT_CS))
write_cs(km, s, mi, t, r, MM_F_CS_NO_EQUAL);
write_cs(km, s, mi, t, r, !(opt_flag&MM_F_OUT_CS_LONG));
}

s->s[s->l] = 0; // we always have room for an extra byte (see str_enlarge)
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32 changes: 24 additions & 8 deletions main.c
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Original file line number Diff line number Diff line change
Expand Up @@ -6,7 +6,7 @@
#include "mmpriv.h"
#include "getopt.h"

#define MM_VERSION "2.2-r473-dirty"
#define MM_VERSION "2.2-r474-dirty"

#ifdef __linux__
#include <sys/resource.h>
Expand Down Expand Up @@ -39,7 +39,7 @@ static struct option long_options[] = {
{ "sr", no_argument, 0, 0 },
{ "multi", optional_argument, 0, 0 },
{ "print-2nd", optional_argument, 0, 0 },
{ "cs-no-equal", no_argument, 0, 0 },
{ "cs", optional_argument, 0, 0 },
{ "help", no_argument, 0, 'h' },
{ "max-intron-len", required_argument, 0, 'G' },
{ "version", no_argument, 0, 'V' },
Expand Down Expand Up @@ -102,7 +102,6 @@ int main(int argc, char *argv[])
else if (c == 'p') opt.pri_ratio = atof(optarg);
else if (c == 'M') opt.mask_level = atof(optarg);
else if (c == 'c') opt.flag |= MM_F_OUT_CG | MM_F_CIGAR;
else if (c == 'S') opt.flag |= MM_F_OUT_CS | 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;
Expand Down Expand Up @@ -130,15 +129,27 @@ int main(int argc, char *argv[])
else if (c == 0 && long_idx ==11) opt.noncan = atoi(optarg); // --cost-non-gt-ag
else if (c == 0 && long_idx ==12) opt.flag |= MM_F_NO_LJOIN; // --no-long-join
else if (c == 0 && long_idx ==13) opt.flag |= MM_F_SR; // --sr
else if (c == 0 && long_idx ==16) opt.flag |= MM_F_CS_NO_EQUAL | MM_F_OUT_CS | MM_F_CIGAR; // --cs-no-equal
else if (c == 0 && long_idx ==14) { // --multi
else if (c == 0 && long_idx == 14) { // --multi
if (optarg == 0 || strcmp(optarg, "yes") == 0 || strcmp(optarg, "y") == 0)
opt.flag |= MM_F_MULTI_SEG;
else opt.flag &= ~MM_F_MULTI_SEG;
} else if (c == 0 && long_idx ==15) { // --print-2nd
} else if (c == 0 && long_idx == 15) { // --print-2nd
if (optarg == 0 || strcmp(optarg, "yes") == 0 || strcmp(optarg, "y") == 0)
opt.flag &= ~MM_F_NO_PRINT_2ND;
else opt.flag |= MM_F_NO_PRINT_2ND;
} else if (c == 0 && long_idx == 16) { // --cs
opt.flag |= MM_F_OUT_CS | MM_F_CIGAR;
if (optarg == 0 || strcmp(optarg, "short") == 0) {
opt.flag &= ~MM_F_OUT_CS_LONG;
} else if (strcmp(optarg, "long") == 0) {
opt.flag |= MM_F_OUT_CS_LONG;
} else if (mm_verbose >= 2) {
fprintf(stderr, "[WARNING]\033[1;31m --cs only takes 'short' or 'long'. Invalid values are assumed to be 'short'.\033[0m\n");
}
} else if (c == 'S') {
opt.flag |= MM_F_OUT_CS | MM_F_CIGAR | MM_F_OUT_CS_LONG;
if (mm_verbose >= 2)
fprintf(stderr, "[WARNING]\033[1;31m option -S is deprecated and may be removed in future. Please use --cs=long instead.\033[0m\n");
} else if (c == 'V') {
puts(MM_VERSION);
return 0;
Expand Down Expand Up @@ -172,6 +183,11 @@ int main(int argc, char *argv[])
if (opt.flag & MM_F_SPLICE)
opt.max_gap_ref = opt.bw = max_gap_ref;
}
if ((opt.flag & MM_F_OUT_SAM) && (opt.flag & MM_F_OUT_CS_LONG)) {
opt.flag &= ~MM_F_OUT_CS_LONG;
if (mm_verbose >= 2)
fprintf(stderr, "[WARNING]\033[1;31m in SAM, only the short form of the cs tag is outputted.\033[0m\n");
}

if (argc == optind || fp_help == stdout) {
fprintf(fp_help, "Usage: minimap2 [options] <target.fa>|<target.idx> [query.fa] [...]\n");
Expand Down Expand Up @@ -206,7 +222,7 @@ int main(int argc, char *argv[])
fprintf(fp_help, " -Q don't output base quality in SAM\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, " -S output the cs tag in PAF (cs encodes both query and ref sequences)\n");
fprintf(fp_help, " --cs[=STR] output the cs tag; STR is 'short' (if absent) or 'long' [no cs]\n");
fprintf(fp_help, " -t INT number of threads [%d]\n", n_threads);
fprintf(fp_help, " -K NUM minibatch size for mapping [200M]\n");
// fprintf(fp_help, " -v INT verbose level [%d]\n", mm_verbose);
Expand Down Expand Up @@ -241,7 +257,7 @@ int main(int argc, char *argv[])
} else {
mm_write_sam_hdr(0, rg, MM_VERSION, argc, argv);
if (mm_verbose >= 2)
fprintf(stderr, "[WARNING] \033[1;31mFor a multi-part index, no @SQ lines will be outputted.\033[0m\n");
fprintf(stderr, "[WARNING]\033[1;31m For a multi-part index, no @SQ lines will be outputted.\033[0m\n");
}
}
if (mm_verbose >= 3)
Expand Down
2 changes: 1 addition & 1 deletion minimap.h
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Original file line number Diff line number Diff line change
Expand Up @@ -16,7 +16,7 @@
#define MM_F_SPLICE_FOR 0x100 // match GT-AG
#define MM_F_SPLICE_REV 0x200 // match CT-AC, the reverse complement of GT-AG
#define MM_F_NO_LJOIN 0x400
#define MM_F_CS_NO_EQUAL 0x800
#define MM_F_OUT_CS_LONG 0x800
#define MM_F_SR 0x1000
#define MM_F_MULTI_SEG 0x2000
#define MM_F_NO_PRINT_2ND 0x4000
Expand Down

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