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r309: improved SAM header output

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This commit is contained in:
Heng Li
2017-08-25 10:35:58 +08:00
parent 240f6caaff
commit 0fe1a224ab
9 changed files with 61 additions and 42 deletions
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main.c
+16 -10
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@@ -8,7 +8,7 @@
#include "minimap.h"
#include "mmpriv.h"
#define MM_VERSION "2.0-r301-dirty"
#define MM_VERSION "2.0-r309-dirty"
void liftrlimit()
{
@@ -33,6 +33,7 @@ static struct option long_options[] = {
{ "print-aln-seq", no_argument, 0, 0 },
{ "splice", no_argument, 0, 0 },
{ "cost-non-gt-ag", required_argument, 0, 0 },
{ "no-sam-sq", no_argument, 0, 0 },
{ "help", no_argument, 0, 'h' },
{ "max-intron-len", required_argument, 0, 'G' },
{ "version", no_argument, 0, 'V' },
@@ -58,11 +59,11 @@ static inline int64_t mm_parse_num(const char *str)
int main(int argc, char *argv[])
{
mm_mapopt_t opt;
int i, c, k = 15, w = -1, bucket_bits = MM_IDX_DEF_B, n_threads = 3, keep_name = 1, is_idx, is_hpc = 0, long_idx, idx_par_set = 0, max_intron_len = 0;
int i, c, k = 15, w = -1, bucket_bits = MM_IDX_DEF_B, n_threads = 3, keep_name = 1, is_idx, is_hpc = 0, long_idx, idx_par_set = 0, max_intron_len = 0, n_idx_part = 0;
int minibatch_size = 200000000;
uint64_t batch_size = 4000000000ULL;
mm_bseq_file_t *fp = 0;
char *fnw = 0, *s;
char *fnw = 0, *rg = 0, *s;
FILE *fpr = 0, *fpw = 0, *fp_help = stderr;
liftrlimit();
@@ -97,7 +98,7 @@ int main(int argc, char *argv[])
else if (c == 's') opt.min_dp_max = atoi(optarg);
else if (c == 'I') batch_size = mm_parse_num(optarg);
else if (c == 'K') minibatch_size = (int)mm_parse_num(optarg);
else if (c == 'R') mm_set_rg(optarg); // WARNING: this modifies global variables in format.c
else if (c == 'R') rg = optarg;
else if (c == 'h') fp_help = stdout;
else if (c == 0 && long_idx == 0) bucket_bits = atoi(optarg); // --bucket-bits
else if (c == 0 && long_idx == 2) keep_name = 0; // --int-rname
@@ -110,6 +111,7 @@ int main(int argc, char *argv[])
else if (c == 0 && long_idx == 9) mm_dbg_flag |= MM_DBG_PRINT_QNAME | MM_DBG_PRINT_ALN_SEQ; // --print-aln-seq
else if (c == 0 && long_idx ==10) opt.flag |= MM_F_SPLICE; // --splice
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_SAM_SQ; // --no-sam-sq
else if (c == 'V') {
puts(MM_VERSION);
return 0;
@@ -222,27 +224,31 @@ int main(int argc, char *argv[])
is_idx = mm_idx_is_idx(argv[optind]);
if (is_idx < 0) {
fprintf(stderr, "[E::%s] failed to open file '%s'\n", __func__, argv[optind]);
fprintf(stderr, "[ERROR] failed to open file '%s'\n", argv[optind]);
return 1;
}
if (!is_idx && fnw == 0 && argc - optind < 2) {
fprintf(stderr, "[E::%s] missing input: please specify a query file or option -d\n", __func__);
fprintf(stderr, "[ERROR] missing input: please specify a query file to map or option -d to keep the index\n");
return 1;
}
if (is_idx) fpr = fopen(argv[optind], "rb");
else fp = mm_bseq_open(argv[optind]);
if (fnw) fpw = fopen(fnw, "wb");
if (opt.flag & MM_F_OUT_SAM)
mm_write_sam_hdr_no_SQ(rg, MM_VERSION, argc, argv);
for (;;) {
mm_idx_t *mi = 0;
mm_idx_t *mi;
if (fpr) {
mi = mm_idx_load(fpr);
if (idx_par_set && mm_verbose >= 2 && (mi->k != k || mi->w != w || mi->is_hpc != is_hpc))
fprintf(stderr, "[W::%s::%.3f*%.2f] Indexing parameters on the command line (-k/-w/-H) overridden by parameters in the prebuilt index.\n",
__func__, realtime() - mm_realtime0, cputime() / (realtime() - mm_realtime0));
} else if (!mm_bseq_eof(fp)) {
fprintf(stderr, "[WARNING] \033[1;31mIndexing parameters on the command line (-k/-w/-H) overridden by parameters in the prebuilt index.\033[0m\n");
} else {
mi = mm_idx_gen(fp, w, k, bucket_bits, is_hpc, minibatch_size, n_threads, batch_size, keep_name);
}
if (mi == 0) break;
++n_idx_part;
if (mm_verbose >= 2 && n_idx_part > 1 && (opt.flag&MM_F_OUT_SAM) && !(opt.flag&MM_F_NO_SAM_SQ))
fprintf(stderr, "[WARNING] \033[1;31mSAM output is malformated due to internal @SQ lines. Please add option --no-sam-sq or filter afterwards.\033[0m\n");
if (mm_verbose >= 3)
fprintf(stderr, "[M::%s::%.3f*%.2f] loaded/built the index for %d target sequence(s)\n",
__func__, realtime() - mm_realtime0, cputime() / (realtime() - mm_realtime0), mi->n_seq);