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main.c
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#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <stdint.h>
#include <assert.h>
#include <limits.h>
#include <unistd.h>
#include <math.h>
#include <sys/stat.h>
#include "ketopt.h"
#include "yak-priv.h"
static inline int64_t mm_parse_num(const char *str)
{
double x;
char *p;
x = strtod(str, &p);
if (*p == 'G' || *p == 'g') x *= 1e9;
else if (*p == 'M' || *p == 'm') x *= 1e6;
else if (*p == 'K' || *p == 'k') x *= 1e3;
return (int64_t)(x + .499);
}
int main_count(int argc, char *argv[])
{
yak_ch_t *h;
int c;
char *fn_out = 0;
yak_copt_t opt;
ketopt_t o = KETOPT_INIT;
yak_copt_init(&opt);
while ((c = ketopt(&o, argc, argv, 1, "k:p:K:t:b:H:o:", 0)) >= 0) {
if (c == 'k') opt.k = atoi(o.arg);
else if (c == 'p') opt.pre = atoi(o.arg);
else if (c == 'K') opt.chunk_size = mm_parse_num(o.arg);
else if (c == 't') opt.n_thread = atoi(o.arg);
else if (c == 'b') opt.bf_shift = atoi(o.arg);
else if (c == 'H') opt.bf_n_hash = mm_parse_num(o.arg);
else if (c == 'o') fn_out = o.arg;
}
if (argc - o.ind < 1) {
fprintf(stderr, "Usage: yak count [options] <in.fa> [in.fa]\n");
fprintf(stderr, "Options:\n");
fprintf(stderr, " -k INT k-mer size [%d]\n", opt.k);
fprintf(stderr, " -p INT prefix length [%d]\n", opt.pre);
fprintf(stderr, " -b INT set Bloom filter size to 2**INT bits; 0 to disable [%d]\n", opt.bf_shift);
fprintf(stderr, " -H INT use INT hash functions for Bloom filter [%d]\n", opt.bf_n_hash);
fprintf(stderr, " -t INT number of worker threads [%d]\n", opt.n_thread);
fprintf(stderr, " -o FILE dump the count hash table to FILE []\n");
fprintf(stderr, " -K INT chunk size [100m]\n");
fprintf(stderr, "Note: -b37 is recommended for human reads\n");
return 1;
}
if (opt.pre < YAK_COUNTER_BITS) {
fprintf(stderr, "ERROR: -p should be at least %d\n", YAK_COUNTER_BITS);
return 1;
}
if (opt.k >= 64) {
fprintf(stderr, "ERROR: -k must be smaller than 64\n");
return 1;
} else if (opt.k >= 32) {
fprintf(stderr, "WARNING: counts are inexact if -k is greater than 31\n");
}
h = yak_count(argv[o.ind], &opt, 0);
if (opt.bf_shift > 0) {
yak_ch_destroy_bf(h);
yak_ch_clear(h, opt.n_thread);
h = yak_count(argc - o.ind >= 2? argv[o.ind+1] : argv[o.ind], &opt, h);
yak_ch_shrink(h, 2, YAK_MAX_COUNT, opt.n_thread);
fprintf(stderr, "[M::%s] %ld distinct k-mers after shrinking\n", __func__, (long)h->tot);
}
if (fn_out) yak_ch_dump(h, fn_out);
yak_ch_destroy(h);
return 0;
}
int main_qv(int argc, char *argv[])
{
yak_qopt_t opt;
yak_ch_t *ch = 0;
ketopt_t o = KETOPT_INIT;
int64_t cnt[YAK_N_COUNTS], hist[YAK_N_COUNTS];
int c, i, kmer;
yak_qstat_t qs;
yak_qopt_init(&opt);
while ((c = ketopt(&o, argc, argv, 1, "K:t:l:f:pe:", 0)) >= 0) {
if (c == 'K') opt.chunk_size = mm_parse_num(o.arg);
else if (c == 'l') opt.min_len = mm_parse_num(o.arg);
else if (c == 'f') opt.min_frac = atof(o.arg);
else if (c == 't') opt.n_threads = atoi(o.arg);
else if (c == 'p') opt.print_each = 1;
else if (c == 'e') opt.fpr = atof(o.arg);
}
if (argc - o.ind < 2) {
fprintf(stderr, "Usage: yak qv [options] <kmer.hash> <seq.fa>\n");
fprintf(stderr, "Options:\n");
fprintf(stderr, " -l NUM min sequence length [%d]\n", opt.min_len);
fprintf(stderr, " -f FLOAT min k-mer fraction [%g]\n", opt.min_frac);
fprintf(stderr, " -e FLOAT false positive rate [%g]\n", opt.fpr);
fprintf(stderr, " -p print QV for each sequence\n");
fprintf(stderr, " -t INT number of threads [%d]\n", opt.n_threads);
fprintf(stderr, " -K NUM batch size [1g]\n");
return 1;
}
ch = yak_ch_restore(argv[o.ind]);
assert(ch);
kmer = ch->k;
yak_ch_hist(ch, hist, opt.n_threads);
printf("CC\tCT kmer_occurrence short_read_kmer_count raw_input_kmer_count adjusted_input_kmer_count\n");
printf("CC\tFR fpr_lower_bound fpr_upper_bound\n");
printf("CC\tER total_input_kmers adjusted_error_kmers\n");
printf("CC\tCV coverage\n");
printf("CC\tQV raw_quality_value adjusted_quality_value\n");
printf("CC\n");
yak_qv(&opt, argv[o.ind+1], ch, cnt);
yak_qv_solve(hist, cnt, kmer, opt.fpr, &qs);
for (i = (1<<YAK_COUNTER_BITS) - 1; i >= 0; --i)
printf("CT\t%d\t%ld\t%ld\t%.3f\n", i, (long)hist[i], (long)cnt[i], qs.adj_cnt[i]);
printf("FR\t%.3g\t%.3g\n", qs.fpr_lower, qs.fpr_upper);
printf("ER\t%ld\t%.3f\n", (long)qs.tot, qs.err);
printf("CV\t%.3f\n", qs.cov);
printf("QV\t%.3f\t%.3f\n", qs.qv_raw, qs.qv);
yak_ch_destroy(ch);
return 0;
}
int main(int argc, char *argv[])
{
extern int main_triobin(int argc, char *argv[]);
extern int main_trioeval(int argc, char *argv[]);
extern int main_inspect(int argc, char *argv[]);
extern int main_chkerr(int argc, char *argv[]);
int ret = 0, i;
yak_reset_realtime();
if (argc == 1) {
fprintf(stderr, "Usage: yak <command> <argument>\n");
fprintf(stderr, "Command:\n");
fprintf(stderr, " count count k-mers\n");
fprintf(stderr, " qv evaluate quality values\n");
fprintf(stderr, " triobin trio binning\n");
fprintf(stderr, " trioeval evaluate phasing accuracy with trio\n");
fprintf(stderr, " inspect k-mer hash tables\n");
fprintf(stderr, " chkerr check errors\n");
fprintf(stderr, " version print version number\n");
return 1;
}
if (strcmp(argv[1], "count") == 0) ret = main_count(argc-1, argv+1);
else if (strcmp(argv[1], "qv") == 0) ret = main_qv(argc-1, argv+1);
else if (strcmp(argv[1], "triobin") == 0) ret = main_triobin(argc-1, argv+1);
else if (strcmp(argv[1], "trioeval") == 0) ret = main_trioeval(argc-1, argv+1);
else if (strcmp(argv[1], "inspect") == 0) ret = main_inspect(argc-1, argv+1);
else if (strcmp(argv[1], "chkerr") == 0) ret = main_chkerr(argc-1, argv+1);
else if (strcmp(argv[1], "version") == 0) {
puts(YAKS_VERSION);
return 0;
} else {
fprintf(stderr, "[E::%s] unknown command\n", __func__);
return 1;
}
if (ret == 0) {
fprintf(stderr, "[M::%s] Version: %s\n", __func__, YAKS_VERSION);
fprintf(stderr, "[M::%s] CMD:", __func__);
for (i = 0; i < argc; ++i)
fprintf(stderr, " %s", argv[i]);
fprintf(stderr, "\n[M::%s] Real time: %.3f sec; CPU: %.3f sec; Peak RSS: %.3f GB\n", __func__, yak_realtime(), yak_cputime(), yak_peakrss() / 1024.0 / 1024.0 / 1024.0);
}
return ret;
}