Merge commit 'upstream/0.1.16'

[samtools.git] / bcftools / main.c

diff --git a/bcftools/main.c b/bcftools/main.c
index 75125f872d0117d287186a72251b0e2eaeb5853f..7293374a19de5abdc31a04366cb75e982fa8eacf 100644 (file)
--- a/bcftools/main.c
+++ b/bcftools/main.c
@@ -1,11 +1,14 @@
 #include <string.h>
 #include <stdlib.h>
 #include <sys/stat.h>
+#include <unistd.h>
 #include "bcf.h"
 
+#include "kseq.h"
+KSTREAM_INIT(gzFile, gzread, 0x10000)
+
 int bcfview(int argc, char *argv[]);
 int bcf_main_index(int argc, char *argv[]);
-int bcf_main_pwld(int argc, char *argv[]);
 
 #define BUF_SIZE 0x10000
 
@@ -43,6 +46,122 @@ int bcf_cat(int n, char * const *fn)
        return 0;
 }
 
+extern double bcf_pair_freq(const bcf1_t *b0, const bcf1_t *b1, double f[4]);
+
+int bcf_main_ldpair(int argc, char *argv[])
+{
+       bcf_t *fp;
+       bcf_hdr_t *h;
+       bcf1_t *b0, *b1;
+       bcf_idx_t *idx;
+       kstring_t str;
+       void *str2id;
+       gzFile fplist;
+       kstream_t *ks;
+       int dret, lineno = 0;
+       if (argc < 3) {
+               fprintf(stderr, "Usage: bcftools ldpair <in.bcf> <in.list>\n");
+               return 1;
+       }
+       fplist = gzopen(argv[2], "rb");
+       ks = ks_init(fplist);
+       memset(&str, 0, sizeof(kstring_t));
+       fp = bcf_open(argv[1], "rb");
+       h = bcf_hdr_read(fp);
+       str2id = bcf_build_refhash(h);
+       idx = bcf_idx_load(argv[1]);
+       if (idx == 0) {
+               fprintf(stderr, "[%s] No bcf index is found. Abort!\n", __func__);
+               return 1;
+       }
+       b0 = calloc(1, sizeof(bcf1_t));
+       b1 = calloc(1, sizeof(bcf1_t));
+       while (ks_getuntil(ks, '\n', &str, &dret) >= 0) {
+               char *p, *q;
+               int k;
+               int tid0 = -1, tid1 = -1, pos0 = -1, pos1 = -1;
+               ++lineno;
+               for (p = q = str.s, k = 0; *p; ++p) {
+                       if (*p == ' ' || *p == '\t') {
+                               *p = '\0';
+                               if (k == 0) tid0 = bcf_str2id(str2id, q);
+                               else if (k == 1) pos0 = atoi(q) - 1;
+                               else if (k == 2) tid1 = strcmp(q, "=")? bcf_str2id(str2id, q) : tid0;
+                               else if (k == 3) pos1 = atoi(q) - 1;
+                               q = p + 1;
+                               ++k;
+                       }
+               }
+               if (k == 3) pos1 = atoi(q) - 1;
+               if (tid0 >= 0 && tid1 >= 0 && pos0 >= 0 && pos1 >= 0) {
+                       uint64_t off;
+                       double r, f[4];
+                       off = bcf_idx_query(idx, tid0, pos0);
+                       bgzf_seek(fp->fp, off, SEEK_SET);
+                       while (bcf_read(fp, h, b0) >= 0 && b0->pos != pos0);
+                       off = bcf_idx_query(idx, tid1, pos1);
+                       bgzf_seek(fp->fp, off, SEEK_SET);
+                       while (bcf_read(fp, h, b1) >= 0 && b1->pos != pos1);
+                       r = bcf_pair_freq(b0, b1, f);
+                       r *= r;
+                       printf("%s\t%d\t%s\t%d\t%.4g\t%.4g\t%.4g\t%.4g\t%.4g\n", h->ns[tid0], pos0+1, h->ns[tid1], pos1+1,
+                               r, f[0], f[1], f[2], f[3]);
+               } //else fprintf(stderr, "[%s] Parse error at line %d.\n", __func__, lineno);
+       }
+       bcf_destroy(b0); bcf_destroy(b1);
+       bcf_idx_destroy(idx);
+       bcf_str2id_destroy(str2id);
+       bcf_hdr_destroy(h);
+       bcf_close(fp);
+       free(str.s);
+       ks_destroy(ks);
+       gzclose(fplist);
+       return 0;
+}
+
+int bcf_main_ld(int argc, char *argv[])
+{
+       bcf_t *fp;
+       bcf_hdr_t *h;
+       bcf1_t **b, *b0;
+       int i, j, m, n;
+       double f[4];
+       if (argc == 1) {
+               fprintf(stderr, "Usage: bcftools ld <in.bcf>\n");
+               return 1;
+       }
+       fp = bcf_open(argv[1], "rb");
+       h = bcf_hdr_read(fp);
+       // read the entire BCF
+       m = n = 0; b = 0;
+       b0 = calloc(1, sizeof(bcf1_t));
+       while (bcf_read(fp, h, b0) >= 0) {
+               if (m == n) {
+                       m = m? m<<1 : 16;
+                       b = realloc(b, sizeof(void*) * m);
+               }
+               b[n] = calloc(1, sizeof(bcf1_t));
+               bcf_cpy(b[n++], b0);
+       }
+       bcf_destroy(b0);
+       // compute pair-wise r^2
+       printf("%d\n", n); // the number of loci
+       for (i = 0; i < n; ++i) {
+               printf("%s:%d", h->ns[b[i]->tid], b[i]->pos + 1);
+               for (j = 0; j < i; ++j) {
+                       double r = bcf_pair_freq(b[i], b[j], f);
+                       printf("\t%.3f", r*r);
+               }
+               printf("\t1.000\n");
+       }
+       // free
+       for (i = 0; i < n; ++i) bcf_destroy(b[i]);
+       free(b);
+       bcf_hdr_destroy(h);
+       bcf_close(fp);
+       return 0;
+}
+
 int main(int argc, char *argv[])
 {
        if (argc == 1) {
@@ -52,12 +171,14 @@ int main(int argc, char *argv[])
                fprintf(stderr, "         index     index BCF\n");
                fprintf(stderr, "         cat       concatenate BCFs\n");
                fprintf(stderr, "         ld        compute all-pair r^2\n");
+               fprintf(stderr, "         ldpair    compute r^2 between requested pairs\n");
                fprintf(stderr, "\n");
                return 1;
        }
        if (strcmp(argv[1], "view") == 0) return bcfview(argc-1, argv+1);
        else if (strcmp(argv[1], "index") == 0) return bcf_main_index(argc-1, argv+1);
-       else if (strcmp(argv[1], "ld") == 0) return bcf_main_pwld(argc-1, argv+1);
+       else if (strcmp(argv[1], "ld") == 0) return bcf_main_ld(argc-1, argv+1);
+       else if (strcmp(argv[1], "ldpair") == 0) return bcf_main_ldpair(argc-1, argv+1);
        else if (strcmp(argv[1], "cat") == 0) return bcf_cat(argc-2, argv+2); // cat is different ...
        else {
                fprintf(stderr, "[main] Unrecognized command.\n");