System libraries go *after* user libraries in link commands, because

[samtools.git] / bcftools / bcf.h

diff --git a/bcftools/bcf.h b/bcftools/bcf.h
index 89feeb89ac3bd2e278329866996d02e7709414aa..84f0c2d941eb24db6a8c3b0cbc015e2402d80a1e 100644 (file)
--- a/bcftools/bcf.h
+++ b/bcftools/bcf.h
@@ -30,7 +30,19 @@
 
 #include <stdint.h>
 #include <zlib.h>
+
+#ifndef BCF_LITE
 #include "bgzf.h"
+typedef BGZF *bcfFile;
+#else
+typedef gzFile bcfFile;
+#define bgzf_open(fn, mode) gzopen(fn, mode)
+#define bgzf_fdopen(fd, mode) gzdopen(fd, mode)
+#define bgzf_close(fp) gzclose(fp)
+#define bgzf_read(fp, buf, len) gzread(fp, buf, len)
+#define bgzf_write(fp, buf, len)
+#define bgzf_flush(fp)
+#endif
 
 /*
   A member in the structs below is said to "primary" if its content
@@ -74,7 +86,7 @@ typedef struct {
 typedef struct {
        int is_vcf; // if the file in operation is a VCF
        void *v; // auxillary data structure for VCF
-       BGZF *fp; // file handler for BCF
+       bcfFile fp; // file handler for BCF
 } bcf_t;
 
 struct __bcf_idx_t;
@@ -130,6 +142,8 @@ extern "C" {
        int bcf_gl2pl(bcf1_t *b);
        // if the site is an indel
        int bcf_is_indel(const bcf1_t *b);
+       bcf_hdr_t *bcf_hdr_subsam(const bcf_hdr_t *h0, int n, char *const* samples, int *list);
+       int bcf_subsam(int n_smpl, int *list, bcf1_t *b);
 
        // string hash table
        void *bcf_build_refhash(bcf_hdr_t *h);