Uploaded samtools_0.1.16-1_amd64.changes.

[samtools.git] / bcftools / bcf.h

diff --git a/bcftools/bcf.h b/bcftools/bcf.h
index 36578956bbae06d4c216c121a2ddb3a94cad94d8..ba6dbe9b42ae033c6b3c179a730a48312cf927dd 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;
@@ -117,6 +129,8 @@ extern "C" {
        int vcf_close(bcf_t *bp);
        // read the VCF/BCF header
        bcf_hdr_t *vcf_hdr_read(bcf_t *bp);
+       // read the sequence dictionary from a separate file; required for VCF->BCF conversion
+       int vcf_dictread(bcf_t *bp, bcf_hdr_t *h, const char *fn);
        // read a VCF/BCF record; return -1 on end-of-file and <-1 for errors
        int vcf_read(bcf_t *bp, bcf_hdr_t *h, bcf1_t *b);
        // write the VCF header
@@ -128,10 +142,19 @@ extern "C" {
        int bcf_shrink_alt(bcf1_t *b, int n);
        // convert GL to PL
        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);
+       // move GT to the first FORMAT field
+       int bcf_fix_gt(bcf1_t *b);
+       // update PL generated by old samtools
+       int bcf_fix_pl(bcf1_t *b);
 
        // string hash table
        void *bcf_build_refhash(bcf_hdr_t *h);
        void bcf_str2id_destroy(void *_hash);
+       void bcf_str2id_thorough_destroy(void *_hash);
        int bcf_str2id_add(void *_hash, const char *str);
        int bcf_str2id(void *_hash, const char *str);
        void *bcf_str2id_init();