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Imported Upstream version 0.1.13
[samtools.git]
/
bcftools
/
bcf.h
diff --git
a/bcftools/bcf.h
b/bcftools/bcf.h
index f87ac1e6fa3021964753f051a944fdc95a59549d..f545a916879ee9f527c3e12b622926dfaf96971b 100644
(file)
--- a/
bcftools/bcf.h
+++ b/
bcftools/bcf.h
@@
-129,6
+129,8
@@
extern "C" {
int vcf_close(bcf_t *bp);
// read the VCF/BCF header
bcf_hdr_t *vcf_hdr_read(bcf_t *bp);
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
// 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
@@
-142,10
+144,13
@@
extern "C" {
int bcf_gl2pl(bcf1_t *b);
// if the site is an indel
int bcf_is_indel(const bcf1_t *b);
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);
void bcf_str2id_destroy(void *_hash);
// 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();
int bcf_str2id_add(void *_hash, const char *str);
int bcf_str2id(void *_hash, const char *str);
void *bcf_str2id_init();