Imported Upstream version 0.1.18

[samtools.git] / bcftools / bcf.h

diff --git a/bcftools/bcf.h b/bcftools/bcf.h
index f87ac1e6fa3021964753f051a944fdc95a59549d..822ae5cf80fd7f9dc375259524935c933f088323 100644 (file)
--- a/bcftools/bcf.h
+++ b/bcftools/bcf.h
@@ -28,6 +28,8 @@
 #ifndef BCF_H
 #define BCF_H
 
+#define BCF_VERSION "0.1.17-dev (r973:277)"
+
 #include <stdint.h>
 #include <zlib.h>
 
@@ -129,6 +131,8 @@ 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
@@ -142,10 +146,21 @@ 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);
+       // 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);
+       // convert PL to GLF-like 10-likelihood GL
+       int bcf_gl10(const bcf1_t *b, uint8_t *gl);
+       // convert up to 4 INDEL alleles to GLF-like 10-likelihood GL
+       int bcf_gl10_indel(const bcf1_t *b, uint8_t *gl);
 
        // 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();