X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bcftools%2Fbcf.h;h=dff439df5d7f2d74a09e8d4b3b327a57f58ccc62;hb=80658e4d152b53bd55927c432ceece7702ab49d7;hp=84f0c2d941eb24db6a8c3b0cbc015e2402d80a1e;hpb=f0b7a686f0f6581bc524353d7e783abbe9a94316;p=samtools.git

diff --git a/bcftools/bcf.h b/bcftools/bcf.h
index 84f0c2d..dff439d 100644
--- a/bcftools/bcf.h
+++ b/bcftools/bcf.h
@@ -28,6 +28,8 @@
 #ifndef BCF_H
 #define BCF_H
 
+#define BCF_VERSION "0.1.16-dev (r963:240)"
+
 #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
@@ -144,10 +148,15 @@ extern "C" {
 	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();