X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=samtools.git;a=blobdiff_plain;f=bcftools%2Fbcf.h;h=822ae5cf80fd7f9dc375259524935c933f088323;hp=36578956bbae06d4c216c121a2ddb3a94cad94d8;hb=0f906dafb2ad22371a753557562ef95c3034480d;hpb=8d2494d1fb7cd0fa7c63be5ffba8dd1a11457522

diff --git a/bcftools/bcf.h b/bcftools/bcf.h
index 3657895..822ae5c 100644
--- a/bcftools/bcf.h
+++ b/bcftools/bcf.h
@@ -28,9 +28,23 @@
 #ifndef BCF_H
 #define BCF_H
 
+#define BCF_VERSION "0.1.17-dev (r973:277)"
+
 #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 +88,7 @@ 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 +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
@@ -128,10 +144,23 @@ 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);
+	// 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();