X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bcftools%2Fbcf.h;h=8c52451f7a40d939a322a2737f922ac44fa9e871;hb=da45f88bac09817fcd87916d3e104f0e4bc53874;hp=f545a916879ee9f527c3e12b622926dfaf96971b;hpb=06021e30abb66d5631a0cd5daadb8f45878e90a3;p=samtools.git

diff --git a/bcftools/bcf.h b/bcftools/bcf.h
index f545a91..8c52451 100644
--- 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>
 
@@ -71,6 +73,7 @@ typedef struct {
 	bcf_ginfo_t *gi; // array of geno fields
 	int n_alleles, n_smpl; // number of alleles and samples
 	// derived info: ref, alt, flt, info, fmt (<-str), n_gi (<-fmt), n_alleles (<-alt), n_smpl (<-bcf_hdr_t::n_smpl)
+    uint8_t *ploidy;    // ploidy of all samples; if NULL, ploidy of 2 is assumed.
 } bcf1_t;
 
 typedef struct {
@@ -120,6 +123,10 @@ extern "C" {
 	char *bcf_fmt(const bcf_hdr_t *h, bcf1_t *b);
 	// append more info
 	int bcf_append_info(bcf1_t *b, const char *info, int l);
+    // remove tag
+    int remove_tag(char *string, const char *tag, char delim);
+    // remove info tag, string is the kstring holder of bcf1_t.str
+    void rm_info(kstring_t *string, const char *key);
 	// copy
 	int bcf_cpy(bcf1_t *r, const bcf1_t *b);
 
@@ -140,12 +147,22 @@ extern "C" {
 
 	// keep the first n alleles and discard the rest
 	int bcf_shrink_alt(bcf1_t *b, int n);
+    // keep the masked alleles and discard the rest
+	void bcf_fit_alt(bcf1_t *b, int mask);
 	// 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);