Updated samtools to 0.1.19

[rsem.git] / sam / bcftools / bcf.h

diff --git a/sam/bcftools/bcf.h b/sam/bcftools/bcf.h
index 822ae5cf80fd7f9dc375259524935c933f088323..f722525bc938cab8f36adfcefe9b527d357e735d 100644 (file)
--- a/sam/bcftools/bcf.h
+++ b/sam/bcftools/bcf.h
@@ -28,7 +28,7 @@
 #ifndef BCF_H
 #define BCF_H
 
-#define BCF_VERSION "0.1.17-dev (r973:277)"
+#define BCF_VERSION "0.1.19-44428cd"
 
 #include <stdint.h>
 #include <zlib.h>
@@ -73,6 +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 {
@@ -122,6 +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);
 
@@ -142,6 +147,8 @@ 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