Compress binary packages with xz.

[samtools.git] / bcftools / bcf.h

diff --git a/bcftools/bcf.h b/bcftools/bcf.h
index f545a916879ee9f527c3e12b622926dfaf96971b..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>
 
@@ -146,6 +148,14 @@ 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);
+       // 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);