Alternative model for multiallelic and rare-variant calling. Proof-of-principle imple...

[samtools.git] / bcftools / bcf.h

diff --git a/bcftools/bcf.h b/bcftools/bcf.h
index 822ae5cf80fd7f9dc375259524935c933f088323..4fe3ed7fb33a3499b3f38d8dd26724f783f5653d 100644 (file)
--- a/bcftools/bcf.h
+++ b/bcftools/bcf.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 {
@@ -142,6 +143,8 @@ 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