X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bam2bcf.h;h=8ac6b79abfb60abaeefc29451923ec197c2f6c7a;hb=607d7a0ab79152be4153fa09861cfa889488f2c7;hp=a4d8ca5128319800c91303a022a4e53ac6aea599;hpb=543a9fc2055575dcc17a7bb9c83ecca17a32cec6;p=samtools.git

diff --git a/bam2bcf.h b/bam2bcf.h
index a4d8ca5..8ac6b79 100644
--- a/bam2bcf.h
+++ b/bam2bcf.h
@@ -14,8 +14,9 @@
 typedef struct __bcf_callaux_t {
 	int capQ, min_baseQ;
 	int openQ, extQ, tandemQ; // for indels
-	int min_support; // for collecting indel candidates
-	double min_frac; // for collecting indel candidates
+	int min_support, max_support; // for collecting indel candidates
+	double min_frac, max_frac; // for collecting indel candidates
+    int per_sample_flt; // indel filtering strategy
 	// for internal uses
 	int max_bases;
 	int indel_types[4];
@@ -35,6 +36,7 @@ typedef struct {
 
 typedef struct {
 	int a[5]; // alleles: ref, alt, alt2, alt3
+    float qsum[4];
 	int n, n_alleles, shift, ori_ref, unseen;
 	int n_supp; // number of supporting non-reference reads
 	int anno[16], depth, ori_depth;