X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=samtools.git;a=blobdiff_plain;f=bam2bcf.h;h=4af080c4753b2070192bec5e04e16174ca5bb5f8;hp=26b022c08e89e3597bd6e400690d42bd7ecabe38;hb=HEAD;hpb=016b50ab60e879a0b8f81cb76ce11ea360a03d4a

diff --git a/bam2bcf.h b/bam2bcf.h
index 26b022c..4af080c 100644
--- a/bam2bcf.h
+++ b/bam2bcf.h
@@ -9,7 +9,9 @@
 
 typedef struct __bcf_callaux_t {
 	int capQ, min_baseQ;
-	int openQ, extQ, tandemQ;
+	int openQ, extQ, tandemQ; // for indels
+	int min_support; // for collecting indel candidates
+	double min_frac; // for collecting indel candidates
 	// for internal uses
 	int max_bases;
 	int indel_types[4];
@@ -24,6 +26,7 @@ typedef struct {
 	int depth, ori_depth, qsum[4];
 	int anno[16];
 	float p[25];
+    int mvd[3]; // mean variant distance, number of variant reads, average read length
 } bcf_callret1_t;
 
 typedef struct {
@@ -31,6 +34,7 @@ typedef struct {
 	int n, n_alleles, shift, ori_ref, unseen;
 	int anno[16], depth, ori_depth;
 	uint8_t *PL;
+    float vdb; // variant distance bias
 } bcf_call_t;
 
 #ifdef __cplusplus