X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bam2bcf.h;h=958567241936a4c54feae501c725ad77a6e3f1be;hb=d382711a770f67a72b9af3bfd98a88fbced34f64;hp=e0673e5e868b3ab4babcd0726f76ff301c42e9be;hpb=165f1d8cb88f04a48b7da3f4e5e5fd2a4f074972;p=samtools.git

diff --git a/bam2bcf.h b/bam2bcf.h
index e0673e5..9585672 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];
@@ -21,7 +23,7 @@ typedef struct __bcf_callaux_t {
 } bcf_callaux_t;
 
 typedef struct {
-	int depth, qsum[4];
+	int depth, ori_depth, qsum[4];
 	int anno[16];
 	float p[25];
 } bcf_callret1_t;
@@ -29,7 +31,7 @@ typedef struct {
 typedef struct {
 	int a[5]; // alleles: ref, alt, alt2, alt3
 	int n, n_alleles, shift, ori_ref, unseen;
-	int anno[16], depth;
+	int anno[16], depth, ori_depth;
 	uint8_t *PL;
 } bcf_call_t;