* bugfix in index: large memory when a read pos is 1

[samtools.git] / bam2bcf.h

diff --git a/bam2bcf.h b/bam2bcf.h
index e0673e5e868b3ab4babcd0726f76ff301c42e9be..4af080c4753b2070192bec5e04e16174ca5bb5f8 100644 (file)
--- 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];
@@ -21,16 +23,18 @@ 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];
+    int mvd[3]; // mean variant distance, number of variant reads, average read length
 } bcf_callret1_t;
 
 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;
+    float vdb; // variant distance bias
 } bcf_call_t;
 
 #ifdef __cplusplus