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[samtools.git] / bam2bcf.h

diff --git a/bam2bcf.h b/bam2bcf.h
index 26b022c08e89e3597bd6e400690d42bd7ecabe38..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];
@@ -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