Complain when BAM cannot be open. Severe bug fixed in -m haploid calling.

[samtools.git] / bam2bcf.h

diff --git a/bam2bcf.h b/bam2bcf.h
index a4d8ca5128319800c91303a022a4e53ac6aea599..8ac6b79abfb60abaeefc29451923ec197c2f6c7a 100644 (file)
--- 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;