mpileup indel hotfix: fix in detecting long stretches of N's. The version string...

[samtools.git] / bam2bcf_indel.c

diff --git a/bam2bcf_indel.c b/bam2bcf_indel.c
index 30b3f46f8431a184fc50524e8f339b70363f6af5..9933586ae0c21b9a1cb5f45fef3b56e6819343ed 100644 (file)
--- a/bam2bcf_indel.c
+++ b/bam2bcf_indel.c
@@ -175,7 +175,7 @@ int bcf_call_gap_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_calla
         // To prevent long stretches of N's to be mistaken for indels (sometimes thousands of bases),
         //  check the number of N's in the sequence and skip places where half or more reference bases are Ns.
         int nN=0; for (i=pos; i-pos<max_rd_len && ref[i]; i++) if ( ref[i]=='N' ) nN++;
-        if ( nN*2>i ) { free(aux); return -1; }
+        if ( nN*2>(i-pos) ) { free(aux); return -1; }
 
                ks_introsort(uint32_t, m, aux);
                // squeeze out identical types