diff --git a/data/db/test_ref.fa.fai b/data/db/test_ref.fa.fai new file mode 100644 index 00000000..607beda7 --- /dev/null +++ b/data/db/test_ref.fa.fai @@ -0,0 +1 @@ +test 401 6 401 402 diff --git a/data/omicron_s_3ins_9del.bam b/data/omicron_s_3ins_9del.bam new file mode 100644 index 00000000..be23874a Binary files /dev/null and b/data/omicron_s_3ins_9del.bam differ diff --git a/data/omicron_s_3ins_9del.bam.bai b/data/omicron_s_3ins_9del.bam.bai new file mode 100644 index 00000000..7d37030b Binary files /dev/null and b/data/omicron_s_3ins_9del.bam.bai differ diff --git a/src/allele_functions.cpp b/src/allele_functions.cpp index 32eca874..09517b79 100644 --- a/src/allele_functions.cpp +++ b/src/allele_functions.cpp @@ -87,7 +87,7 @@ std::vector update_allele_depth(char ref,std::string bases, std::string i += n + j; if(indel[0]>=97 && indel[0] <= 122) forward=false; - q = min_qual; // For insertions and deletion ust use minimum quality. + q = min_qual; // For insertions and deletion use minimum quality. break; default: int asc_val = bases[i]; diff --git a/src/call_consensus_pileup.cpp b/src/call_consensus_pileup.cpp index 997f2d6c..58e6e87a 100644 --- a/src/call_consensus_pileup.cpp +++ b/src/call_consensus_pileup.cpp @@ -104,7 +104,7 @@ ret_t get_consensus_allele(std::vector ad, uint8_t min_qual, double thre it++; ambg_n = 1; if(i > 0){ - cur_threshold = threshold * (double) total_indel_depth; + cur_threshold = threshold * 0.3333 * (double) total_indel_depth; } else { cur_threshold = threshold * (double)total_max_depth; }