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Indel discount feature #115

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Indel discount feature #115

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417f1ab
adds example omicron reads
bwlang Jan 7, 2022
7c7704f
comment typo
bwlang Jan 7, 2022
771e68d
POC indel depth, need to add a real option to enable this instead of …
bwlang Jan 7, 2022
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1 change: 1 addition & 0 deletions data/db/test_ref.fa.fai
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@@ -0,0 +1 @@
test 401 6 401 402
Binary file added data/omicron_s_3ins_9del.bam
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Binary file added data/omicron_s_3ins_9del.bam.bai
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2 changes: 1 addition & 1 deletion src/allele_functions.cpp
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Expand Up @@ -87,7 +87,7 @@ std::vector<allele> 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];
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2 changes: 1 addition & 1 deletion src/call_consensus_pileup.cpp
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Expand Up @@ -104,7 +104,7 @@ ret_t get_consensus_allele(std::vector<allele> 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;
}
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