Merge pull request #95 from J35P312/master

3.3.1
SciLifeLab · Sep 7, 2022 · 6072296 · 6072296
2 parents 3c40013 + 3dada4d
commit 6072296
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diff --git a/README.md b/README.md
@@ -111,7 +111,6 @@ optional parameters:
 
     -o - the prefix of the output files
     -z - compute the coverage within bins of a specified size across the entire genome, default bin size is 500
-    -u - do not print per bin quality values
     -w - generate a wig file instead of bed
  --ref - reference sequence (fasta), required for reading cram file.
 

diff --git a/tiddit/tiddit_variant.pyx b/tiddit/tiddit_variant.pyx
@@ -238,7 +238,7 @@ def define_variant(str chrA, str bam_file_name,dict sv_clusters,args,dict librar
 
 				sample_data[sample]={}
 				sample_data[sample]={"covA":coverageA,"QA":frac_low_qA,"discA":n_discsA,"splitA":n_splitsA,"refRA":crossing_r_A,"refFA":crossing_f_A}
-				sample_data[sample].update({"covB":coverageB,"QB":frac_low_qA,"discB":n_discsB,"splitB":n_splitsB,"refRB":crossing_r_B,"refFB":crossing_f_B})
+				sample_data[sample].update({"covB":coverageB,"QB":frac_low_qB,"discB":n_discsB,"splitB":n_splitsB,"refRB":crossing_r_B,"refFB":crossing_f_B})
 
 				if chrA != chrB:
 					sample_data[sample]["covM"]=0