Typos

README.md

@@ -95,7 +95,7 @@ The output JSON file contains input information, genotypes at all SNP positions,
         "summary": {
             "snps": {
                 "total": 1041,
-                "snps-genotyped": 1016
+                "genotyped": 1016
             },
             "heterozygotes-fraction": 0.4744,
             "mean-maf-homozygote-sites": 0.0022,
@@ -145,7 +145,7 @@ Output is similar to that in germline mode. Only sites which are genotyping in b
         "summary": {
             "snps": {
                 "total": 1041,
-                "snps-genotyped": 1000
+                "genotyped": 1000
             },
             "tumor": {
                 "heterozygotes-fraction": 0.474,

src/snpahoy/client.py

@@ -98,7 +98,7 @@ def somatic(ctx, bed_file, tumor_bam_file, germline_bam_file, output_json_file):
     germline_snps_at_homozygote_positions = [pair['germline'] for pair in genotyped_snp_pairs if pair['germline'].is_homozygote()]
     tumor_snps_at_homozygote_positions = [pair['tumor'] for pair in genotyped_snp_pairs if pair['germline'].is_homozygote()]
 
-    results['output']['summary'] = {'snps': {'total': len(snp_coordinates), 'snps-genotyped': len(genotyped_snp_pairs)}}
+    results['output']['summary'] = {'snps': {'total': len(snp_coordinates), 'genotyped': len(genotyped_snp_pairs)}}
 
     if genotyped_snp_pairs:
         results['output']['summary']['tumor'] = {
@@ -141,7 +141,7 @@ def germline(ctx, bed_file, bam_file, output_json_file):
     genotyped_snps = [snp for snp in snps if snp.genotype]
 
     results['output']['details'] = get_details(snps=snps)
-    results['output']['summary'] = {'snps': {'total': len(snps), 'snps-genotyped': len(genotyped_snps)}}
+    results['output']['summary'] = {'snps': {'total': len(snps), 'genotyped': len(genotyped_snps)}}
 
     number_of_heterozygotes = count_heterozygotes(snps=genotyped_snps)
     homozygote_snps = [snp for snp in snps if snp.is_homozygote()]