Merge pull request #379 from mgcam/better_contam_comparison

reduce uncertainty in ranking close results
wtsi-npg · Nov 29, 2016 · ae94c0f · ae94c0f
2 parents 6e006b4 + 45596a3
commit ae94c0f
Show file tree

Hide file tree

Showing 3 changed files with 7 additions and 5 deletions.
diff --git a/Changes b/Changes
@@ -5,6 +5,8 @@ LIST OF CHANGES FOR NPG-QC PACKAGE
  - back to testing with mysql 5.7.13 in travis
  - drop node 0.12 from node travis matrix
  - add perl 5.22-shrplib to travis matrix
+ - to reduce uncertainty in ranking close results, increase precision
+   used for ranking contamination results
 
 release 62.5
  - a very concise replacement for NPG_QC pages

diff --git a/lib/npg_qc/autoqc/role/contamination.pm b/lib/npg_qc/autoqc/role/contamination.pm
@@ -26,7 +26,7 @@ sub normalised_contamination {
         my $value =  ( $raw_count / $fastq_size )
                              * $genome_correction{$organism}
                              * $PERCENT;
-        $normalized_value{$organism} = sprintf '%.1f', $value;
+        $normalized_value{$organism} = sprintf '%.2f', $value;
     }
 
     return \%normalized_value;

diff --git a/t/60-autoqc-results-contamination.t b/t/60-autoqc-results-contamination.t
@@ -37,10 +37,10 @@ ok(!$r->normalised_contamination(), 'normalized measure not defined if read_coun
 $r->read_count(100_000);
 
 is_deeply( $r->normalised_contamination(),
-           { Homo_sapiens          => '62.0',
-             Danio_rerio           =>  '0.0',
-             Mus_musculus          =>  '1.3',
-             Clostridium_difficile =>  '0.3', },
+           { Homo_sapiens          => '62.00',
+             Danio_rerio           =>  '0.00',
+             Mus_musculus          =>  '1.34',
+             Clostridium_difficile =>  '0.30', },
            'Calculate normalized measures' );
 
 my $comment1 = 'ABC';