Merge pull request #17 from Illumina/omni5-issue

Omni5 issue
Illumina · Feb 17, 2020 · af0ba22 · af0ba22
2 parents 881bbac + 8a83221
commit af0ba22
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Showing 2 changed files with 6 additions and 3 deletions.
diff --git a/examples/gtc_final_report.py b/examples/gtc_final_report.py
@@ -39,15 +39,16 @@
     output_handle.write(delim.join(["Total Samples", str(len(samples))]) + "\n")
 
     output_handle.write("[Data]\n")
-    output_handle.write(delim.join(["SNP Name", "Sample ID", "Chr", "MapInfo", "Alleles - AB", "Alleles - Plus", "Alleles - Forward"]) + "\n")
+    output_handle.write(delim.join(["SNP Name", "Sample ID", "Chr", "MapInfo", "Alleles - AB", "Alleles - Plus", "Alleles - Forward", "X",	"Y"]) + "\n")
     for gtc_file in samples:
         sys.stderr.write("Processing " + gtc_file + "\n")
         gtc_file = os.path.join(args.gtc_directory, gtc_file)
         gtc = GenotypeCalls(gtc_file)
         genotypes = gtc.get_genotypes()
         plus_strand_genotypes = gtc.get_base_calls_plus_strand(manifest.snps, manifest.ref_strands)
         forward_strand_genotypes = gtc.get_base_calls_forward_strand(manifest.snps, manifest.source_strands)
+        normalized_intensities = gtc.get_normalized_intensities(manifest.normalization_lookups)
 
         assert len(genotypes) == len(manifest.names)
-        for (name, chrom, map_info, genotype, ref_strand_genotype, source_strand_genotype) in zip(manifest.names, manifest.chroms, manifest.map_infos, genotypes, plus_strand_genotypes, forward_strand_genotypes):
-            output_handle.write(delim.join([name, os.path.basename(gtc_file)[:-4], chrom, str(map_info), code2genotype[genotype], ref_strand_genotype, source_strand_genotype]) + "\n")
+        for (name, chrom, map_info, genotype, ref_strand_genotype, source_strand_genotype, (x_norm, y_norm)) in zip(manifest.names, manifest.chroms, manifest.map_infos, genotypes, plus_strand_genotypes, forward_strand_genotypes, normalized_intensities):
+            output_handle.write(delim.join([name, os.path.basename(gtc_file)[:-4], chrom, str(map_info), code2genotype[genotype], ref_strand_genotype, source_strand_genotype, str(x_norm), str(y_norm)]) + "\n")
diff --git a/module/BeadPoolManifest.py b/module/BeadPoolManifest.py
@@ -118,6 +118,8 @@ def __parse_file(self, manifest_file):
             for locus_idx in xrange(self.num_loci):
                 self.normalization_ids[locus_idx] += 100 * \
                     self.assay_types[locus_idx]
+                # To mimic the byte-wrapping behavior from GenomeStudio, AutoCall, IAAP take the mod of 256
+                self.normalization_ids[locus_idx] %= 256
                 all_norm_ids.add(self.normalization_ids[locus_idx])
             sorted_norm_ids = sorted(all_norm_ids)
             lookup_dictionary = {}