Add VCF detectedChip meta-information

src/snps/io/writer.py

@@ -177,6 +177,16 @@ def _write_vcf(self):
         if self._snps.determine_sex():
             comment.append(f"##detectedSex={self._snps.determine_sex()}")
 
+        if self._vcf_qc_only or self._vcf_qc_filter:
+            chip_version = ""
+            if self._snps.chip_version:
+                chip_version = f" {self._snps.chip_version}"
+
+            if self._snps.chip:
+                comment.append(
+                    f'##detectedChip="{self._snps.chip}{chip_version} per Lu et al.: https://doi.org/10.1016/j.csbj.2021.06.040"'
+                )
+
         df = self._snps.snps
 
         p = self._snps._parallelizer

src/snps/snps.py

@@ -83,6 +83,7 @@ def __init__(
         self._cluster = ""
         self._chip = ""
         self._chip_version = ""
+        self._cluster_overlap_computed = False
 
         if file:
             d = self._read_raw_data(file, only_detect_source, rsids)
@@ -2021,6 +2022,8 @@ def compute_cluster_overlap(self, cluster_overlap_threshold=0.95):
                     "Detected SNPs data source not found in cluster's company composition"
                 )
 
+        self._cluster_overlap_computed = True
+
         return df
 
     def identify_low_quality_snps(self):