fix the bug for matching donor VCF to cell VCF

single-cell-genetics · Oct 29, 2019 · f859090 · f859090
1 parent 1342b7f
commit f859090
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diff --git a/doc/release.rst b/doc/release.rst
@@ -2,6 +2,10 @@
 History
 =======
 
+Release v0.1.8 (29/10/2019)
+===========================
+* Further fix the bug when variants in donor genotype are not in cell vcf file
+
 Release v0.1.7 (05/10/2019)
 ===========================
 * Support donor genotype vcf file with different FORMAT for different variants

diff --git a/vireoSNP/version.py b/vireoSNP/version.py
@@ -1 +1 @@
-__version__ = "0.1.7"
+__version__ = "0.1.8"
diff --git a/vireoSNP/vireo.py b/vireoSNP/vireo.py
@@ -143,7 +143,15 @@ def main():
             options.geno_tag)
 
         mm_idx = match(cell_vcf['variants'], donor_vcf['variants'])
+        mm_idx = mm_idx.astype(float)
         idx1 = np.where(mm_idx == mm_idx)[0] #remove None
+        # TODO: check when chr is not compatible! given warning.
+        if len(idx1) == 0:
+            print("[vireo] warning: no variants matched to donor VCF, " + 
+                  "please check chr format!")
+        else:
+            print("[vireo] %d out %d variants matched to donor VCF" 
+                  %(len(idx1), len(cell_vcf['variants'])))
         idx2 = mm_idx[idx1].astype(int)
 
         donor_GPb = donor_GPb[idx2, :, :]