edge case where segment is completely masked (#46)

* edge case where segment is completely masked

* Update meta.yaml

Author: andrewkern

diploshic/makeFeatureVecsForChrArmFromVcfDiploid.py

@@ -141,6 +141,10 @@ def readSampleToPopFile(sampleToPopFileName):
         for i in range(len(positions))
         if segmentStart <= positions[i] <= segmentEnd
     ]
+    if len(snpIndicesToKeep) == 0:
+        sys.exit(
+            "Error: no SNPs in the given segment of the chr arm; exiting\n"
+        )
     positions = [positions[i] for i in snpIndicesToKeep]
     genos = allel.GenotypeArray(genos.subset(sel0=snpIndicesToKeep))
 

diploshic/makeFeatureVecsForChrArmFromVcf_ogSHIC.py

@@ -123,6 +123,10 @@ def getSnpIndicesInSubWins(subWinSize, lastSubWinEnd, snpLocs):
         for i in range(len(positions))
         if segmentStart <= positions[i] <= segmentEnd
     ]
+    if len(snpIndicesToKeep) == 0:
+        sys.exit(
+            "Error: no SNPs in the given segment of the chr arm; exiting\n"
+        )
     positions = [positions[i] for i in snpIndicesToKeep]
     refAlleles = [refAlleles[i] for i in snpIndicesToKeep]
     altAlleles = [altAlleles[i] for i in snpIndicesToKeep]

meta.yaml

@@ -1,6 +1,6 @@
 package:
  name: diploshic
- version: "0.34"
+ version: "0.4"
 
 source:
  git_url: https://github.com/kr-colab/diploshic