edge case where segment is completely masked (#46)

* edge case where segment is completely masked

* Update meta.yaml

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