- hitDict = hitRDS.getReadsDict(doMulti=True, findallOptimize=True)
-
- hg = Genome(genome)
- geneinfoDict = getGeneInfoDict(genome, cache=doCache)
- if doFlank:
- locusByChromDict = getLocusByChromDict(hg, upstream=upstreamBp, downstream=downstreamBp, useCDS=doCDS, additionalRegionsDict=acceptDict, keepSense=True, adjustToNeighbor = limitNeighbor)
- else:
- locusByChromDict = getLocusByChromDict(hg, additionalRegionsDict=acceptDict, keepSense=True)
-
- gidList = hg.allGIDs()
- gidList.sort()
- for chrom in acceptDict:
- for region in acceptDict[chrom]:
- if region.label not in gidList:
- gidList.append(region.label)
-