X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=erange.git;a=blobdiff_plain;f=findall.py;fp=findall.py;h=f6fb9e618ae7ebd72830e75b84aa536a455c07e8;hp=f2c70432b1ccc477ca3ccee55b708a0e3e82f4bf;hb=f367a00b0a47e22c96cacccc1ffb4934746629cb;hpb=47bd897210cb85e042f11d7400b46d94400cc428

diff --git a/findall.py b/findall.py
index f2c7043..f6fb9e6 100755
--- a/findall.py
+++ b/findall.py
@@ -700,7 +700,11 @@ def previousRegionIsDone(pos, previousHit, maxSpacing, maxCoord):
 
 
 def regionPassesCriteria(regionFinder, sumAll, numStarts, regionLength, stringency=1):
-    return sumAll >= stringency * regionFinder.minHits and numStarts > stringency * regionFinder.minRatio and regionLength > stringency * regionFinder.readlen
+    minTotalReads = stringency * regionFinder.minHits
+    minNumReadStarts = stringency * regionFinder.minRatio
+    minRegionLength = stringency * regionFinder.readlen
+
+    return sumAll >= minTotalReads and numStarts > minNumReadStarts and regionLength > minRegionLength
 
 
 def trimRegion(region, regionFinder, peak, regionStop, trimValue, currentReadList, totalReadCount):
@@ -829,7 +833,7 @@ def setMultireadPercentage(region, hitRDS, hitRDSsize, currentTotalWeight, curre
     except ZeroDivisionError:
         return
 
-    region.multiP = multiP
+    region.multiP = min(multiP, 100.)
 
 
 def regionAndPeakPass(regionFinder, region, regionLength, peakScore, plusRatio):
@@ -907,6 +911,7 @@ def writeRegions(outregions, outfile, doPvalue, poissonmean, shiftValue=0, repor
 
 def calculatePValue(sum, poissonmean):
     pValue = math.exp(-poissonmean)
+    #TODO: 798: DeprecationWarning: integer argument expected, got float - for i in xrange(sum)
     for i in xrange(sum):
         pValue *= poissonmean
         pValue /= i+1