Fixes negative BED coordinates bug

Pointed out by @joshuak94. When chromosome coordinates of a peak
were too close to the beginning of the chromosome, some reads would
either contain (a) negative start/end coordinates, (b) have an end
coordinate lower than the start, or (c) have an incorrect read length.
This commit fixes this bug by ensuring that all fragment start
coordinates are positive.

chipulate.py

@@ -212,6 +212,14 @@ def makeBed( bedDf, genome, chipFragmentNumbers, controlFragmentNumbers, chromSi
             lengths = bedDf['end'].values - bedDf['start'].values
             lengths = np.repeat( lengths, genome[uniqueFragmentStr] )
             uniqueFragmentStartPos = np.int64( uniqueFragmentMidPoints + lengths * np.random.random( size=numUniqueFragments ) - fragmentLength/2 )
+
+        #Deal with fragments whose left ends are assigned negative start coordinates
+        idxes = np.arange( len(uniqueFragmentStartPos), dtype=np.int )
+        negStarts = uniqueFragmentStartPos < 0
+        negIdxes = idxes[negStarts]
+        maxVals = uniqueFragmentMidPoints[negStarts]
+        for idx in range(len(negIdxes)):
+            uniqueFragmentStartPos[negIdxes[idx]] = np.random.randint( low=1, high=maxVals[idx], size=1 )
 
         uniqueReadNames = np.zeros( numUniqueFragments, dtype=np.object ) 
 
@@ -229,6 +237,7 @@ def makeBed( bedDf, genome, chipFragmentNumbers, controlFragmentNumbers, chromSi
 
         fragmentStartPos = np.repeat( uniqueFragmentStartPos.astype(np.int64), readsToDuplicate )
         readNames = np.repeat( uniqueReadNames, readsToDuplicate )
+        print( np.sum( fragmentStartPos < 0 ) )
         if libraryType == 'single-end':
             strand = np.repeat( uniqueStrand, readsToDuplicate )
             posStrand = strand == '+'
@@ -240,15 +249,16 @@ def makeBed( bedDf, genome, chipFragmentNumbers, controlFragmentNumbers, chromSi
         if libraryType == 'single-end':
             readsDf.loc[:,'strand'] = strand
             readsDf.loc[:,'name'] = readNames
-            readsDf.loc[posStrand,'start'] = np.maximum( 1, fragmentStartPos[posStrand] )
+            readsDf.loc[posStrand,'start'] = fragmentStartPos[posStrand]
             readsDf.loc[posStrand,'end'] = fragmentStartPos[posStrand] + readLength
             readsDf.loc[negStrand,'start'] = fragmentStartPos[negStrand] + fragmentLength - readLength
             readsDf.loc[negStrand,'end'] = fragmentStartPos[negStrand] + fragmentLength
         elif libraryType == 'paired-end':
+            print("Paired end")
             readsDf2 = readsDf.copy(deep=True)
             readNames2 = np.repeat( uniqueReadNames2, readsToDuplicate )
 
-            readsDf.loc[:,'start'] = np.maximum( 1, fragmentStartPos )
+            readsDf.loc[:,'start'] = fragmentStartPos
             readsDf.loc[:,'end'] = fragmentStartPos + readLength 
             readsDf.loc[:,'strand'] = '+'
             readsDf.loc[:,'name'] = readNames
@@ -259,11 +269,21 @@ def makeBed( bedDf, genome, chipFragmentNumbers, controlFragmentNumbers, chromSi
             readsDf2.loc[:,'name'] = readNames2
 
         outOfBounds = readsDf.query( 'end > maxEntry' ).index.tolist()
-        readsLeftShift = 1 + np.random.randint( 10, size=len(outOfBounds) )
-        readsDf.loc[outOfBounds,'end'] = readsDf.loc[outOfBounds,'maxEntry'] - readsLeftShift
-        readsDf.loc[outOfBounds,'start'] = readsDf.loc[outOfBounds,'start'] - readsLeftShift
+        readsShift = 1 + np.random.randint( 10, size=len(outOfBounds) )
+        readsDf.loc[outOfBounds,'end'] = readsDf.loc[outOfBounds,'maxEntry'] - readsShift
+        readsDf.loc[outOfBounds,'start'] = readsDf.loc[outOfBounds,'end'] - readLength
+
+        incorrectReadsDf = readsDf.query('end - start != {}'.format( readLength ))
+        print( incorrectReadsDf.head() )
+
+        if libraryType == 'paired-end':
+            outOfBounds = readsDf2.query( 'end > maxEntry' ).index.tolist()
+            readsShift = 1 + np.random.randint( 10, size=len(outOfBounds) )
+            readsDf2.loc[outOfBounds,'end'] = readsDf2.loc[outOfBounds,'maxEntry'] - readsShift
+            readsDf2.loc[outOfBounds,'start'] = readsDf2.loc[outOfBounds,'end'] - readLength
+
         if len( outOfBounds ) > 0:
-            print( "For the following {} fragment(s) in the {} sample, their right ends were at positions beyond the length of the chromosome. They were shifted to the left by upto 10 base pairs. This can be avoided by either setting a shorter fragment length, or choosing genomic regions away from chromosome ends.".format( len(outOfBounds), fragmentStr[:-6] ) )
+            print( "NOTE : For the following {} fragment(s) in the {} sample, their right ends were at positions beyond the length of the chromosome. They were shifted to the left by upto 10 base pairs. This can be avoided by either setting a shorter fragment length, or choosing genomic regions away from chromosome ends.".format( len(outOfBounds), fragmentStr[:-6] ) )
             print( readsDf[['chr','start','end','name','score','strand']].loc[outOfBounds,:] )
 
         if libraryType == 'single-end':