--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/PsiCLASS-1.0.2/blocks.hpp	Fri Mar 26 16:52:45 2021 +0000
@@ -0,0 +1,1580 @@
+// The class manage the blocks
+// Li Song
+
+#ifndef _LSONG_CLASSES_BLOCKS_HEADER
+#define _LSONG_CLASSES_BLOCKS_HEADER
+
+#include <stdlib.h> 
+#include <vector>
+#include <map>
+#include <assert.h>
+#include <math.h>
+#include <set>
+#include <inttypes.h>
+
+#include "defs.h"
+
+extern bool VERBOSE ;
+extern FILE *fpOut ;
+
+extern int gMinDepth ; 
+
+
+struct _splitSite // means the next position belongs to another block
+{
+	int64_t pos ;
+	char strand ;
+	int chrId ;
+	int type ; // 1-start of an exon. 2-end of an exon.
+	
+	int support ;
+	int uniqSupport ;
+
+	int mismatchSum ;
+
+	int64_t oppositePos ; // the position of the other sites to form the intron.
+} ;
+
+struct _block
+{
+	int chrId ;
+	int contigId ;
+	int64_t start, end ;
+	int64_t leftSplice, rightSplice ; // Some information about the left splice site and right splice site.
+					  // record the leftmost and rightmost coordinates of a splice site within this block 
+				          //or the length of read alignment support the splice sites. 
+					  //Or the number of support.
+	int64_t depthSum ;
+
+	int leftType, rightType ; //0-soft boundary, 1-start of an exon, 2-end of an exon.
+	
+	double leftRatio, rightRatio ; // the adjusted ratio-like value to the left and right anchor subexons.      
+	double ratio ;
+
+	char leftStrand, rightStrand ;
+
+	int *depth ;
+	int prevCnt, nextCnt ; // Some connection information for the subexons.
+	int *prev ;
+	int *next ;
+} ;
+
+// adjacent graph
+struct _adj
+{
+	int ind ;
+	int info ;
+	int support ;
+	int next ;
+} ;
+
+class Blocks
+{
+	private:
+		std::map<int, int> exonBlocksChrIdOffset ;
+
+		int64_t Overlap( int64_t s0, int64_t e0, int64_t s1, int64_t e1, int64_t &s, int64_t &e )
+		{
+			s = e = -1 ;
+			if ( e0 < s1 || s0 > e1 )
+				return 0 ;
+			s = s0 > s1 ? s0 : s1 ;
+			e = e0 < e1 ? e0 : e1 ;
+			return e - s + 1 ;
+		}
+
+		void Split( const char *s, char delimit, std::vector<std::string> &fields )
+		{
+			int i ;
+			fields.clear() ;
+			if ( s == NULL )
+				return ;
+
+			std::string f ;
+			for ( i = 0 ; s[i] ; ++i )
+			{
+				if ( s[i] == delimit || s[i] == '\n' )	
+				{
+					fields.push_back( f ) ;
+					f.clear() ;
+				}
+				else
+					f.append( 1, s[i] ) ;
+			}
+			fields.push_back( f ) ;
+			f.clear() ;
+		}
+		
+		void BuildBlockChrIdOffset()
+		{
+			// Build the map for the offsets of chr id in the exonBlock list.
+			exonBlocksChrIdOffset[ exonBlocks[0].chrId] = 0 ;
+			int cnt = exonBlocks.size() ;
+			for ( int i = 1 ; i < cnt ; ++i )
+			{
+				if ( exonBlocks[i].chrId != exonBlocks[i - 1].chrId )
+					exonBlocksChrIdOffset[ exonBlocks[i].chrId ] = i ;
+			}
+		}
+		
+		bool CanReach( int from, int to, struct _adj *adj, bool *visited )
+		{
+			if ( visited[from] )
+				return false ;
+			visited[from] = true ;
+			int p ;
+			p = adj[from].next ;
+			while ( p != -1 )
+			{
+				if ( adj[p].ind == to )
+					return true ;
+				if ( adj[p].ind < to 
+					&& CanReach( adj[p].ind, to, adj, visited ) )
+					return true ;
+				p = adj[p].next ;
+			}
+			return false ;
+		}
+
+		void AdjustAndCreateExonBlocks( int tag, std::vector<struct _block> &newExonBlocks )
+		{
+			int i, j ;
+			if ( exonBlocks[tag].depth != NULL )
+			{	
+				// Convert the increment and decrement into actual depth.
+				int len = exonBlocks[tag].end - exonBlocks[tag].start + 1 ;
+				int *depth = exonBlocks[tag].depth ;
+				for ( i = 1 ; i < len ; ++i )
+					depth[i] = depth[i - 1] + depth[i] ;
+
+				struct _block island ; // the portion created by the hollow.
+				island.start = island.end = -1 ;
+				island.depthSum = 0 ;
+
+				/*if ( exonBlocks[tag].start == 1562344 )
+				{
+					for ( i = 0 ; i < len ; ++i )
+						printf( "%d\n", depth[i] ) ;
+				}*/
+				// Adjust boundary accordingly. 
+				int64_t adjustStart = exonBlocks[tag].start ; 
+				int64_t adjustEnd = exonBlocks[tag].end ;
+				
+				if ( exonBlocks[tag].leftType == 0 && exonBlocks[tag].rightType != 0 )		
+				{
+					for ( i = len - 1 ; i >= 0 ; --i )
+						if ( depth[i] < gMinDepth )
+							break ;
+					++i ;
+					if ( exonBlocks[tag].rightType == 2 && i + exonBlocks[tag].start > exonBlocks[tag].rightSplice )
+						i = exonBlocks[tag].rightSplice - exonBlocks[tag].start ;
+					adjustStart = i  + exonBlocks[tag].start ;
+
+					if ( adjustStart > exonBlocks[tag].start )
+					{
+						int s, e ;
+						// firstly [s,e] is the range of depth array.
+						for ( s = 0 ; s < i ; ++s )
+							if ( depth[s] >= gMinDepth )
+								break ;
+						for ( e = i - 1 ; e >= s ; -- e )
+							if ( depth[e] >= gMinDepth )
+								break ;
+						if ( e >= s )
+						{
+							island = exonBlocks[tag] ;
+							island.depthSum = 0 ;
+							island.leftType = island.rightType = 0 ;
+							for ( j = s ; j <= e ; ++j )
+								island.depthSum += depth[j] ;
+							island.start = s + exonBlocks[tag].start ; // offset the coordinate.
+							island.end = e + exonBlocks[tag].start ;
+						}
+					}
+				}
+				else if ( exonBlocks[tag].leftType != 0 && exonBlocks[tag].rightType == 0 )
+				{
+					for ( i = 0 ; i < len ; ++i )	
+						if ( depth[i] < gMinDepth )			
+							break ;
+					--i ;
+					if ( exonBlocks[tag].leftType == 1 && i + exonBlocks[tag].start < exonBlocks[tag].leftSplice )
+						i = exonBlocks[tag].leftSplice - exonBlocks[tag].start ;
+					adjustEnd = i + exonBlocks[tag].start ; 
+
+					if ( adjustEnd < exonBlocks[tag].end )
+					{
+						int s, e ;
+						// firstly [s,e] is the range of depth array.
+						for ( s = i + 1 ; s < len ; ++s )
+							if ( depth[s] >= gMinDepth )
+								break ;
+						for ( e = len - 1 ; e >= s ; --e )
+							if ( depth[e] >= gMinDepth )
+								break ;
+						if ( e >= s )
+						{
+							island = exonBlocks[tag] ;
+							island.depthSum = 0 ;
+							island.leftType = island.rightType = 0 ;
+							for ( j = s ; j <= e ; ++j )
+								island.depthSum += depth[j] ;
+							island.start = s + exonBlocks[tag].start ; // offset the coordinate.
+							island.end = e + exonBlocks[tag].start ;
+						}
+					}
+				}
+				else if ( exonBlocks[tag].leftType == 0 && exonBlocks[tag].rightType == 0 )
+				{
+					for ( i = 0 ; i < len ; ++i )			
+						if ( depth[i] >= gMinDepth )
+							break ;
+					adjustStart = i + exonBlocks[tag].start ;
+
+					for ( i = len - 1 ; i >= 0 ; --i )
+						if ( depth[i] >= gMinDepth )
+							break ;
+					adjustEnd = i + exonBlocks[tag].start ;
+				}
+				else if ( exonBlocks[tag].leftType == 1 && exonBlocks[tag].rightType == 2
+					&& exonBlocks[tag].end - exonBlocks[tag].start + 1 >= 1000 )
+				{
+					// The possible merge of two genes or merge of UTRs, if we don't break the low coverage part.
+					// If we decide to cut, I'll reuse the variable "island" to represent the subexon on right hand side.
+					int l ;
+					int gapSize = 30 ;
+					for ( i = 0 ; i <= len - ( gapSize + 1 ) ; ++i )
+					{
+						if ( depth[i] < gMinDepth )
+						{
+							for ( l = i ; l < i + ( gapSize + 1 )  ; ++l )
+								if ( depth[l] >= gMinDepth )
+									break ;
+							if ( l < i + ( gapSize + 1 ) )
+							{
+								i = l - 1 ;
+								continue ;
+							}
+							else
+								break ;
+						}
+					}
+
+					for ( j = len - 1 ; j >= ( gapSize + 1 ) - 1 ; --j )
+					{
+						if ( depth[j] < gMinDepth )
+						{
+							for ( l = j ; l >= j - ( gapSize + 1 ) + 1 ; --l )
+								if ( depth[l] >= gMinDepth )
+									break ;
+
+							if ( l >= j - ( gapSize + 1 ) + 1 )
+							{
+								j = l + 1 ;
+								continue ;
+							}
+							else
+								break ;
+						}
+					}
+
+					if ( j - i + 1 > gapSize )
+					{
+						// we break.	
+						--i ; ++j ;
+
+						adjustEnd = i + exonBlocks[tag].start ;
+
+						if ( j < len - 1 )
+						{
+							island = exonBlocks[tag] ;
+							island.depthSum = 0 ;
+							island.leftType = 0 ; 
+							for ( l = j ; l <= len - 1 ; ++l )
+								island.depthSum += depth[j] ;
+							island.start = j + exonBlocks[tag].start ; // offset the coordinate.
+							island.end = exonBlocks[tag].end ;
+						}
+						
+						exonBlocks[tag].rightType = 0 ; // put it here, so the island can get the right info
+						//fprintf( stderr, "break %d %d %d %d.\n", (int)exonBlocks[tag].start, (int)adjustEnd, i + (int)exonBlocks[tag].start, j + (int)exonBlocks[tag].start ) ;
+					}
+				}
+
+				int lostDepthSum = 0 ;
+				for ( i = exonBlocks[tag].start ; i < adjustStart ; ++i  )
+					lostDepthSum += depth[i - exonBlocks[tag].start ] ;
+				for ( i = adjustEnd + 1 ; i < exonBlocks[tag].end ; ++i  )
+					lostDepthSum += depth[i - exonBlocks[tag].start ] ;
+				exonBlocks[tag].depthSum -= lostDepthSum ;
+
+				delete[] exonBlocks[tag].depth ;
+				exonBlocks[tag].depth = NULL ;
+				
+				//if ( exonBlocks[tag].start == 1562344 )
+				//	printf( "%d %d\n", adjustStart, adjustEnd ) ;
+				if ( ( len > 1 && adjustEnd - adjustStart + 1 <= 1 ) || ( adjustEnd - adjustStart + 1 <= 0 ) )
+					return ;
+				exonBlocks[tag].start = adjustStart ;
+				exonBlocks[tag].end = adjustEnd ;
+				
+				if ( island.start != -1 && island.end < exonBlocks[tag].start )
+					newExonBlocks.push_back( island ) ;
+
+				newExonBlocks.push_back( exonBlocks[tag] ) ;
+				if ( island.start != -1 && island.start > exonBlocks[tag].end )
+					newExonBlocks.push_back( island ) ;
+			}
+		}
+	public:
+		std::vector<struct _block> exonBlocks ;
+
+		Blocks() { } 	
+		~Blocks() 
+		{
+			int blockCnt = exonBlocks.size() ;
+			for ( int i = 0 ; i <  blockCnt ; ++i ) 
+			{
+				if ( exonBlocks[i].next != NULL )
+				{
+					delete[] exonBlocks[i].next ;
+				}
+				if ( exonBlocks[i].prev != NULL )
+				{
+					delete[] exonBlocks[i].prev ;
+				}
+			}
+		}
+		
+		double GetAvgDepth( const struct _block &block )
+		{
+			return block.depthSum / (double)( block.end - block.start + 1 ) ;
+		}
+
+		int BuildExonBlocks( Alignments &alignments )
+		{
+			int tag = 0 ;
+			while ( alignments.Next() )
+			{
+				int i, j, k ;
+				int segCnt = alignments.segCnt ;
+				struct _pair *segments = alignments.segments ;
+				int eid = 0 ; // the exonblock id that the segment update
+				
+				// locate the first exonblock that beyond the start of the read.
+				while ( tag < (int)exonBlocks.size() && ( exonBlocks[tag].end < segments[0].a - 1 
+							|| exonBlocks[tag].chrId != alignments.GetChromId() ) )  
+				{
+					++tag ;
+				}
+				// due to the merge of exon blocks, we might need roll back
+				--tag ;
+				while ( tag >= 0 && ( exonBlocks[tag].end >= segments[0].a - 1 
+							&& exonBlocks[tag].chrId == alignments.GetChromId() ) )
+				{
+					--tag ;
+				}
+				++tag ;
+
+				for ( i = 0 ; i < segCnt ; ++i )
+				{
+					//if ( i == 0 )
+					//	printf( "hi %d %s %d %d\n", i, alignments.GetReadId(), segments[i].a, segments[i].b ) ;
+					for ( j = tag ; j < (int)exonBlocks.size() ; ++j )
+					{
+						if ( exonBlocks[j].end >= segments[i].a - 1 )
+							break ;
+					}
+					if ( j >= (int)exonBlocks.size() )
+					{
+						// Append a new block
+						struct _block newSeg ;
+						newSeg.chrId = alignments.GetChromId() ;
+						newSeg.start = segments[i].a ;
+						newSeg.end = segments[i].b ;
+
+						newSeg.leftSplice = -1 ;
+						newSeg.rightSplice = -1 ;
+						if ( i > 0 )
+							newSeg.leftSplice = segments[i].a ; 
+						if ( i < segCnt - 1 )
+							newSeg.rightSplice = segments[i].b ;
+
+						exonBlocks.push_back( newSeg ) ;
+
+						eid = exonBlocks.size() - 1 ;
+					}
+					else if ( exonBlocks[j].end < segments[i].b || 
+							( exonBlocks[j].start > segments[i].a && exonBlocks[j].start <= segments[i].b + 1 ) ) 
+					{
+						// If overlaps with a current exon block, so we extend it
+						if ( exonBlocks[j].end < segments[i].b )
+						{
+							// extends toward right 
+							exonBlocks[j].end = segments[i].b ;
+							if ( i > 0 && ( exonBlocks[j].leftSplice == -1 || segments[i].a < exonBlocks[j].leftSplice ) )
+								exonBlocks[j].leftSplice = segments[i].a ;
+							if ( i < segCnt - 1 && segments[i].b > exonBlocks[j].rightSplice )
+								exonBlocks[j].rightSplice = segments[i].b ;
+							eid = j ;
+
+							// Merge with next few exon blocks
+							for ( k = j + 1 ; k < (int)exonBlocks.size() ; ++k )
+							{
+								if ( exonBlocks[k].start <= exonBlocks[j].end + 1 )
+								{
+									if ( exonBlocks[k].end > exonBlocks[j].end )
+										exonBlocks[j].end = exonBlocks[k].end ;
+
+									if ( exonBlocks[k].leftSplice != -1 && ( exonBlocks[j].leftSplice == -1 || exonBlocks[k].leftSplice < exonBlocks[j].leftSplice ) )
+										exonBlocks[j].leftSplice = exonBlocks[k].leftSplice ;
+									if ( exonBlocks[k].rightSplice != -1 && exonBlocks[k].rightSplice > exonBlocks[j].rightSplice )
+										exonBlocks[j].rightSplice = exonBlocks[k].rightSplice ;
+
+								}
+								else
+									break ;
+							}
+
+							if ( k > j + 1 )
+							{
+								// Remove the merged blocks
+								int a, b ;
+								for ( a = j + 1, b = k ; b < (int)exonBlocks.size() ; ++a, ++b )
+									exonBlocks[a] = exonBlocks[b] ;
+								for ( a = 0 ; a < k - ( j + 1 ) ; ++a )
+									exonBlocks.pop_back() ;
+							}
+						}
+						else if ( exonBlocks[j].start > segments[i].a && exonBlocks[j].start <= segments[i].b + 1 ) 
+						{
+							// extends toward left
+							exonBlocks[j].start = segments[i].a ;
+							if ( i > 0 && ( exonBlocks[j].leftSplice == -1 || segments[i].a < exonBlocks[j].leftSplice ) )
+								exonBlocks[j].leftSplice = segments[i].a ;
+							if ( i < segCnt - 1 && segments[i].b > exonBlocks[j].rightSplice )
+								exonBlocks[j].rightSplice = segments[i].b ;
+							eid = j ;
+
+							// Merge with few previous exon blocks
+							for ( k = j - 1 ; k >= 0 ; --k )
+							{
+								if ( exonBlocks[k].end >= exonBlocks[k + 1].start - 1 )
+								{
+									if ( exonBlocks[k + 1].start < exonBlocks[k].start )
+									{
+										exonBlocks[k].start = exonBlocks[k + 1].start ;
+									}
+
+									if ( exonBlocks[k].leftSplice != -1 && ( exonBlocks[j].leftSplice == -1 || exonBlocks[k].leftSplice < exonBlocks[j].leftSplice ) )
+										exonBlocks[j].leftSplice = exonBlocks[k].leftSplice ;
+									if ( exonBlocks[k].rightSplice != -1 && exonBlocks[k].rightSplice > exonBlocks[j].rightSplice )
+										exonBlocks[j].rightSplice = exonBlocks[k].rightSplice ;
+
+								}
+								else
+									break ;
+							}
+
+							if ( k < j - 1 )
+							{
+								int a, b ;
+								eid = k + 1 ;
+								for ( a = k + 2, b = j + 1 ; b < (int)exonBlocks.size() ; ++a, ++b )
+									exonBlocks[a] = exonBlocks[b] ;
+								for ( a = 0 ; a < ( j - 1 ) - k ; ++a )
+									exonBlocks.pop_back() ;
+
+							}
+						}
+					}
+					else if ( exonBlocks[j].start > segments[i].b + 1 )
+					{
+						int size = exonBlocks.size() ;
+						int a ;
+						// No overlap, insert a new block
+						struct _block newSeg ;
+						newSeg.chrId = alignments.GetChromId() ;
+						newSeg.start = segments[i].a ;
+						newSeg.end = segments[i].b ;
+
+						newSeg.leftSplice = -1 ;
+						newSeg.rightSplice = -1 ;
+						if ( i > 0 )
+							newSeg.leftSplice = segments[i].a ; 
+						if ( i < segCnt - 1 )
+							newSeg.rightSplice = segments[i].b ;
+
+						// Insert at position j
+						exonBlocks.push_back( newSeg ) ;	
+						for ( a = size ; a > j ; --a )
+							exonBlocks[a] = exonBlocks[a - 1] ;
+						exonBlocks[a] = newSeg ;
+
+						eid = a ;
+					}
+					else
+					{
+						// The segment is contained in j
+						eid = -1 ;
+					}
+
+					// Merge the block with the mate if the gap is very small
+					// Note that since reads are already sorted by coordinate,
+					//    the previous exon blocks is built completely. 
+					/*int64_t matePos ;
+					int mateChrId ;
+					alignments.GetMatePosition( mateChrId, matePos ) ;
+					if ( i == 0 && eid > 0 && mateChrId == exonBlocks[ eid ].chrId 
+						&& matePos < segments[0].a 
+						&& matePos >= exonBlocks[eid - 1].start 
+						&& matePos <= exonBlocks[eid - 1].end
+						&& segments[0].a - matePos + 1 <= 500
+						&& exonBlocks[eid-1].chrId == exonBlocks[eid].chrId 
+						&& exonBlocks[eid].start - exonBlocks[eid - 1].end - 1 <= 30 )
+					{
+						printf( "%d: (%d-%d) (%d-%d). %d %d\n",  ( segments[0].a + alignments.readLen - 1 ) - matePos + 1, exonBlocks[eid - 1].start, exonBlocks[eid - 1].end,
+							exonBlocks[eid].start,
+							exonBlocks[eid].end, eid, exonBlocks.size() ) ;
+						exonBlocks[eid - 1].end = exonBlocks[eid].end ;
+
+						if ( exonBlocks[eid].leftSplice != -1 && ( exonBlocks[eid - 1].leftSplice == -1 || exonBlocks[eid].leftSplice < exonBlocks[eid - 1].leftSplice ) )
+							exonBlocks[eid - 1].leftSplice = exonBlocks[k].leftSplice ;
+						if ( exonBlocks[eid].rightSplice != -1 && exonBlocks[eid].rightSplice > exonBlocks[eid - 1].rightSplice )
+							exonBlocks[eid - 1].rightSplice = exonBlocks[eid].rightSplice ;
+
+						int size = exonBlocks.size() ;
+						for ( j = eid ; j < size - 1 ; ++j )
+							exonBlocks[j] = exonBlocks[j + 1] ;
+						exonBlocks.pop_back() ;
+					}*/
+				}
+			}
+			/*for ( int i = 0 ; i < (int)exonBlocks.size() ; ++i )
+			  {
+			  printf( "%d %d\n", exonBlocks[i].start, exonBlocks[i].end ) ;
+			  }*/
+
+			if ( exonBlocks.size() > 0 )
+			{
+				BuildBlockChrIdOffset() ;
+				int cnt = exonBlocks.size() ;
+				for ( int i = 0 ; i < cnt ; ++i )
+				{
+					exonBlocks[i].contigId = exonBlocks[i].chrId ;
+					
+					exonBlocks[i].leftType = 0 ;
+					exonBlocks[i].rightType = 0 ;
+					exonBlocks[i].depth = NULL ;
+					exonBlocks[i].nextCnt = 0 ;
+					exonBlocks[i].prevCnt = 0 ;
+					exonBlocks[i].leftStrand = '.' ;
+					exonBlocks[i].rightStrand = '.' ;
+				}
+			}
+			return exonBlocks.size() ;
+		}
+
+		void FilterSplitSitesInRegions( std::vector<struct _splitSite> &sites )
+		{
+			int i, j, k ;
+			int size = sites.size() ;
+			int bsize = exonBlocks.size() ;
+			int tag = 0 ;
+
+			for ( i = 0 ; i < bsize ; ++i )
+			{
+				while ( tag < size && ( sites[tag].chrId < exonBlocks[i].chrId || 
+					( sites[tag].chrId == exonBlocks[i].chrId && sites[tag].pos < exonBlocks[i].start ) ) )
+				{
+					++tag ;
+				}
+				if ( tag >= size )
+					break ;
+
+				if ( sites[tag].chrId != exonBlocks[i].chrId || sites[tag].pos > exonBlocks[i].end )
+					continue ;
+
+				for ( j = tag + 1 ; j < size ; ++j )
+					if ( sites[j].chrId != exonBlocks[i].chrId || sites[j].pos > exonBlocks[i].end )
+						break ;
+
+				// [tag,j) holds the split sites in this region.
+				int leftStrandSupport[2] = {0, 0} ;
+				int rightStrandSupport[2] = {0, 0} ;
+				int strandCnt[2] = { 0, 0 } ;
+				for ( k = tag ; k < j ; ++k )			
+				{
+					if ( sites[k].strand == '-' )
+					{
+						++strandCnt[0] ;
+						if ( sites[k].oppositePos < exonBlocks[i].start )
+							leftStrandSupport[0] += sites[k].support ;
+						else if ( sites[k].oppositePos > exonBlocks[i].end )
+							rightStrandSupport[0]  += sites[k].support ;
+					}
+					else if ( sites[k].strand == '+' )
+					{
+						++strandCnt[1] ;
+						if ( sites[k].oppositePos < exonBlocks[i].start )
+							leftStrandSupport[1] += sites[k].support ;
+						else if ( sites[k].oppositePos > exonBlocks[i].end )
+							rightStrandSupport[1]  += sites[k].support ;
+					}
+					
+				}
+
+
+				if ( leftStrandSupport[0] == 0 && rightStrandSupport[0] == 0  
+					&& leftStrandSupport[1] != 0 && rightStrandSupport[1] != 0 && strandCnt[0] == 2 )
+				{
+					// check whether a different strand accidentally show up in this region.
+					bool remove = false ;
+					for ( k = tag ; k < j ; ++k )
+					{
+						if ( sites[k].strand == '-' &&
+							sites[k].oppositePos >= sites[k].pos && sites[k].oppositePos <= exonBlocks[i].end &&
+							sites[k].support <= 2 )
+						{
+							remove = true ;
+							break ;
+						}
+					}
+					
+					if ( remove )
+						for ( k = tag ; k < j ; ++k )
+							if ( sites[k].strand == '-' )
+								sites[k].support = -1 ;
+				}
+				else if ( leftStrandSupport[1] == 0 && rightStrandSupport[1] == 0  
+					&& leftStrandSupport[0] != 0 && rightStrandSupport[0] != 0 && strandCnt[1] == 2 )
+				{
+					// check whether a different strand accidentally show up in this region.
+					bool remove = false ;
+					for ( k = tag ; k < j ; ++k )
+					{
+						if ( sites[k].strand == '+' &&
+							sites[k].oppositePos >= sites[k].pos && sites[k].oppositePos <= exonBlocks[i].end &&
+							sites[k].support <= 2 )
+						{
+							remove = true ;
+							break ;
+						}
+					}
+					
+					if ( remove )
+						for ( k = tag ; k < j ; ++k )
+							if ( sites[k].strand == '+' )
+								sites[k].support = -1 ;
+				}
+	
+				tag = j ;
+			}
+
+			k = 0 ;
+			for ( i = 0 ; i < size ; ++i )
+				if ( sites[i].support > 0 )
+				{
+					sites[k] = sites[i] ;
+					++k ;
+				}
+			sites.resize( k ) ;
+		}
+		
+		// Filter the pair of split sites that is likely merge two genes.
+		// We filter the case like [..]------------------------[..]
+		// 			   [..]--[..]            [..]-[...]
+		void FilterGeneMergeSplitSites( std::vector<struct _splitSite> &sites )
+		{
+			int i, j, k ;
+			int bsize = exonBlocks.size() ;
+			int ssize = sites.size() ;
+
+			struct _pair32 *siteToBlock = new struct _pair32[ ssize ] ;
+			struct _adj *adj = new struct _adj[ ssize / 2 + bsize ] ; 
+			bool *visited = new bool[bsize] ;
+
+			int adjCnt = 0 ;
+			for ( i = 0 ; i < bsize ; ++i )
+			{
+				adj[i].info = 0 ; // in the header, info means the number of next block
+				adj[i].support = 0 ;
+				adj[i].next = -1 ;
+			}
+			adjCnt = i ;
+			memset( siteToBlock, -1, sizeof( struct _pair32 ) * ssize ) ;
+			memset( visited, false, sizeof( bool ) * bsize ) ;
+			
+			// Build the graph.
+			k = 0 ; 
+			for ( i = 0 ; i < bsize ; ++i )
+			{
+				for ( ; k < ssize ; ++k )
+				{
+					if ( sites[k].oppositePos < sites[k].pos )	
+						continue ;
+					if ( sites[k].chrId < exonBlocks[i].chrId 
+						|| ( sites[k].chrId == exonBlocks[i].chrId && sites[k].pos < exonBlocks[i].start ) )
+						continue ;
+					break ;
+				}
+
+				for ( ; k < ssize ; ++k )
+				{
+					if ( sites[k].chrId > exonBlocks[i].chrId 
+						|| sites[k].pos > exonBlocks[i].end )
+						break ;
+					
+					if ( sites[k].oppositePos <= exonBlocks[i].end ) // ignore self-loop
+						continue ;
+					
+					for ( j = i + 1 ; j < bsize ; ++j )
+						if ( sites[k].oppositePos >= exonBlocks[j].start && sites[k].oppositePos <= exonBlocks[j].end )
+							break ;
+					if ( sites[k].oppositePos >= exonBlocks[j].start && sites[k].oppositePos <= exonBlocks[j].end )
+					{
+						int p ;
+						p = adj[i].next ;
+						while ( p != -1 )
+						{
+							if ( adj[p].ind == j )
+							{
+								++adj[p].info ;
+								adj[p].support += sites[k].uniqSupport ;
+								break ;
+							}
+							p = adj[p].next ;
+						}
+						if ( p == -1 )
+						{
+							adj[ adjCnt ].ind = j ;
+							adj[ adjCnt ].info = 1 ;
+							adj[ adjCnt ].support = sites[k].uniqSupport ;
+							adj[ adjCnt ].next = adj[i].next ;
+							adj[i].next = adjCnt ;
+							++adj[i].info ;
+							++adjCnt ;
+						}
+
+						siteToBlock[k].a = i ;
+						siteToBlock[k].b = j ;
+					}
+				}
+			}
+			for ( k = 0 ; k < ssize ; ++k )
+			{
+				if ( sites[k].oppositePos - sites[k].pos + 1 < 20000 || sites[k].uniqSupport >= 30 )
+					continue ;
+
+				int from = siteToBlock[k].a ;
+				int to = siteToBlock[k].b ;
+				if ( to - from - 1 < 2 || adj[from].info <= 1 )
+					continue ;
+					
+				memset( &visited[from], false, sizeof( bool ) * ( to - from + 1 ) ) ;	
+				
+				int cnt = 0 ;
+				int p = adj[from].next ;
+				int max = -1 ;
+				int maxP = 0 ;
+				while ( p != -1 )
+				{
+					if ( adj[p].support >= 10 && adj[p].ind <= to )
+						++cnt ;
+					if ( adj[p].support > max || ( adj[p].support == max && adj[p].ind == to ) )
+					{
+						max = adj[p].support ;
+						maxP = p ;
+					}
+
+					if ( adj[p].ind == to && adj[p].info > 1 )
+					{
+						cnt = 0 ;
+						break ;
+					}
+					p = adj[p].next ;
+				}
+				if ( cnt <= 1 )
+					continue ;
+
+				if ( max != -1 && adj[maxP].ind == to )
+					continue ;
+
+				// No other path can reach "to"
+				p = adj[from].next ;
+				while ( p != -1 )
+				{
+					if ( adj[p].ind != to )
+					{
+						//if ( sites[k].pos ==43917158 )
+						//	printf( "hi %d %d. (%d %d)\n", from, adj[p].ind, exonBlocks[ adj[p].ind ].start, exonBlocks[ adj[p].ind ].end ) ;
+						if ( CanReach( adj[p].ind, to, adj, visited ) )
+							break ;
+					}
+					p = adj[p].next ;
+				}
+				if ( p != -1 )
+					continue ;
+
+				//if ( sites[k].pos == 34073267 )
+				//	printf( "hi %d %d. (%d %d)\n", from, to, exonBlocks[to].start, exonBlocks[to].end ) ;
+				
+				// There are some blocks between that can reach "to"
+				for ( i = from + 1 ; i < to ; ++i )
+				{
+					p = adj[i].next ;
+					while ( p != -1 )
+					{
+						if ( adj[p].ind == to && adj[p].support >= 10 )
+							break ;
+						p = adj[p].next ;
+					}
+					if ( p != -1 )
+						break ;
+				}
+				if ( i >= to )
+					continue ;
+			
+				// Filter the site
+				//printf( "filtered: %d %d\n", sites[k].pos, sites[k].oppositePos ) ;
+				sites[k].support = -1 ;
+				for ( j = k + 1 ; j < ssize ; ++j )
+				{
+					if ( sites[j].pos == sites[k].oppositePos && sites[j].oppositePos == sites[k].pos )
+						sites[j].support = -1 ;
+					if ( sites[j].pos > sites[k].oppositePos )
+						break ;
+				}
+			}
+
+			k = 0 ;
+			for ( i = 0 ; i < ssize ; ++i )
+				if ( sites[i].support > 0 )
+				{
+					sites[k] = sites[i] ;
+					++k ;
+				}
+			sites.resize( k ) ;
+
+			// Filter the intron on the different strand of a gene.
+			ssize = k ;
+			k = 0 ;
+			for ( i = 0 ; i < bsize ;  )
+			{
+				int farthest = exonBlocks[i].end ;
+				
+				for ( j = i ; j < bsize ; ++j )
+				{
+					if ( exonBlocks[j].start > farthest || exonBlocks[i].chrId != exonBlocks[j].chrId )
+						break ;
+					int p = adj[i].next ;
+					while ( p != -1 )
+					{
+						if ( exonBlocks[ adj[p].ind ].end > farthest )
+							farthest = exonBlocks[ adj[p].ind ].end ;
+						p = adj[p].next ;
+					}
+				}
+
+				for ( ; k < ssize ; ++k )
+				{
+					if ( sites[k].chrId < exonBlocks[i].chrId || 
+						( sites[k].chrId == exonBlocks[i].chrId && sites[k].pos < exonBlocks[i].start ) )
+							continue ;
+					break ;
+				}
+				
+				if ( sites[k].chrId > exonBlocks[i].chrId || sites[k].pos > farthest )
+				{
+					i = j ;
+					continue ;
+				}
+				//printf( "%d %d. %d %d. %d %d\n", i, j, exonBlocks[i].start, farthest, k, sites[k].pos ) ;
+
+
+				int from = k ;
+				int to ;
+				for ( to = k ; to < ssize ; ++to )
+					if ( sites[to].chrId != exonBlocks[i].chrId || sites[to].pos > farthest )
+						break ;
+
+				int strandSupport[2] = {0, 0};
+				int strandCount[2] = {0, 0};
+				for ( k = from ; k < to ; ++k )
+				{
+					if ( sites[k].oppositePos <= sites[k].pos )
+						continue ;
+
+					int tag = ( sites[k].strand == '+' ? 1 : 0 ) ;
+					strandSupport[tag] += sites[k].support ;
+					++strandCount[tag] ;
+				}
+				
+				// Not mixtured.
+				if ( strandCount[0] * strandCount[1] == 0 )
+				{
+					i = j ;
+					k = to ;
+					continue ;
+				}
+				
+				char removeStrand = 0 ;
+				if ( strandCount[0] == 1 && strandCount[1] >= 3 
+					&& strandSupport[1] >= 20 * strandSupport[0] && strandSupport[0] <= 5 )
+				{
+					removeStrand = '-' ;
+				}
+				else if ( strandCount[1] == 1 && strandCount[0] >= 3 
+						&& strandSupport[0] >= 20 * strandSupport[1] && strandSupport[1] <= 5 )
+				{
+					removeStrand = '+' ;
+				}
+
+				if ( removeStrand == 0 )
+				{
+					i = j ; k = to ;
+					continue ;
+				}
+
+				for ( k = from ; k < to ; ++k )
+				{
+					if ( sites[k].strand == removeStrand && sites[k].oppositePos >= exonBlocks[i].start && sites[k].oppositePos <= farthest )
+					{
+						//printf( "filtered: %d %d\n", sites[k].pos, sites[k].oppositePos ) ;
+						sites[k].support = -1 ;
+					}
+				}
+
+				i = j ;
+				k = to ;	
+			}
+			
+			k = 0 ;
+			for ( i = 0 ; i < ssize ; ++i )
+				if ( sites[i].support > 0 )
+				{
+					sites[k] = sites[i] ;
+					++k ;
+				}
+			sites.resize( k ) ;
+
+			delete[] visited ;
+			delete[] siteToBlock ;
+			delete[] adj ;
+		}
+
+		void SplitBlocks( Alignments &alignments, std::vector< struct _splitSite > &splitSites )	
+		{
+			std::vector<struct _block> rawExonBlocks = exonBlocks ;
+			int i, j ;
+			int tag = 0 ;
+			int bsize = rawExonBlocks.size() ; 
+			int ssize = splitSites.size() ;
+
+			// Make sure not overflow
+			struct _splitSite tmp ;
+			tmp.pos = -1 ;
+			splitSites.push_back( tmp ) ;
+
+			exonBlocks.clear() ;
+			for ( i = 0 ; i < bsize ; ++i )
+			{
+				while ( tag < ssize && ( splitSites[tag].chrId < rawExonBlocks[i].chrId ||
+							( splitSites[tag].chrId == rawExonBlocks[i].chrId && splitSites[tag].pos < rawExonBlocks[i].start ) ) )
+					++tag ;
+
+				int l ;
+				for ( l = tag ; l < ssize ; ++l )
+					if ( splitSites[l].chrId != rawExonBlocks[i].chrId || splitSites[l].pos > rawExonBlocks[i].end )
+						break ;
+				int64_t start = rawExonBlocks[i].start ;
+				int64_t end = rawExonBlocks[i].end ;
+				//printf( "%lld %lld\n", start, end ) ;
+				//printf( "%s %s: %d %d\n", alignments.GetChromName( splitSites[tag].chrId ), alignments.GetChromName( rawExonBlocks[i].chrId ), tag, l ) ;
+				for ( j = tag ; j <= l ; ++j )
+				{
+					int leftType = 0 ;
+					int rightType = 0 ;
+					if ( j > tag )	
+					{
+						start = splitSites[j - 1].pos ; // end is from previous stage
+						leftType = splitSites[j - 1].type ;
+					}
+					else
+						start = rawExonBlocks[i].start ;
+
+					if ( j <= l - 1 )
+					{
+						end = splitSites[j].pos ;
+						rightType = splitSites[j].type ;
+					}
+					else
+						end = rawExonBlocks[i].end ;
+
+					if ( leftType == 2 )
+						++start ;
+					if ( rightType == 1 )
+						--end ;
+
+					struct _block tmpB ;
+					tmpB = rawExonBlocks[i] ;
+					tmpB.start = start ;
+					tmpB.end = end ;
+					tmpB.depthSum = 0 ;
+					tmpB.ratio = 0 ;
+					//printf( "\t%lld %lld\n", start, end ) ;
+					tmpB.leftType = leftType ;
+					tmpB.rightType = rightType ;
+					tmpB.depth = NULL ;
+
+					exonBlocks.push_back( tmpB ) ;
+					// handle the soft boundary is the same as the hard boundary case 
+					// or adjacent splice sites
+					/*if ( j == tag && start == end )
+					{
+						exonBlocks.pop_back() ;
+						--end ;
+					}
+					else if ( j == l && start > end )
+					{
+						exonBlocks.pop_back() ;
+					}*/
+					if ( start > end 
+						//|| ( tmpB.start == rawExonBlocks[i].start && tmpB.end != rawExonBlocks[i].end && tmpB.end - tmpB.start + 1 <= 7 ) 
+						//|| ( tmpB.end == rawExonBlocks[i].end && tmpB.start != rawExonBlocks[i].start && tmpB.end - tmpB.start + 1 <= 7  )) // the case of too short overhang
+						|| ( tmpB.leftType == 0 && tmpB.rightType == 2 && tmpB.end - tmpB.start + 1 <= 9 )
+						|| ( tmpB.leftType == 1 && tmpB.rightType == 0 && tmpB.end - tmpB.start + 1 <= 9 ) )
+					{
+						exonBlocks.pop_back() ;
+					}
+					/*else if ( start == end )
+					{
+
+					}*/
+				}
+			}
+			BuildBlockChrIdOffset() ;
+		}
+
+		void ComputeDepth( Alignments &alignments ) 
+		{
+			// Go through the alignment list again to fill in the depthSum;
+			int i ;
+			int j ;
+			int tag = 0 ;
+			int blockCnt = exonBlocks.size() ;
+
+			std::vector<struct _block> newExonBlocks ;
+			while ( alignments.Next() )
+			{
+				int segCnt = alignments.segCnt ;
+				struct _pair *segments = alignments.segments ;
+
+				while ( tag < blockCnt && ( exonBlocks[tag].chrId < alignments.GetChromId() || 
+							( exonBlocks[tag].chrId == alignments.GetChromId() && exonBlocks[tag].end < segments[0].a ) ) )
+				{
+					AdjustAndCreateExonBlocks( tag, newExonBlocks ) ;
+					++tag ;
+				}
+				for ( i = 0 ; i < segCnt ; ++i )
+				{
+					for ( j = tag ; j < blockCnt && ( exonBlocks[j].chrId == alignments.GetChromId() && exonBlocks[j].start <= segments[i].b ) ; ++j )
+					{
+						int64_t s = -1, e = -1 ;
+						exonBlocks[j].depthSum += Overlap( segments[i].a, segments[i].b, exonBlocks[j].start, exonBlocks[j].end, s, e ) ; 
+						if ( s == -1 )
+							continue ;
+
+						if ( exonBlocks[j].depth == NULL )
+						{
+							int len = exonBlocks[j].end - exonBlocks[j].start + 1 ;
+							exonBlocks[j].depth = new int[len + 1] ;
+							memset( exonBlocks[j].depth, 0, sizeof( int ) * ( len + 1 ) ) ;
+							exonBlocks[j].leftSplice = exonBlocks[j].start ;
+							exonBlocks[j].rightSplice = exonBlocks[j].end ;
+						}
+						int *depth = exonBlocks[j].depth ;
+						++depth[s - exonBlocks[j].start] ;
+						--depth[e - exonBlocks[j].start + 1] ; // notice the +1 here, since the decrease of coverage actually happens at next base.
+
+						// record the longest alignment stretch support the splice site.
+						if ( exonBlocks[j].leftType == 1 && segments[i].a == exonBlocks[j].start 
+							&& e > exonBlocks[j].leftSplice )
+						{
+							exonBlocks[j].leftSplice = e ;	
+						}
+						if ( exonBlocks[j].rightType == 2 && segments[i].b == exonBlocks[j].end 
+							&& s < exonBlocks[j].rightSplice )
+						{
+							exonBlocks[j].rightSplice = s ;	
+						}
+					}
+				}
+			}
+
+			for ( ; tag < blockCnt ; ++tag )
+				AdjustAndCreateExonBlocks( tag, newExonBlocks ) ;
+			exonBlocks.clear() ;
+
+			// Due to multi-alignment, we may skip some alignments that determines leftSplice and
+			// rightSplice, hence filtered some subexons. As a result, some subexons' anchor subexon will disapper
+			// and we need to change its boundary type.
+			blockCnt = newExonBlocks.size() ;
+			for ( i = 0 ; i < blockCnt ; ++i )
+			{
+				if ( ( i == 0 && newExonBlocks[i].leftType == 2 ) ||
+					( i > 0 && newExonBlocks[i].leftType == 2 && newExonBlocks[i - 1].end + 1 != newExonBlocks[i].start ) )
+				{
+					newExonBlocks[i].leftType = 0 ;
+				}
+
+				if ( ( i == blockCnt - 1 && newExonBlocks[i].rightType == 1 ) ||
+					( i < blockCnt - 1 && newExonBlocks[i].rightType == 1 && 
+						newExonBlocks[i].end + 1 != newExonBlocks[i + 1].start ) )
+					newExonBlocks[i].rightType = 0 ;
+			}
+			exonBlocks = newExonBlocks ;
+		}
+
+		// If two blocks whose soft boundary are close to each other, we can merge them.
+		void MergeNearBlocks()
+		{
+			std::vector<struct _block> rawExonBlocks = exonBlocks ;
+			int i, k ;
+			int bsize = rawExonBlocks.size() ; 
+			int *newIdx = new int[bsize] ; // used for adjust prev and next. Note that by merging, it won't change the number of prevCnt or nextCnt.
+			
+			exonBlocks.clear() ;
+			exonBlocks.push_back( rawExonBlocks[0] ) ;
+			k = 0 ;
+			newIdx[0] = 0 ;
+			for ( i = 1 ; i < bsize ; ++i )	
+			{
+				if ( rawExonBlocks[i].chrId == exonBlocks[k].chrId 
+					&& rawExonBlocks[i].leftType == 0 && exonBlocks[k].rightType == 0 
+					&& rawExonBlocks[i].start - exonBlocks[k].end - 1 <= 50 
+					&& rawExonBlocks[i].depthSum / double( rawExonBlocks[i].end - rawExonBlocks[i].start + 1 ) < 3.0 
+					&& exonBlocks[k].depthSum / double( exonBlocks[k].end - exonBlocks[i].start + 1 ) < 3.0 )
+				{
+					exonBlocks[k].end = rawExonBlocks[i].end ;
+					exonBlocks[k].rightType = rawExonBlocks[i].rightType ;
+					exonBlocks[k].rightStrand = rawExonBlocks[i].rightStrand ;
+					exonBlocks[k].depthSum += rawExonBlocks[i].depthSum ;
+					if ( rawExonBlocks[i].rightSplice != -1 )
+						exonBlocks[k].rightSplice = rawExonBlocks[i].rightSplice ;
+
+					if ( exonBlocks[k].nextCnt > 0 )	
+						delete[] exonBlocks[k].next ;
+					exonBlocks[k].nextCnt = rawExonBlocks[i].nextCnt ;
+					exonBlocks[k].next = rawExonBlocks[i].next ;
+				}
+				else
+				{
+					exonBlocks.push_back( rawExonBlocks[i] ) ;
+					++k ;
+				}
+				newIdx[i] = k ;
+			}
+			BuildBlockChrIdOffset() ;
+			bsize = exonBlocks.size() ;
+			for ( i = 0 ; i < bsize ; ++i )
+			{
+				int cnt = exonBlocks[i].prevCnt ;
+				for ( k = 0 ; k < cnt ; ++k )
+					exonBlocks[i].prev[k] = newIdx[ exonBlocks[i].prev[k] ] ;
+
+				cnt = exonBlocks[i].nextCnt ;
+				for ( k = 0 ; k < cnt ; ++k )
+					exonBlocks[i].next[k] = newIdx[ exonBlocks[i].next[k] ] ;
+			}
+			delete[] newIdx ;
+		}
+
+		void AddIntronInformation( std::vector<struct _splitSite> &sites, Alignments &alignments )
+		{
+			// Add the connection information, support information and the strand information.
+			int i, j, k, tag ;
+			tag = 0 ;
+			int scnt = sites.size() ;
+			int exonBlockCnt = exonBlocks.size() ;
+			bool flag ;
+
+			for ( i = 0 ; i < exonBlockCnt ; ++i )
+			{
+				exonBlocks[i].prevCnt = exonBlocks[i].nextCnt = 0 ;
+				exonBlocks[i].prev = exonBlocks[i].next = NULL ;
+				exonBlocks[i].leftStrand = exonBlocks[i].rightStrand = '.' ;
+				exonBlocks[i].leftSplice = exonBlocks[i].rightSplice = 0 ;
+			}
+			
+			// Now, we add the region id and compute the length of each region, here the region does not contain possible IR event.
+			int regionId = 0 ;
+			for ( i = 0 ; i < exonBlockCnt ; )
+			{
+				if ( exonBlocks[i].leftType == 2 && exonBlocks[i].rightType == 1 )
+				{
+					j = i + 1 ;
+				}
+				else
+					for ( j = i + 1 ; j < exonBlockCnt ; ++j )
+						if ( exonBlocks[j].start > exonBlocks[j - 1].end + 1 || ( exonBlocks[j].leftType == 2 && exonBlocks[j].rightType == 1 ) )
+							break ;
+				for ( k = i ; k < j ; ++k )
+					exonBlocks[k].contigId = regionId ;
+				++regionId ;
+				i = j ;
+			}
+			int *regionLength = new int[regionId] ;
+			memset( regionLength, 0, sizeof( int ) * regionId ) ;
+			for ( i = 0 ; i < exonBlockCnt ; ++i )
+			{
+				regionLength[ exonBlocks[i].contigId ] += exonBlocks[i].end - exonBlocks[i].start + 1 ;
+			}
+
+			for ( i = 0 ; i < scnt ; )	
+			{
+				for ( j = i ; j < scnt ; ++j )		
+				{
+					if ( sites[j].chrId != sites[i].chrId ||
+							sites[j].pos != sites[i].pos ||
+							sites[j].type != sites[i].type )
+						break ;
+				}
+				// [i,j-1] are the indices of the sites with same coordinate
+				// It is possible a sites corresponds to 2 strands, then we should only keep one of them.
+				char strand = '.' ;
+				int strandSupport[2] = {0, 0};
+				for ( k = i ; k < j ; ++k )
+				{
+					if ( sites[k].strand == '-' )
+						strandSupport[0] += sites[k].support ;
+					else if ( sites[k].strand == '+' )
+						strandSupport[1] += sites[k].support ;
+				}
+				if ( strandSupport[0] > strandSupport[1] )
+					strand = '-' ;
+				else if ( strandSupport[1] > strandSupport[0] )
+					strand = '+' ;
+
+
+				int cnt = j - i ;
+				// Locate the first subexon that can overlap with this site
+				while ( tag < exonBlockCnt )
+				{
+					if ( ( exonBlocks[tag].chrId == sites[i].chrId && exonBlocks[tag].end >= sites[i].pos ) 
+						|| exonBlocks[tag].chrId > sites[i].chrId )
+						break ;
+					++tag ;
+				}
+				flag = false ;
+				for ( k = tag; k < exonBlockCnt ; ++k )
+				{
+					if ( exonBlocks[tag].start > sites[i].pos ||
+						exonBlocks[tag].chrId > sites[i].chrId )
+						break ;
+
+					if ( exonBlocks[tag].start == sites[i].pos ||
+						exonBlocks[tag].end == sites[i].pos )
+					{
+						flag = true ;
+						break ;
+					}
+				}
+				
+				if ( !flag )
+				{
+					i = j ; 
+					continue ;
+				}
+
+				if ( sites[i].type == 1 && exonBlocks[tag].start == sites[i].pos )
+				{
+					exonBlocks[tag].prevCnt = 0 ;
+					exonBlocks[tag].prev = new int[cnt] ;
+					exonBlocks[tag].leftStrand = strand ;
+
+					// And we also need to put the "next" here.
+					// Here we assume the oppositePos sorted in increasing order
+					k = tag - 1 ;
+					for ( int l = j - 1 ; l >= i ; --l )
+					{
+						for ( ; k >= 0 ; --k )			
+						{
+							if ( exonBlocks[k].end < sites[l].oppositePos || exonBlocks[k].chrId != sites[l].chrId )
+								break ;
+							if ( exonBlocks[k].end == sites[l].oppositePos ) //&& exonBlocks[k].rightType == sites[l].type )
+							{
+								if ( sites[l].strand != strand || 
+									sites[l].strand != exonBlocks[k].rightStrand )
+									break ;
+								exonBlocks[k].next[ exonBlocks[k].nextCnt ] = tag ;
+								exonBlocks[tag].prev[ exonBlocks[tag].prevCnt] = k ; // Note that the prev are sorted in decreasing order
+								++exonBlocks[k].nextCnt ;
+								++exonBlocks[tag].prevCnt ;
+								double factor = 1.0 ;
+								if ( regionLength[ exonBlocks[k].contigId ] < alignments.readLen )
+								{
+									int left ;
+									for ( left = k ; left >= 0 ; --left )
+										if ( exonBlocks[left].contigId != exonBlocks[k].contigId )
+											break ;
+									++left ;
+
+									int prevType = 0 ;
+									// only consider the portion upto k.
+									for ( int m = left ; m <= k ; ++m )
+										if ( exonBlocks[m].leftType == 1 )	
+											++prevType ;
+
+									if ( prevType == 0 )
+										factor = 2 * (double)alignments.readLen / regionLength[ exonBlocks[k].contigId ] ;
+								}
+								if ( regionLength[ exonBlocks[tag].contigId ] < alignments.readLen )
+								{
+									int right ;
+									for ( right = tag ; right < exonBlockCnt ; ++right )
+										if ( exonBlocks[right].contigId != exonBlocks[tag].contigId )
+											break ;
+									--right ;
+
+									int nextType = 0 ;
+									for ( int m = tag ; m <= right ; ++m )
+										if ( exonBlocks[m].rightType == 2 )
+											++nextType ;
+
+									if ( nextType == 0 )
+										factor = 2 * (double)alignments.readLen / regionLength[ exonBlocks[tag].contigId ] ;
+								}
+								if ( factor > 10 )
+									factor = 10 ;
+								
+								if ( exonBlocks[k].contigId != exonBlocks[tag].contigId ) // the support of introns between regions.
+								{
+									// Adjust the support if one of the anchor exon is too short.
+									// This avoid the creation of alternative 3'/5' end due to low coverage from too short anchor.
+									exonBlocks[tag].leftSplice += sites[l].support * factor ;
+									exonBlocks[k].rightSplice += sites[l].support * factor ;
+								}
+								break ;
+							}
+						}
+					}
+				}
+				else if ( sites[i].type == 2 && exonBlocks[tag].end == sites[i].pos )
+				{
+					exonBlocks[tag].nextCnt = 0 ; // cnt ; it should reach cnt after putting the ids in
+					exonBlocks[tag].next = new int[cnt] ;
+					exonBlocks[tag].rightStrand = strand ;
+				}
+
+				i = j ;
+			}
+			// Reverse the prev list
+			for ( i = 0 ; i < exonBlockCnt ; ++i )
+			{
+				for ( j = 0, k = exonBlocks[i].prevCnt - 1 ; j < k ; ++j, --k )
+				{
+					int tmp = exonBlocks[i].prev[j] ;
+					exonBlocks[i].prev[j] = exonBlocks[i].prev[k] ;
+					exonBlocks[i].prev[k] = tmp ;
+				}
+			}
+
+			// If all of the subexon anchored the intron are filtered, we need to change the type of the other anchor.
+			for ( i = 0 ; i < exonBlockCnt ; ++i )		
+			{
+				if ( exonBlocks[i].leftType == 1 && exonBlocks[i].prevCnt == 0 )	
+				{
+					exonBlocks[i].leftType = 0 ;
+					exonBlocks[i].leftStrand = '.' ;
+					if ( i > 0 && exonBlocks[i - 1].rightType == 1 )	
+						exonBlocks[i - 1].rightType = 0 ;
+				}
+				if ( exonBlocks[i].rightType == 2 && exonBlocks[i].nextCnt == 0 )
+				{
+					exonBlocks[i].rightType = 0 ;
+					exonBlocks[i].rightStrand = '.' ;
+					if ( i < exonBlockCnt - 1 && exonBlocks[i + 1].leftType == 2 )
+						exonBlocks[i + 1].leftType = 0 ;
+				}
+			}
+			MergeNearBlocks() ;
+
+			delete[] regionLength ;
+		}
+
+		double PickLeftAndRightRatio( double l, double r )
+		{
+			if ( l >= 0 && r >= 0 )
+				return l < r ? l : r ;
+			else if ( l < 0 && r < 0 )
+				return -1 ;
+			else if ( l < 0 )
+				return r ;
+			else
+				return l ;
+		}
+			
+		double PickLeftAndRightRatio( const struct _block &b )
+		{
+			return PickLeftAndRightRatio( b.leftRatio, b.rightRatio ) ;
+		}
+
+		void ComputeRatios()
+		{
+			int i, j ;
+			int exonBlockCnt = exonBlocks.size() ;		
+			for ( i = 0 ; i < exonBlockCnt ; ++i )
+			{
+				exonBlocks[i].leftRatio = -1 ;
+				exonBlocks[i].rightRatio = -1 ;
+				if ( exonBlocks[i].leftType == 2 && exonBlocks[i].rightType == 1 )
+				{
+					// ]...[
+					double anchorAvg = 0 ;
+					double avgDepth = GetAvgDepth( exonBlocks[i] ) ;
+					if ( i >= 1 && exonBlocks[i - 1].chrId == exonBlocks[i].chrId )
+					{
+						anchorAvg = GetAvgDepth( exonBlocks[i - 1] ) ;	
+						if ( anchorAvg > 1 && avgDepth > 1 )
+							exonBlocks[i].leftRatio = ( avgDepth - 1 ) / ( anchorAvg - 1 ) ;  
+					}
+					if ( i < exonBlockCnt - 1 && exonBlocks[i + 1].chrId == exonBlocks[i].chrId )
+					{
+						anchorAvg = GetAvgDepth( exonBlocks[i + 1] ) ;	
+						if ( anchorAvg > 1 && avgDepth > 1 )
+							exonBlocks[i].rightRatio = ( avgDepth - 1 ) / ( anchorAvg - 1 ) ;  
+					}
+				}
+
+				if ( exonBlocks[i].leftType == 0 && exonBlocks[i].rightType == 1 ) 
+				{
+					// (..[ , overhang subexon.
+					double avgDepth = GetAvgDepth( exonBlocks[i] ) ;
+					double anchorAvg = GetAvgDepth( exonBlocks[i + 1] ) ;
+					if ( avgDepth > 1 && anchorAvg > 1 )
+						exonBlocks[i].rightRatio = ( avgDepth - 1 ) / ( anchorAvg - 1 ) ;
+				}
+
+				/*if ( exonBlocks[i].leftType == 1 )
+				{
+					// For the case (...[, the leftRatio is actuall the leftratio of the subexon on its right. 	
+					int len = 0 ;
+					double depthSum = 0 ;
+					int tag = i ;
+					
+					for ( j = 0 ; j < exonBlocks[tag].prevCnt ; ++j )
+					{
+						int k = exonBlocks[tag].prev[j] ;
+						len += ( exonBlocks[k].end - exonBlocks[k].start + 1 ) ;		
+						depthSum += exonBlocks[k].depthSum ;	
+					}
+					double otherAvgDepth = depthSum / len ;
+					double avgDepth = GetAvgDepth( exonBlocks[tag] ) ;
+
+					// adjust avgDepth by looking into the following exon blocks(subexon) in the same region whose left side is not hard end
+					for ( j = tag + 1 ; j < exonBlockCnt ; ++j )
+					{
+						if ( exonBlocks[j].start != exonBlocks[j - 1].end + 1 || exonBlocks[j].leftType == 1 )
+							break ;
+						double tmp = GetAvgDepth( exonBlocks[j] ) ;
+						if ( tmp > avgDepth )
+							avgDepth = tmp ;
+					}
+
+					if ( avgDepth < 1 )
+						avgDepth = 1 ;
+					if ( otherAvgDepth < 1 )
+						otherAvgDepth = 1 ;
+
+					//exonBlocks[i].leftRatio = pow( log( avgDepth ) / log(2.0), 2.0 / 3.0 ) - pow( log( otherAvgDepth ) / log( 2.0 ), 2.0 / 3.0 );
+					exonBlocks[i].leftRatio = sqrt( avgDepth ) - log( avgDepth ) - ( sqrt( otherAvgDepth ) + log( otherAvgDepth ) ) ;
+
+				}*/
+				if ( exonBlocks[i].rightType == 0 && exonBlocks[i].leftType == 2  ) 
+				{
+					// for overhang subexon.
+					double avgDepth = GetAvgDepth( exonBlocks[i] ) ;
+					double anchorAvg = GetAvgDepth( exonBlocks[i - 1] ) ;
+					if ( avgDepth > 1 && anchorAvg > 1 )
+						exonBlocks[i].leftRatio = ( avgDepth - 1 ) / ( anchorAvg - 1 ) ;
+
+				}
+				/*if ( exonBlocks[i].rightType == 2 ) 
+				{
+					int len = 0 ;
+					double depthSum = 0 ;
+					int tag = i ;
+					
+					for ( j = 0 ; j < exonBlocks[tag].nextCnt ; ++j )
+					{
+						int k = exonBlocks[tag].next[j] ;
+						len += ( exonBlocks[k].end - exonBlocks[k].start + 1 ) ;		
+						depthSum += exonBlocks[k].depthSum ;	
+					}
+					double otherAvgDepth = depthSum / len ;
+					double avgDepth = GetAvgDepth( exonBlocks[tag] ) ;
+					
+					// adjust avgDepth by looking into the earlier exon blocks(subexon) in the same region whose right side is not hard end
+					for ( j = tag - 1 ; j >= 0 ; --j )
+					{
+						if ( exonBlocks[j].end + 1 != exonBlocks[j + 1].start || exonBlocks[j].rightType == 2 )
+							break ;
+						double tmp = GetAvgDepth( exonBlocks[j] ) ;
+						if ( tmp > avgDepth )
+							avgDepth = tmp ;
+					}
+
+					if ( avgDepth < 1 )
+						avgDepth = 1 ;
+					if ( otherAvgDepth < 1 )
+						otherAvgDepth = 1 ;
+
+					exonBlocks[i].rightRatio = sqrt( avgDepth ) - log( avgDepth ) - ( sqrt( otherAvgDepth ) + log( otherAvgDepth ) ) ;
+					//pow( log( avgDepth ) / log(2.0), 2.0 / 3.0 ) - pow( log( otherAvgDepth ) / log(2.0), 2.0 / 3.0 );
+				}*/
+				// The remaining case the islands, (...)
+			}
+
+			// go through each region of subexons, and only compute the ratio for the first and last hard boundary
+			for ( i = 0 ; i < exonBlockCnt ; )
+			{
+				// the blocks from [i,j) corresponds to a region, namely consecutive subexons.
+				for ( j = i + 1 ; j < exonBlockCnt ; ++j )
+					if ( exonBlocks[j].contigId != exonBlocks[i].contigId )
+						break ;
+
+				int leftSupport = 0 ;
+				int rightSupport = 0 ;
+				int leftTag = j, rightTag = i - 1  ; 
+				for ( int k = i ; k < j ; ++k )
+				{
+					if ( exonBlocks[k].leftType == 1 && exonBlocks[k].leftSplice > 0 )	
+					{
+						leftSupport += exonBlocks[k].leftSplice ;
+						if ( k < leftTag )
+							leftTag = k ;
+					}
+					if ( exonBlocks[k].rightType == 2 && exonBlocks[k].rightSplice > 0 )
+					{
+						rightSupport += exonBlocks[k].rightSplice ;
+						if ( k > rightTag )
+							rightTag = k ;
+					}
+				}
+
+				if ( leftSupport > 0 && rightSupport > 0 )
+				{
+					// when the right splice support is much greater than that of the left side, there should be a soft boundary for the left side.
+					// Wether we want to include this soft boundary or not will be determined in class, when it looked at whether the overhang block
+					// 	should be kept or not.
+					exonBlocks[ leftTag ].leftRatio = sqrt( rightSupport ) - log( ( rightSupport + leftSupport ) * 0.5 ) - ( sqrt( leftSupport ) ) ; //+ log( leftSupport ) ) ;
+					exonBlocks[ rightTag ].rightRatio = sqrt( leftSupport ) - log( ( rightSupport + leftSupport ) * 0.5 ) - ( sqrt( rightSupport ) ) ; //+ log( rightSupport ) ) ;
+				}
+
+				i = j ; // don't forget this.
+			}
+		}
+} ;
+
+#endif