Description: Fix wrong function parameters in ungap tool
 This missing parameter in a function call was likely missed as the ungap
 tool is not built if simply 'make' is run.
Author: Sascha Steinbiss <sascha@steinbiss.name>
--- a/src/ungap.cpp
+++ b/src/ungap.cpp
@@ -17,7 +17,7 @@
 	TRegionScan ( chrvec &_chrs , TChromosomalIndices &_index ) : TChromosomeAlign ( _chrs , _index ) {} ;
 	void assemble_leftovers ( int cnt ) ;
 	vector <TLeftovers> leftovers ;
-	
+
 	protected:
 	virtual uint align_solexa_paired_read ( const string &name , const string &sequence , string quality , uint read_length_1 , uint fragment_length , uint range ) ;
 	int get_overlap ( TLeftovers &l1 , TLeftovers &l2 ) ;
@@ -52,7 +52,7 @@
 /*
 	string s1 = l1.seq.substr ( o , l1.seq.length() - o ) ;
 	string s2 = l2.seq ;
-	
+
 	if ( s1.length() < s2.length() ) s2 = s2.substr ( 0 , s1.length() ) ;
 	else if ( s2.length() < s1.length() ) s1 = s1.substr ( 0 , s2.length() ) ;
 	if ( s1 != s2 ) return -1 ; // No match
@@ -63,9 +63,9 @@
 void TRegionScan::assemble_leftovers ( int cnt ) {
 	uint a , b ;
 	vector <TLeftovers> lo ;
-	
+
 	cout << "Assembling, depth " << cnt << endl ;
-	
+
 	for ( a = 0 ; a+1 < leftovers.size() ; a++ ) {
 		for ( b = a+1 ; b < leftovers.size() ; b++ ) {
 			int o = get_overlap ( leftovers[a] , leftovers[b] ) ;
@@ -77,30 +77,30 @@
 		}
 	}
 	if ( cnt <= 0 ) return ;
-	
+
 	for ( a = 0 ; a < leftovers.size() ; a++ ) {
 		if ( leftovers[a].used ) continue ;
 		lo.push_back ( leftovers[a] ) ;
 	}
-	
+
 	// Add unique sequences as new source set
 	sort ( lo.begin() , lo.end() ) ;
 	leftovers.clear() ;
 	for ( a = 0 ; a < lo.size() ; a++ ) {
 		if ( a == 0 || lo[a-1].seq != lo[a].seq ) leftovers.push_back ( lo[a] ) ;
 	}
-	
+
 	assemble_leftovers ( cnt - 1 ) ;
 }
 
 uint TRegionScan::align_solexa_paired_read ( const string &name , const string &sequence , string quality , uint read_length_1 , uint fragment_length , uint range ) {
 	string seq1 = sequence.substr ( 0 , read_length_1 ) ;
 	string seq2 = sequence.substr ( read_length_1 , sequence.length() - read_length_1 ) ;
-	
+
 	while ( quality.length() < sequence.length() ) quality += (char) 33+30 ;
 	string qual1 = quality.substr ( 0 , read_length_1 ) ;
 	string qual2 = quality.substr ( read_length_1 , sequence.length() - read_length_1 ) ;
-	
+
 	pwi_vector res1 , res2 ;
 	get_align_solexa_read ( seq1.c_str() , res1 ) ;
 	get_align_solexa_read ( seq2.c_str() , res2 ) ;
@@ -112,7 +112,7 @@
 	int ret = 0 ;
 	ret += paired_read_combine ( res1 , res2 , maxfrag/2 , maxfrag/2 , read_length_1 , seq1 , qual1 , seq2 , qual2 ) ;
 	ret += paired_read_combine ( res2 , res1 , maxfrag/2 , maxfrag/2 , read_length_1 , seq2 , qual2 , seq1 , qual1 ) ;
-	
+
 	if ( ret == 0 && res1.size() + res2.size() == 1 ) {
 		string seq ;
 		int newpos , chr ;
@@ -136,7 +136,7 @@
 			leftovers.push_back ( l ) ;
 		}
 	}
-	
+
 	return ret ;
 }
 
@@ -185,7 +185,7 @@
 	int c ;
 	int option_index = 0;
 	while ( -1 != ( c = getopt_long (argc, argv, "g:a::q::s::f::p::b::r::w::n::",long_options, NULL) ) ) {
-		
+
 		switch ( c ) {
 			case 0 : break ;
 			case 'g' : genome_file = optarg ; break ;
@@ -214,7 +214,7 @@
 	if ( name.empty() ) die_with_description("No name given!") ; // Need one
 	if ( from == 0 ) die_with_description("Needs --from!") ; // Need one
 	if ( to == 0 ) die_with_description("Needs --to!") ; // Need one
-	
+
 
 	// Incorporating known SNPs and indexing chromosomes
 	init_iupac () ;
@@ -223,7 +223,7 @@
 	index.max_snps_per_index = mspi ;
 	vector <TChromosome> chrs ;
 	load_all_chromosomes ( genome_file , chrs ) ;
-	
+
 	if ( !gff_file.empty() ) incorporate_all_gff ( gff_file , chrs ) ;
 	if ( !simple_snp_file.empty() ) incorporate_simple_snps ( simple_snp_file , chrs ) ;
 
@@ -240,7 +240,7 @@
 	cout << "Keeping " << chrs[0].sequence.length() << " bases from " << chromosome << endl ;
 
 	index.run ( &chrs ) ;
-	
+
 	// Now look at the SOlexa reads and do the thing
 	TRegionScan ca ( chrs , index ) ;
 	if ( !coverage_file.empty() ) ca.coverage = fopen ( coverage_file.c_str() , "w" ) ;
@@ -258,9 +258,9 @@
 		ca.using_bins = true ;
 	}
 */
-	ca.align_solexa_paired ( fastq_file , pair_length , fragment_length , variance ) ;
+	ca.align_solexa_paired ( genome_file, fastq_file , pair_length , fragment_length , variance ) ;
 //	ca.assemble_leftovers ( 2 ) ;
-	
+
 	string fasta_output = name + ".fasta" ;
 	fstream filestr;
 	filestr.open ( fasta_output.c_str() , fstream::out ); //| fstream::app);
