[med-svn] [snpomatic] 01/01: remove whitespace-only patch hunks

[Sascha Steinbiss]

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sascha-guest pushed a commit to branch master
in repository snpomatic.

commit 5f9fedfb00c6a7d2ab4b3a87724fc0f7dc77f90d
Author: Sascha Steinbiss <sascha at steinbiss.name>
Date:   Wed Dec 16 09:58:20 2015 +0000

    remove whitespace-only patch hunks
---
 debian/patches/fix_ungap | 120 -----------------------------------------------
 1 file changed, 120 deletions(-)

diff --git a/debian/patches/fix_ungap b/debian/patches/fix_ungap
index 524147b..69ae900 100644
--- a/debian/patches/fix_ungap
+++ b/debian/patches/fix_ungap
@@ -4,126 +4,6 @@ Description: Fix wrong function parameters in ungap tool
 Author: Sascha Steinbiss <sascha at 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 ;
  	}

-- 
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