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(-)wise2.4.0alpha.old/src/HMMer2/prior.c (+1 lines)
Lines 4-9 Link Here
4 
 * Support for Dirichlet prior data structure, p7prior_s.
 4 
 * Support for Dirichlet prior data structure, p7prior_s.
5 
 */
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 */
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              7
              
#include <string.h>

            

        

          7
          
#include "config.h"

          8
          
#include "config.h"

        

        

          8
          
#include "structs.h"

          9
          
#include "structs.h"

        

        

          9
          
#include "funcs.h" 

          10
          
#include "funcs.h" 

        

        

          10
          

          11
          

        



(-)wise2.4.0alpha.old/src/dynlibsrc/hsplookupthreaded.h
      (-1 / +1 lines)




  

    
      
            Lines 6-12
          
      
      
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          6
          
#include "hsplookupscan.h"

          6
          
#include "hsplookupscan.h"

        

        

          7
          
#include "hsphandler.h"

          7
          
#include "hsphandler.h"

        

        

          8
          
#include "arrayseqlookup.h"

          8
          
#include "arrayseqlookup.h"

        

          
            

              9
              


              9
              
#include <sys/time.h>

            

        

          10
          

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#define MAX_HSP_THREADS 64

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#define MAX_HSP_THREADS 64

        

        

          12
          

          12
          

        



(-)wise2.4.0alpha.old/src/external/mott/mott_api.c
      (+2 lines)




  

    
      
            Lines 1-6
          
      
      
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          1
          
#include<stdio.h>

          1
          
#include<stdio.h>

        

        

          2
          
#include<limits.h>

          2
          
#include<limits.h>

        

        

          3
          
#include<math.h>

          3
          
#include<math.h>

        

            

              
              
              4
              
#include <stdlib.h>

            

            

              5
              
#include <ctype.h>

            

        

          4
          
#include"gapstat.h"

          6
          
#include"gapstat.h"

        

        

          5
          

          7
          

        

        

          6
          
double default_lambda0, default_K0, default_Kplus, default_H, default_r, default_s, default_alpha;

          8
          
double default_lambda0, default_K0, default_Kplus, default_H, default_r, default_s, default_alpha;

        



(-)wise2.4.0alpha.old/src/socket/functionclient.c
      (-1 / +1 lines)




  

    
      
            Lines 181-187
          
      
      
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          181
          
  bcopy( hp->h_addr, &server.sin_addr, hp->h_length);

          181
          
  bcopy( hp->h_addr, &server.sin_addr, hp->h_length);

        

        

          182
          
  server.sin_port = htons(port);

          182
          
  server.sin_port = htons(port);

        

        

          183
          

          183
          

        

          
            

              184
              
  connect(out->socket, &server, sizeof(server));


              184
              
  connect(out->socket, (struct sockaddr *)&server, sizeof(server));

            

        

          185
          
  

          185
          
  

        

        

          186
          

          186
          

        

        

          187
          
  return out;

          187
          
  return out;

        



(-)wise2.4.0alpha.old/src/dnaindex/kmer_assembly_untangler.c
      (-1 / +1 lines)




  

    
      
            Lines 641-647
          
      
      
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          641
          

        

        

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          643
          
# line 660 "kmer_assembly_untangler.dy"

          643
          
# line 660 "kmer_assembly_untangler.dy"

        

          
            

              644
              
void lift_backward_tangled_tail(KmerAssemblyIndex * kai,KmerAssemblyLink * new,KmerAssemblyPath * tail,int * start_label,SinglePosSequence ** positions,int label_len)


              644
              
void lift_backward_tangled_tail(KmerAssemblyIndex * kai,KmerAssemblyLink * new,KmerAssemblyPath * tail,long int * start_label,SinglePosSequence ** positions,int label_len)

            

        

          645
          
{

          645
          
{

        

        

          646
          
  int i;

          646
          
  int i;

        

        

          647
          
  int j;

          647
          
  int j;

        



(-)wise2.4.0alpha.old/src/dnaindex/kmer_assembly_untangler.h
      (-1 / +1 lines)




  

    
      
            Lines 171-177
          
      
      
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          171
          
#define old_attempt_forward_untangle_KmerAssembly Wise2_old_attempt_forward_untangle_KmerAssembly

          171
          
#define old_attempt_forward_untangle_KmerAssembly Wise2_old_attempt_forward_untangle_KmerAssembly

        

        

          172
          
void Wise2_lift_forward_tangled_tail(KmerAssemblyIndex * kai,KmerAssemblyPath * tail,long int * start_label,int label_len);

          172
          
void Wise2_lift_forward_tangled_tail(KmerAssemblyIndex * kai,KmerAssemblyPath * tail,long int * start_label,int label_len);

        

        

          173
          
#define lift_forward_tangled_tail Wise2_lift_forward_tangled_tail

          173
          
#define lift_forward_tangled_tail Wise2_lift_forward_tangled_tail

        

          
            

              174
              
void Wise2_lift_backward_tangled_tail(KmerAssemblyIndex * kai,KmerAssemblyLink * new,KmerAssemblyPath * tail,int * start_label,SinglePosSequence ** positions,int label_len);


              174
              
void Wise2_lift_backward_tangled_tail(KmerAssemblyIndex * kai,KmerAssemblyLink * new,KmerAssemblyPath * tail,long int * start_label,SinglePosSequence ** positions,int label_len);

            

        

          175
          
#define lift_backward_tangled_tail Wise2_lift_backward_tangled_tail

          175
          
#define lift_backward_tangled_tail Wise2_lift_backward_tangled_tail

        

        

          176
          
KmerAssemblyPath * Wise2_lift_forward_tangled_KmerAssemblyPath(KmerAssemblyIndex * kai,KmerAssemblyPath * kap,long int * start_label,int label_len);

          176
          
KmerAssemblyPath * Wise2_lift_forward_tangled_KmerAssemblyPath(KmerAssemblyIndex * kai,KmerAssemblyPath * kap,long int * start_label,int label_len);

        

        

          177
          
#define lift_forward_tangled_KmerAssemblyPath Wise2_lift_forward_tangled_KmerAssemblyPath

          177
          
#define lift_forward_tangled_KmerAssemblyPath Wise2_lift_forward_tangled_KmerAssemblyPath

        



(-)wise2.4.0alpha.old/src/dnaindex/compressed_protein_index.c
      (-1 / +1 lines)




  

    
      
            Lines 199-205
          
      
      
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          199
          
{

          199
          
{

        

        

          200
          
  fatal("For compressed protein indexes, impossible to add numbers directly");

          200
          
  fatal("For compressed protein indexes, impossible to add numbers directly");

        

        

          201
          

          201
          

        

          
            

              202
              
  return NULL;


              202
              
  return FALSE;

            

        

          203
          
}

          203
          
}

        

        

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# line 226 "compressed_protein_index.dy"

          205
          
# line 226 "compressed_protein_index.dy"

        






  

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