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init.cpp
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#include "init.h"
extern int INDEX_RESOLUTION;
extern int EXONGAP;
extern int READLEN;
extern int RQFACTOR;
extern unsigned CONVERSION_FACTOR;
extern char Char_To_CodeC[256];
extern char Char_To_Code[256];
extern unsigned RQ_Hits;
extern SA* SA_Index;
extern char COMPRESS;
extern int *SA_Blocks;
extern std::map <unsigned, Ann_Info> Annotations;
extern unsigned Location_Array[80];
extern pthread_mutex_t OpenGenomeFileslock;
extern bool SAM_READER;
extern int ORG_STRINGLENGTH;
void Init(BWT *revfmi,unsigned & SOURCELENGTH,FILE* & Input_File,FILE* & Mate_File,FILETYPE & File_Info,Parameters & CL,Index_Info & Genome_Files,int & INIT_MIS_SCAN)
{
EXONGAP=CL.EXONGAP;
SOURCELENGTH = revfmi->textLength;
CONVERSION_FACTOR=revfmi->textLength-RQFACTOR;//+1;
Char_To_Code['N']=0;Char_To_Code['n']=0;
Char_To_Code['A']=0;Char_To_Code['C']=1;Char_To_Code['G']=2;Char_To_Code['T']=3;
Char_To_Code['a']=0;Char_To_Code['c']=1;Char_To_Code['g']=2;Char_To_Code['t']=3;
Char_To_Code['+']='+';Char_To_Code['-']='-';//we are using character count to store the fmicode for acgt
Char_To_CodeC['N']=3;Char_To_CodeC['n']=3;
Char_To_CodeC[0]=3;Char_To_CodeC[1]=2;Char_To_CodeC[2]=1;Char_To_CodeC[3]=0;
Char_To_CodeC['A']=3;Char_To_CodeC['C']=2;Char_To_CodeC['G']=1;Char_To_CodeC['T']=0;
Char_To_CodeC['a']=3;Char_To_CodeC['c']=2;Char_To_CodeC['g']=1;Char_To_CodeC['t']=0;
Char_To_CodeC['-']='-';Char_To_CodeC['+']='+';//we are using character count to store the fmicode for acgt
Open_Files(Input_File,Mate_File,CL);
if(SAM_READER)
{
char SAM_Line[5000];
int Flag;READ Head;SAMREAD SAM;
Read_Again:
if (fgets(SAM_Line,5000,Input_File)!=0)// read a tag...
{
if(*SAM_Line=='@')
goto Read_Again;
sscanf(SAM_Line,"%s %d %s %u %d %s %s %*d %*d %s ",Head.Description,&Flag,SAM.Chr,&SAM.Loc,&SAM.MapQ,SAM.Cigar,Head.Quality,Head.Tag_Copy);
}
else
{
cout << "Init():Error reading file..\n";exit (100);
}
File_Info.STRINGLENGTH=strlen(Head.Tag_Copy);
if (Head.Quality[0]=='*')
{
File_Info.FILETYPE=FA;
}
else
{
assert(strlen(Head.Quality)==File_Info.STRINGLENGTH);
File_Info.FILETYPE=FQ;
}
fseek(Input_File, 0L, SEEK_END);
File_Info.File_Size = ftello64(Input_File);
File_Info.Org_File=Input_File;
fseek(Input_File,0,SEEK_SET);//go top
READLEN=File_Info.TAG_COPY_LEN=File_Info.STRINGLENGTH;
ORG_STRINGLENGTH=READLEN;
}
else
Detect_Input(File_Info,Input_File,Mate_File);
FILE* Inf_File;
if((Inf_File=File_Exist_Open(Genome_Files.INFOFILE)))
{
char String[40];
int Num;
fscanf(Inf_File,"%s%d",String,&Num);
fscanf(Inf_File,"%s%d",String,&INDEX_RESOLUTION);
}
else
{
INDEX_RESOLUTION=30000;
}
if(INIT_MIS_SCAN==-1)
{
if (File_Info.STRINGLENGTH<=80)
{
INIT_MIS_SCAN=1;
}
else if (File_Info.STRINGLENGTH<=100)
{
INIT_MIS_SCAN=2;
}
else
{
INIT_MIS_SCAN=3;
}
}
//fclose(Inf_File);
}
bool Progress_Bar(Parameters & CL,unsigned & Number_of_Tags,unsigned & Progress,unsigned & Tag_Count,FILETYPE & File_Info)
{
Tag_Count++;
Progress++;
if (CL.MAX_TAGS_TO_PROCESS && Tag_Count >= CL.MAX_TAGS_TO_PROCESS) return false;
if (Progress==Number_of_Tags)
{
if (CL.MAX_TAGS_TO_PROCESS)
{
Number_of_Tags=(CL.MAX_TAGS_TO_PROCESS)/20;
Progress=0;
Show_Progress(Tag_Count*100/CL.MAX_TAGS_TO_PROCESS);
}
else
{
off64_t Current_Pos=ftello64(File_Info.Org_File);
unsigned Average_Length=Current_Pos/Tag_Count+1;//+1 avoids divide by zero..
Number_of_Tags=(File_Info.File_Size/Average_Length)/20;
Progress=0;
off64_t Perc= Current_Pos*100/File_Info.File_Size;
Show_Progress(Perc);
}
}
return true;
}
void Load_All_Indexes(Index_Info Genome_Files,BWT* & fwfmi,BWT* & revfmi,MMPool* & mmPool,RANGEINDEX & Range_Index)
{
if(mkdir("Raw_Out",S_IRWXU | S_IRWXG | S_IROTH | S_IXOTH) && errno != EEXIST) {fprintf(stderr,"Cannot create Temp directory..\n");exit(-1);};
fprintf (stderr,"Loading index %s\n",Genome_Files.BWTFILE);
fwfmi= Load_Indexes(Genome_Files.BWTFILE,Genome_Files.OCCFILE,Genome_Files.SAFILE,mmPool);
fprintf (stderr,"Loading index %s\n",Genome_Files.REVBWTINDEX);
revfmi= Load_Indexes(Genome_Files.REVBWTINDEX,Genome_Files.REVOCCFILE,Genome_Files.REVSAFILE,mmPool);
fwfmi->saInterval=revfmi->saInterval;
fprintf (stderr,"Loading Location %s\n",Genome_Files.LOCATIONFILE);
int Genome_Count= Load_Location(Genome_Files.LOCATIONFILE,Annotations,Location_Array);
fprintf (stderr,"Loading packed genome %s\n",Genome_Files.BINFILE);
loadPac(Genome_Files.BINFILE);
fprintf (stderr,"Loading index %s\n",Genome_Files.INDFILE);
Load_Range_Index(Genome_Files.INDFILE,Genome_Files.BLKFILE,Range_Index);
SA_Index=Range_Index.SA_Index;
SA_Blocks=Range_Index.SA_Blocks;
COMPRESS=Range_Index.COMPRESS;
RQ_Hits=Range_Index.Hits;
fprintf(stderr,"Done...\n");
}
/*
* === FUNCTION ======================================================================
* Name: Open_Genome_Files
* Description: Creates an array of existing chromosomes and associates auxilliary files
* and data structures with it.
* =====================================================================================
*/
int Open_Genome_Files(char* LOCATIONFILE,Offset_Record* Genome_Offsets,unsigned Offsets[])
{
pthread_mutex_lock(&OpenGenomeFileslock);
FILE* Location_File=File_Open(LOCATIONFILE,"r");
int Genome_Count=0;
/*if(mkdir("Raw_Out",S_IRWXU | S_IRWXG | S_IROTH | S_IXOTH) && errno != EEXIST)
{
printf("Open_Genome_Files():Cannot create Temp directory..\n");
exit(-1);
}*/
while (fgets(Genome_Offsets[Genome_Count].Genome,39,Location_File)!=0 && Genome_Count<80)
{
Genome_Offsets[Genome_Count].Offset=atoi(Genome_Offsets[Genome_Count].Genome);
fgets(Genome_Offsets[Genome_Count].Genome,39,Location_File);
strcpy(Genome_Offsets[Genome_Count].GenomeM,Genome_Offsets[Genome_Count].Genome);
for(int i=0;i<40;i++)
{
if (Genome_Offsets[Genome_Count].Genome[i] == '\n' ||Genome_Offsets[Genome_Count].Genome[i] == '\r')
{
Genome_Offsets[Genome_Count].Genome[i]=0;
Genome_Offsets[Genome_Count].GenomeM[i]='-';
Genome_Offsets[Genome_Count].GenomeM[i+1]=0;
break;
}
}
//if(MAPMODE) Genome_Offsets[Genome_Count].Out_File=File_Open(Genome_Offsets[Genome_Count].Genome,"w+b");
//else Genome_Offsets[Genome_Count].Out_File=File_Open(Genome_Offsets[Genome_Count].Genome,"r");
Genome_Count++;
}
fclose(Location_File);
for ( int i=1;i<Genome_Count;i++)
{
Offsets[i]=Offsets[i-1]+Genome_Offsets[i].Offset;
//if(MAPMODE)
{
Genome_Offsets[i-1].Junc_Hash=new Hash;
/*string S=Genome_Offsets[i-1].Genome;S="Raw_Out/"+S;Genome_Offsets[i-1].Out_File=File_Open(S.c_str(),"w+b");
S=Genome_Offsets[i-1].GenomeM;S="Raw_Out/"+S;Genome_Offsets[i-1].Out_FileM=File_Open(S.c_str(),"w+b");
S=Genome_Offsets[i-1].Genome;S="Raw_Out/"+S+".U";Genome_Offsets[i-1].Unmapped=File_Open(S.c_str(),"w+b");
S=Genome_Offsets[i-1].GenomeM;S="Raw_Out/"+S+".U";Genome_Offsets[i-1].UnmappedM=File_Open(S.c_str(),"w+b");
S=Genome_Offsets[i-1].Genome;S="Raw_Out/"+S+".UX";Genome_Offsets[i-1].UnmappedX=File_Open(S.c_str(),"w+b");
S=Genome_Offsets[i-1].GenomeM;S="Raw_Out/"+S+".UX";Genome_Offsets[i-1].UnmappedXM=File_Open(S.c_str(),"w+b");*/
}
/*else
{
string S=Genome_Offsets[i-1].Genome;S="Raw_Out/"+S;Genome_Offsets[i-1].Out_File=File_Open(S.c_str(),"r");
S=Genome_Offsets[i-1].GenomeM;S="Raw_Out/"+S;Genome_Offsets[i-1].Out_FileM=File_Open(S.c_str(),"r");
S=Genome_Offsets[i-1].Genome;S="Raw_Out/"+S+".U";Genome_Offsets[i-1].Unmapped=File_Open(S.c_str(),"r");
S=Genome_Offsets[i-1].GenomeM;S="Raw_Out/"+S+".U";Genome_Offsets[i-1].UnmappedM=File_Open(S.c_str(),"r");
S=Genome_Offsets[i-1].Genome;S="Raw_Out/"+S+".UX";Genome_Offsets[i-1].UnmappedX=File_Open(S.c_str(),"r");
S=Genome_Offsets[i-1].GenomeM;S="Raw_Out/"+S+".UX";Genome_Offsets[i-1].UnmappedXM=File_Open(S.c_str(),"r");
}*/
/*if (USEREFGENE)
{
string S=Genome_String+Genome_Offsets[i-1].Genome+".ref";
Genome_Offsets[i-1].Ref_File=File_Open(S.c_str(),"r");
}*/
}
Genome_Offsets[Genome_Count-1].Offset=INT_MAX;
pthread_mutex_unlock(&OpenGenomeFileslock);
return Genome_Count-1;
}
void Load_FM_Indexes(Index_Info Genome_Files,BWT* & fwfmi,BWT* & revfmi,MMPool* & mmPool)
{
fprintf (stderr,"Loading index %s\n",Genome_Files.BWTFILE);
fwfmi= Load_Indexes(Genome_Files.BWTFILE,Genome_Files.OCCFILE,Genome_Files.SAFILE,mmPool);
fprintf (stderr,"Loading index %s\n",Genome_Files.REVBWTINDEX);
revfmi= Load_Indexes(Genome_Files.REVBWTINDEX,Genome_Files.REVOCCFILE,Genome_Files.REVSAFILE,mmPool);
fwfmi->saInterval=revfmi->saInterval;
fprintf (stderr,"Loading Location %s\n",Genome_Files.LOCATIONFILE);
int Genome_Count= Load_Location(Genome_Files.LOCATIONFILE,Annotations,Location_Array);
/*fprintf (stderr,"Loading packed genome %s\n",Genome_Files.BINFILE);
loadPac(Genome_Files.BINFILE);*/
fprintf (stderr,"Loading index %s\n",Genome_Files.INDFILE);
fprintf(stderr,"Done...\n");
}