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/*
* GFastaIndex.cpp
*
* Created on: Aug 25, 2010
* Author: gpertea
*/
#include "GFastaIndex.h"
#define ERR_FAIDXLINE "Error parsing fasta index line: \n%s\n"
#define ERR_FALINELEN "Error: sequence lines in a FASTA record must have the same length!\n"
void GFastaIndex::addRecord(const char* seqname, uint seqlen, off_t foffs, int llen, int llen_full) {
GFastaRec* farec=records.Find(seqname);
if (farec!=NULL) {
GMessage("Warning: duplicate sequence ID (%s) added to the fasta index! Only last entry data will be kept.\n");
farec->seqlen=seqlen;
farec->fpos=foffs;
farec->line_len=llen;
farec->line_blen=llen_full;
}
else {
farec=new GFastaRec(seqlen,foffs,llen,llen_full);
records.Add(seqname,farec);
farec->seqname=records.getLastKey();
}
}
int GFastaIndex::loadIndex(const char* finame) { //load record info from existing fasta index
if (finame==NULL) finame=fai_name;
if (finame!=fai_name) {
fai_name=Gstrdup(finame);
}
if (fai_name==NULL) GError("Error: GFastaIndex::loadIndex() called with no file name!\n");
records.Clear();
haveFai=false;
FILE* fi=fopen(fai_name,"rb");
if (fi==NULL) {
GMessage("Warning: cannot open fasta index file: %s!\n",fai_name);
return 0;
}
GLineReader fl(fi);
char* s=NULL;
while ((s=fl.nextLine())!=NULL) {
if (*s=='#') continue;
char* p=strchrs(s,"\t ");
if (p==NULL) GError(ERR_FAIDXLINE,s);
*p=0; //s now holds the genomic sequence name
p++;
uint len=0;
int line_len=0, line_blen=0;
#ifdef _WIN32
long offset=-1;
sscanf(p, "%d%ld%d%d", &len, &offset, &line_len, &line_blen);
#else
long long offset=-1;
sscanf(p, "%u%lld%d%d", &len, &offset, &line_len, &line_blen);
#endif
if (len==0 || line_len==0 || line_blen==0 || line_blen<line_len)
GError(ERR_FAIDXLINE,p);
addRecord(s,len,offset,line_len, line_blen);
}
fclose(fi);
haveFai=(records.Count()>0);
return records.Count();
}
int GFastaIndex::buildIndex() {
//this parses the whole fasta file, so it could be slow for large files
//builds the index in memory only
if (fa_name==NULL)
GError("Error: GFastaIndex::buildIndex() called with no fasta file!\n");
FILE* fa=fopen(fa_name,"rb");
if (fa==NULL) {
GMessage("Warning: cannot open fasta index file: %s!\n",fa_name);
return 0;
}
records.Clear();
GLineReader fl(fa);
char* s=NULL;
uint seqlen=0;
int line_len=0,line_blen=0;
bool newSeq=false; //set when FASTA header is encountered
off_t newSeqOffset=0;
//int prevOffset=0;
char* seqname=NULL;
int last_len=0;
bool mustbeLastLine=false; //true if the line length decreases
while ((s=fl.nextLine())!=NULL) {
if (s[0]=='>') {
if (seqname!=NULL) {
if (seqlen==0)
GError("Warning: empty FASTA record skipped (%s)!\n",seqname);
else { //seqlen!=0
addRecord(seqname, seqlen,newSeqOffset, line_len, line_blen);
}
}
char *p=s;
while (*p > 32) p++;
*p=0;
GFREE(seqname);
seqname=Gstrdup(&s[1]);
newSeq=true;
newSeqOffset=fl.getfpos();
last_len=0;
line_len=0;
line_blen=0;
seqlen=0;
mustbeLastLine=false;
} //defline parsing
else { //sequence line
int llen=fl.tlength();
int lblen=fl.blength(); //fl.getFpos()-prevOffset;
if (newSeq) { //first sequence line after defline
line_len=llen;
line_blen=lblen;
}
else {//next seq lines after first
if (mustbeLastLine) {
//could be empty line, adjust for possible spaces
if (llen>0) {
char *p=s;
//trim spaces, tabs etc. on the last line
while (*p > 32) ++p;
llen=(p-s);
}
if (llen>0) GError(ERR_FALINELEN);
}
else {
if (llen<last_len) mustbeLastLine=true;
else if (llen>last_len) GError(ERR_FALINELEN);
}
}
seqlen+=llen;
last_len=llen;
newSeq=false;
} //sequence line
//prevOffset=fl.getfpos();
}//for each line of the fasta file
if (seqlen>0)
addRecord(seqname, seqlen, newSeqOffset, line_len, line_blen);
GFREE(seqname);
fclose(fa);
return records.Count();
}
int GFastaIndex::storeIndex(const char* finame) { //write the hash to a file
if (records.Count()==0)
GError("Error at GFastaIndex:storeIndex(): no records found!\n");
FILE* fai=fopen(finame, "w");
if (fai==NULL) GError("Error creating fasta index file: %s\n",finame);
int rcount=storeIndex(fai);
GFREE(fai_name);
fai_name=Gstrdup(finame);
return rcount;
}
int GFastaIndex::storeIndex(FILE* fai) {
int rcount=0;
GList<GFastaRec> reclist(true,false,true); //sorted, don't free members, unique
records.startIterate();
GFastaRec* rec=NULL;
while ((rec=records.NextData())!=NULL) {
reclist.Add(rec);
}
//reclist has records sorted by file offset
for (int i=0;i<reclist.Count();i++) {
#ifdef _WIN32
int written=fprintf(fai, "%s\t%d\t%ld\t%d\t%d\n",
reclist[i]->seqname,reclist[i]->seqlen,(long)reclist[i]->fpos,
reclist[i]->line_len, reclist[i]->line_blen);
#else
int written=fprintf(fai, "%s\t%d\t%lld\t%d\t%d\n",
reclist[i]->seqname, reclist[i]->seqlen, (long long)(reclist[i]->fpos),
reclist[i]->line_len, reclist[i]->line_blen);
#endif
if (written>0) rcount++;
else break; //couldn't write anymore
}
fclose(fai);
haveFai=(rcount>0);
return rcount;
}
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