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/* |
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* GFaIdx.h |
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* |
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* Created on: Aug 25, 2010 |
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* Author: gpertea |
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*/ |
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|
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#ifndef GFAIDX_H_ |
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#define GFAIDX_H_ |
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|
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#include "GHash.hh" |
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#include "GList.hh" |
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|
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class GFastaRec { |
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public: |
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char* seqname; |
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uint seqlen; |
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off_t fpos; |
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int line_len; //effective line length (without EoL) |
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int line_blen; //length of line including EoL characters |
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GFastaRec(uint slen=0, off_t fp=0, int llen=0, int llenb=0) { |
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seqname=NULL; //only a pointer copy |
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seqlen=slen; |
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fpos=fp; |
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line_len=llen; |
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line_blen=llenb; |
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} |
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bool operator==(GFastaRec& d){ |
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return (fpos==d.fpos); |
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} |
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bool operator>(GFastaRec& d){ |
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return (fpos>d.fpos); |
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} |
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bool operator<(GFastaRec& d){ |
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return (fpos<d.fpos); |
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} |
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|
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}; |
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|
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class GFastaIndex { |
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char* fa_name; |
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char* fai_name; |
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bool haveFai; |
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public: |
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GHash<GFastaRec> records; |
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void addRecord(const char* seqname, uint seqlen, |
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off_t foffs, int llen, int llen_full); |
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|
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GFastaRec* getRecord(const char* seqname) { |
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return records.Find(seqname); |
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} |
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bool hasIndex() { return haveFai; } |
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int loadIndex(const char* finame); |
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int buildIndex(); //build index in memory by parsing the whole fasta file |
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int storeIndex(const char* finame); |
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int storeIndex(FILE* fai); |
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int getCount() { return records.Count(); } |
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GFastaIndex(const char* fname, const char* finame=NULL):records() { |
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if (fileExists(fname)!=2) GError("Error: fasta file %s not found!\n",fname); |
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if (fileSize(fname)<=0) GError("Error: invalid fasta file %s !\n",fname); |
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fa_name=Gstrdup(fname); |
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fai_name=finame!=NULL ? Gstrdup(finame) : NULL; |
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if (fileSize(fa_name)==0) { |
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GError("Error creating GFastaIndex(%s): invalid fasta file!\n",fa_name); |
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} |
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haveFai=false; |
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if (fai_name!=NULL && fileSize(fai_name)>0) { |
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//try to load the index file if it exists |
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loadIndex(fai_name); |
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haveFai=(records.Count()>0); |
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} |
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} |
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~GFastaIndex() { |
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GFREE(fa_name); |
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GFREE(fai_name); |
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} |
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}; |
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|
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#endif /* GFAIDX_H_ */ |
