//' The reads in the read collection. //' //' This simply returns the full read count. //' //' @param acc An accession or a path to an actual SRA file (with .sra suffix) //' @param n The number of reads to return //' @return the reads in the collection //' @export //' @examples //' reads('SRR000123') // [[Rcpp::export]] SEXP reads(Rcpp::String acc, int n, SEXP lkup) { ReadCollection run = ncbi::NGS::openReadCollection ( acc ); ReadIterator rgi = run.getReads( Read::all ); SEXP r_ans_width, r_ans; XVectorList_holder r_ans_holder; PROTECT(r_ans_width = IntegerVector(1,1000)); PROTECT(r_ans = alloc_XRawList("DNAStringSet", "DNAString", r_ans_width)); vector<std::string> out; for(int i = 0; rgi.nextRead() & (i < 3) ; i++) { cout << i; while ( rgi.nextFragment() ) { std::string str1 = rgi.getFragmentBases().toString(); const char * abc = str1.c_str(); cout << abc; Chars_holder r_ans_elt_holder = get_elt_from_XRawList_holder(&r_ans_holder, i); Ocopy_bytes_to_i1i2_with_lkup(0, r_ans_elt_holder.length - 1, (char *)r_ans_elt_holder.ptr, r_ans_elt_holder.length, abc, str1.length(), INTEGER(lkup), LENGTH(lkup)); } } UNPROTECT(2); return r_ans; }
static void run ( String acc, int splitNum, int splitNo ) { // open requested accession using SRA implementation of the API ReadCollection run = ncbi::NGS::openReadCollection ( acc ); String run_name = run.getName (); // compute window to iterate through long MAX_ROW = run.getReadCount (); double chunk = ( double ) MAX_ROW / splitNum; long first = ( long ) round ( chunk * ( splitNo-1 ) ); long next_first = ( long ) round ( chunk * ( splitNo ) ); if ( next_first > MAX_ROW ) next_first = MAX_ROW; //start iterator on reads long count = next_first - first; ReadIterator it = run.getReadRange ( first+1, count, Read::all ); long i; for ( i = 0; it.nextRead (); ++ i ) { cout << it.getReadId(); //iterate through fragments while ( it.nextFragment () ) cout << '\t' << it.getFragmentBases (); cout << '\n'; } cerr << "Read " << i << " spots for " << run_name << '\n'; }
static void run ( const DumpArgs & TheArgs ) { if ( ! TheArgs . good () ) { throw ErrorMsg ( "Invalid arguments" ); } ngs :: String Acc ( TheArgs . accession () . c_str () ); ReadCollection RCol = ncbi :: NGS :: openReadCollection ( Acc ); int64_t minSpot = TheArgs . minSpotId (); int64_t maxSpot = TheArgs . maxSpotId (); if ( minSpot == 0 ) { minSpot = 1; } if ( maxSpot == 0 ) { maxSpot = RCol . getReadCount (); } if ( maxSpot < minSpot ) { int64_t Id = minSpot; minSpot = maxSpot; maxSpot = Id; } ReadIterator Iterator = RCol.getReadRange ( minSpot, maxSpot - minSpot + 1, TheArgs . category () ); ngs :: String ReadCollectionName = RCol.getName (); AFilters Filters ( TheArgs . accession () ); setupFilters ( Filters, TheArgs ); for ( int64_t llp = TheArgs . minSpotId () ; Iterator.nextRead (); llp ++ ) { if ( Filters . checkIt ( Iterator ) ) { if ( TheArgs . fastaDump () ) { dumpFastA ( llp, ReadCollectionName, Iterator, TheArgs . fastaDumpWidth () ); } else { dumpFastQ ( llp, ReadCollectionName, Iterator ); } } } kout.flush (); std :: cerr << Filters . report ( TheArgs . legacyReport () ); } /* run () */