void output_contig ( EDGE * ed_array, unsigned int ed_num, char * outfile, int cut_len ) { char temp[256]; FILE * fp, *fp_contig; int flag, count, len_c; int signI; unsigned int i; long long sum = 0, N90, N50; unsigned int * length_array; boolean tip; sprintf ( temp, "%s.contig", outfile ); fp = ckopen ( temp, "w" ); qsort ( &ed_array[1], ed_num, sizeof ( EDGE ), cmp_edge ); length_array = ( unsigned int * ) ckalloc ( ed_num * sizeof ( unsigned int ) ); kmerSeq = ( char * ) ckalloc ( overlaplen * sizeof ( char ) ); //first scan for number counting count = len_c = 0; for ( i = 1; i <= ed_num; i++ ) { if ( ( ed_array[i].length + overlaplen ) >= len_bar ) { length_array[len_c++] = ed_array[i].length + overlaplen; } if ( ed_array[i].length < 1 || ed_array[i].deleted ) { continue; } count++; if ( EdSmallerThanTwin ( i ) ) { i++; } } sum = 0; for ( signI = len_c - 1; signI >= 0; signI-- ) { sum += length_array[signI]; } if ( len_c > 0 ) { printf ( "%d ctgs longer than %d, sum up %lldbp, with average length %lld\n", len_c, len_bar, sum, sum / len_c ); } qsort ( length_array, len_c, sizeof ( length_array[0] ), cmp_int ); printf ( "the longest is %dbp, ", length_array[len_c - 1] ); N50 = sum * 0.5; N90 = sum * 0.9; sum = flag = 0; for ( signI = len_c - 1; signI >= 0; signI-- ) { sum += length_array[signI]; if ( !flag && sum >= N50 ) { printf ( "contig N50 is %d bp,", length_array[signI] ); flag = 1; } if ( sum >= N90 ) { printf ( "contig N90 is %d bp\n", length_array[signI] ); break; } } //fprintf(fp,"Number %d\n",count); for ( i = 1; i <= ed_num; i++ ) { //if(ed_array[i].multi!=1||ed_array[i].length<1||(ed_array[i].length+overlaplen)<cut_len) if ( ed_array[i].deleted || ed_array[i].length < 1 ) { continue; } if ( ed_array[i].arcs && ed_array[getTwinEdge ( i )].arcs ) { tip = 0; } else { tip = 1; } output_1contig ( i, & ( ed_array[i] ), fp, tip ); if ( EdSmallerThanTwin ( i ) ) { i++; } } fclose ( fp ); free ( ( void * ) kmerSeq ); free ( ( void * ) length_array ); printf ( "%d contigs longer than %d output\n", count, cut_len ); sprintf ( temp, "%s.ContigIndex", outfile ); fp_contig = ckopen ( temp, "w" ); fprintf ( fp_contig, "Edge_num %d %d\n", ed_num, count ); fprintf ( fp_contig, "index\tlength\treverseComplement\n" ); for ( i = 1; i <= num_ed; i++ ) { fprintf ( fp_contig, "%d\t%d\t", i, edge_array[i].length + overlaplen ); if ( EdSmallerThanTwin ( i ) ) { fprintf ( fp_contig, "1\n" ); i++; } else if ( EdLargerThanTwin ( i ) ) { fprintf ( fp_contig, "-1\n" ); } else { fprintf ( fp_contig, "0\n" ); } } fclose ( fp_contig ); }
void output_contig (EDGE * ed_array, unsigned int ed_num, char *outfile, int cut_len) { char temp[256]; FILE * fp, *fp_contig; int flag, count, len_c; int signI; unsigned int i, j, diff_len=0; long long sum = 0, N90, N50; unsigned int *length_array; boolean tip; sprintf (temp, "%s.contig", outfile); fp = ckopen (temp, "w"); index_array = (unsigned int *)ckalloc((ed_num+1)*sizeof(unsigned int)); unsigned int * all_length_arr = (unsigned int*) ckalloc((ed_num+1)*sizeof(unsigned int)); flag_array = (unsigned int*)ckalloc((ed_num+1)*sizeof(unsigned int)); for (i=1; i<=ed_num; ++i) { index_array[i] = ed_array[i].length; all_length_arr[i] = ed_array[i].length; } qsort(&all_length_arr[1], ed_num, sizeof(all_length_arr[0]), cmp_int); for (i=1; i<=ed_num; ++i) { for (j=i+1; j<=ed_num; ++j) { if (all_length_arr[i] != all_length_arr[j]) break; } all_length_arr[++diff_len] = all_length_arr[i]; flag_array[diff_len] = i; i = j-1; } for (i=1; i<=ed_num; ++i) { index_array[i] = uniqueLenSearch(all_length_arr, flag_array, diff_len, index_array[i]); } for (i=1; i<=ed_num; ++i) { flag_array[index_array[i]] = i; } free((void*)all_length_arr); length_array = (unsigned int *) ckalloc (ed_num * sizeof (unsigned int)); kmerSeq = (char *) ckalloc (overlaplen * sizeof (char)); count = len_c = 0; for (i = 1; i <= ed_num; i++) { if ((ed_array[i].length + overlaplen) >= len_bar) { length_array[len_c++] = ed_array[i].length + overlaplen; } if (ed_array[i].length < 1 || ed_array[i].deleted) { continue; } count++; if (EdSmallerThanTwin (i)) { i++; } } sum = 0; for (signI = len_c - 1; signI >= 0; signI--) { sum += length_array[signI]; } qsort ( length_array, len_c, sizeof ( length_array[0] ), cmp_int ); if ( len_c > 0 ) { printf ( "%d ctgs longer than %d, sum up %lldbp, with average length %lld\n", len_c, len_bar, sum, sum / len_c ); printf ( "the longest is %dbp, ", length_array[len_c - 1] ); } N50 = sum * 0.5; N90 = sum * 0.9; sum = flag = 0; for (signI = len_c - 1; signI >= 0; signI--) { sum += length_array[signI]; if (!flag && sum >= N50) { printf ("contig N50 is %d bp,", length_array[signI]); flag = 1; } if (sum >= N90) { printf ("contig N90 is %d bp\n", length_array[signI]); break; } } for (i = 1; i <= ed_num; i++) { j = flag_array[i]; if (ed_array[j].deleted || ed_array[j].length < 1) { continue; } if (ed_array[j].arcs && ed_array[getTwinEdge (j)].arcs) { tip = 0; } else { tip = 1; } output_1contig (i, &(ed_array[j]), fp, tip); if (EdSmallerThanTwin (j)) { i++; } } fclose (fp); free ((void *) kmerSeq); free ((void *) length_array); printf ("%d contigs longer than %d output\n", count, cut_len); sprintf (temp, "%s.ContigIndex", outfile); fp_contig = ckopen (temp, "w"); fprintf (fp_contig, "Edge_num %d %d\n", ed_num, count); fprintf (fp_contig, "index\tlength\treverseComplement\n"); for (i = 1; i <= num_ed; i++) { j = flag_array[i]; fprintf (fp_contig, "%d\t%d\t", i, edge_array[j].length + overlaplen); if (EdSmallerThanTwin (j)) { fprintf (fp_contig, "1\n"); i++; } else if (EdLargerThanTwin (j)) { fprintf (fp_contig, "-1\n"); } else { fprintf (fp_contig, "0\n"); } } fclose (fp_contig); }