static void parse1read (int t, int threadID) { unsigned int j, retain = 0; unsigned int edge_index = 0; kmer_t *node; boolean isSmaller; Kmer wordplus, bal_wordplus; unsigned int start, finish, pos; Kmer prevKmer, currentKmer; boolean IsPrevKmer = 0; start = indexArray[t]; finish = indexArray[t + 1]; pos = start; for (j = start; j < finish; j++) { #ifdef MER127 if( kmerBuffer[j].low2== 0 && N_kmer) #endif #ifdef MER63 if( kmerBuffer[j].low== 0 && N_kmer) #endif #ifdef MER31 if( kmerBuffer[j]== 0 && N_kmer) #endif { IsPrevKmer=0; continue; } node = nodeBuffer[j]; //extract edges or keep kmers if ((node->deleted) || (node->linear && !node->inEdge)) // deleted or in a floating loop { if (retain < 2) { retain = 0; pos = start; } else { break; } continue; } isSmaller = smallerBuffer[j]; if (node->linear) { if (isSmaller) { edge_index = node->l_links; } else { edge_index = node->l_links + node->twin - 1; } #ifdef MER127 if (retain == 0 || IsPrevKmer) { retain++; mixBuffer[pos].low2 = edge_index; flagArray[pos++] = 0; IsPrevKmer = 0; } else if (edge_index != mixBuffer[pos - 1].low2) { retain++; mixBuffer[pos].low2 = edge_index; flagArray[pos++] = 0; } #endif #ifdef MER63 if (retain == 0 || IsPrevKmer) { retain++; mixBuffer[pos].low= edge_index; flagArray[pos++] = 0; IsPrevKmer = 0; } else if (edge_index != mixBuffer[pos - 1].low) { retain++; mixBuffer[pos].low= edge_index; flagArray[pos++] = 0; } #endif #ifdef MER31 if (retain == 0 || IsPrevKmer) { retain++; mixBuffer[pos] = edge_index; flagArray[pos++] = 0; IsPrevKmer = 0; } else if (edge_index != mixBuffer[pos - 1]) { retain++; mixBuffer[pos] = edge_index; flagArray[pos++] = 0; } #endif } else { if (isSmaller) { currentKmer = node->seq; } else { currentKmer = reverseComplement (node->seq, overlaplen); } if (IsPrevKmer) { retain++; wordplus = KmerPlus (prevKmer, lastCharInKmer (currentKmer)); bal_wordplus = reverseComplement (wordplus, overlaplen + 1); if (KmerSmaller (wordplus, bal_wordplus)) { smallerBuffer[pos] = 1; hashBanBuffer[pos] = hash_kmer (wordplus); mixBuffer[pos] = wordplus; } else { smallerBuffer[pos] = 0; hashBanBuffer[pos] = hash_kmer (bal_wordplus); mixBuffer[pos] = bal_wordplus; } // fprintf(stderr,"%lld\n",hashBanBuffer[pos]); flagArray[pos++] = 1; } IsPrevKmer = 1; prevKmer = currentKmer; } } /* for(j=start;j<pos;j++) fprintf(stderr,"%d ",flagArray[j]); fprintf(stderr,"\n"); */ if (retain < 1) { deletion[threadID]++; } if (retain < 2) { flagArray[start] = 0; mixBuffer[start] = kmerZero; return; } if ((pos - start) != retain) { printf ("read %d, %d vs %d\n", t, retain, edge_index - start); } if (pos < finish) { flagArray[pos] = 0; mixBuffer[pos] = kmerZero; } }
static void merge_linearV2 ( char bal_edge, STACK * nStack, int count, FILE * fp ) { int length, char_index; preEDGE * newedge; kmer_t * del_node, *longNode; char * tightSeq, firstCh; long long symbol = 0; int len_tSeq; Kmer wordplus, bal_wordplus; ubyte8 hash_ban; KMER_PT * last_np = ( KMER_PT * ) stackPop ( nStack ); KMER_PT * second_last_np = ( KMER_PT * ) stackPop ( nStack ); KMER_PT * first_np, *second_np = NULL; KMER_PT * temp; boolean found, lastOne = 1, single = 1; int setPicker; length = count - 1; len_tSeq = length; if ( len_tSeq >= edge_length_limit ) { tightSeq = ( char * ) ckalloc ( len_tSeq * sizeof ( char ) ); } else { tightSeq = edge_seq; } char_index = length - 1; newedge = &temp_edge; newedge->to_node = last_np->kmer; newedge->length = length; newedge->bal_edge = bal_edge; tightSeq[char_index--] = lastCharInKmer ( last_np->kmer ); firstCh = firstCharInKmer ( second_last_np->kmer ); dislink2prevUncertain ( last_np->node, firstCh, last_np->isSmaller ); stackRecover ( nStack ); while ( nStack->item_c > 1 ) { second_np = ( KMER_PT * ) stackPop ( nStack ); } first_np = ( KMER_PT * ) stackPop ( nStack ); //unlink first node to the second one dislink2nextUncertain ( first_np->node, lastCharInKmer ( second_np->kmer ), first_np->isSmaller ); //printf("from %llx, to %llx\n",first_np->node->seq,last_np->node->seq); //now temp is the last node in line, out_node is the second last node in line newedge->from_node = first_np->kmer; //create a long kmer for edge with length 1 if ( length == 1 ) { nodeCounter++; wordplus = KmerPlus ( newedge->from_node, lastCharInKmer ( newedge->to_node ) ); bal_wordplus = reverseComplement ( wordplus, overlaplen + 1 ); /* Kmer temp = KmerPlus(reverseComplement(newedge->to_node,overlaplen), lastCharInKmer(reverseComplement(newedge->from_node,overlaplen))); fprintf(stderr,"(%llx %llx) (%llx %llx) (%llx %llx)\n", wordplus.high,wordplus.low,temp.high,temp.low, bal_wordplus.high,bal_wordplus.low); */ edge_c++; edgeCounter++; if ( KmerSmaller ( wordplus, bal_wordplus ) ) { hash_ban = hash_kmer ( wordplus ); setPicker = hash_ban % thrd_num; found = put_kmerset ( KmerSetsPatch[setPicker], wordplus, 4, 4, &longNode ); if ( found ) { printf ( "longNode %llx %llx already exist\n", wordplus.high, wordplus.low ); } longNode->l_links = edge_c; longNode->twin = ( unsigned char ) ( bal_edge + 1 ); } else { hash_ban = hash_kmer ( bal_wordplus ); setPicker = hash_ban % thrd_num; found = put_kmerset ( KmerSetsPatch[setPicker], bal_wordplus, 4, 4, &longNode ); if ( found ) { printf ( "longNode %llx %llx already exist\n", bal_wordplus.high, bal_wordplus.low ); } longNode->l_links = edge_c + bal_edge; longNode->twin = ( unsigned char ) ( -bal_edge + 1 ); } } else { edge_c++; edgeCounter++; } stackRecover ( nStack ); //mark all the internal nodes temp = ( KMER_PT * ) stackPop ( nStack ); while ( nStack->item_c > 1 ) { temp = ( KMER_PT * ) stackPop ( nStack ); del_node = temp->node; del_node->inEdge = 1; symbol += get_kmer_left_covs ( *del_node ); if ( temp->isSmaller ) { del_node->l_links = edge_c; del_node->twin = ( unsigned char ) ( bal_edge + 1 ); } else { del_node->l_links = edge_c + bal_edge; del_node->twin = ( unsigned char ) ( -bal_edge + 1 ); } tightSeq[char_index--] = lastCharInKmer ( temp->kmer ); } newedge->seq = tightSeq; if ( length > 1 ) { newedge->cvg = symbol / ( length - 1 ) * 10 > MaxEdgeCov ? MaxEdgeCov : symbol / ( length - 1 ) * 10; } else { newedge->cvg = 0; } output_1edge ( newedge, fp ); if ( len_tSeq >= edge_length_limit ) { free ( ( void * ) tightSeq ); } edge_c += bal_edge; if ( edge_c % 10000000 == 0 ) { printf ( "--- %d edges built\n", edge_c ); } return; }