// Orient supernode
// Once oriented, supernode has lowest possible kmerkey at the beginning,
// oriented FORWARDs if possible
void supernode_normalise(dBNode *nlist, size_t len, const dBGraph *db_graph)
{
// Sort supernode into forward orientation
ctx_assert(len > 0);
if(len == 1) {
nlist[0].orient = FORWARD;
return;
}
BinaryKmer bkmer0 = db_node_get_bkmer(db_graph, nlist[0].key);
BinaryKmer bkmer1 = db_node_get_bkmer(db_graph, nlist[len-1].key);
// Check if closed cycle
if(supernode_is_closed_cycle(nlist, len, bkmer0, bkmer1, db_graph))
{
// find lowest kmer to start from
BinaryKmer lowest = bkmer0, tmp;
size_t i, idx = 0;
for(i = 1; i < len; i++) {
tmp = db_node_get_bkmer(db_graph, nlist[i].key);
if(binary_kmer_less_than(tmp, lowest)) {
lowest = tmp;
idx = i;
}
}
// If already starting from the lowest kmer no change needed
if(idx > 0 || nlist[0].orient != FORWARD)
{
// a->b->c->d->e->f->a
// if c is lowest and FORWARD: c->d->e->f->a->b (keep orientations)
// if c is lowest and REVERSE: c->b->a->f->e->d (reverse orientations)
if(nlist[idx].orient == FORWARD) {
// Shift left by idx, without affecting orientations
db_nodes_left_shift(nlist, len, idx);
} else {
db_nodes_reverse_complement(nlist, idx+1);
db_nodes_reverse_complement(nlist+idx+1, len-idx-1);
}
}
}
else if(binary_kmer_less_than(bkmer1,bkmer0)) {
db_nodes_reverse_complement(nlist, len);
}
}
// For a given kmer, get the BinaryKmer 'key':
// the lower of the kmer vs reverse complement of itself
// kmer and kmer_key must NOT point to overlapping memory
BinaryKmer bkmer_get_key(const BinaryKmer bkmer, size_t kmer_size)
{
BinaryKmer bkey;
// Get first and last nucleotides
Nucleotide first = binary_kmer_first_nuc(bkmer, kmer_size);
Nucleotide last = binary_kmer_last_nuc(bkmer);
Nucleotide rev_last = dna_nuc_complement(last);
if(first < rev_last) return bkmer;
// Don't know which is going to be correct -- this will happen 1 in 4 times
bkey = binary_kmer_reverse_complement(bkmer, kmer_size);
return (binary_kmer_less_than(bkmer, bkey) ? bkmer : bkey);
}
Key element_get_key(BinaryKmer * kmer, short kmer_size, Key preallocated_key)
{
BinaryKmer local_rev_kmer;
binary_kmer_initialise_to_zero(&local_rev_kmer);
binary_kmer_reverse_complement(kmer, kmer_size, &local_rev_kmer);
if (binary_kmer_less_than(local_rev_kmer, *kmer, kmer_size)) {
binary_kmer_assignment_operator(*((BinaryKmer *)
preallocated_key),
local_rev_kmer);
} else {
binary_kmer_assignment_operator(*((BinaryKmer *)
preallocated_key), *kmer);
}
return preallocated_key;
}
int ctx_index(int argc, char **argv)
{
const char *out_path = NULL;
size_t block_size = 0, block_kmers = 0;
// Arg parsing
char cmd[100];
char shortopts[300];
cmd_long_opts_to_short(longopts, shortopts, sizeof(shortopts));
int c;
// silence error messages from getopt_long
// opterr = 0;
while((c = getopt_long_only(argc, argv, shortopts, longopts, NULL)) != -1) {
cmd_get_longopt_str(longopts, c, cmd, sizeof(cmd));
switch(c) {
case 0: /* flag set */ break;
case 'h': cmd_print_usage(NULL); break;
case 'o': cmd_check(!out_path, cmd); out_path = optarg; break;
case 'b':
cmd_check(!block_kmers, cmd);
block_kmers = cmd_size_nonzero(cmd, optarg);
break;
case 's':
cmd_check(!block_size, cmd);
block_size = cmd_size_nonzero(cmd, optarg);
break;
case ':': /* BADARG */
case '?': /* BADCH getopt_long has already printed error */
// cmd_print_usage(NULL);
die("`"CMD" index -h` for help. Bad option: %s", argv[optind-1]);
default: abort();
}
}
if(optind+1 != argc)
cmd_print_usage("Require exactly one input graph file (.ctx)");
if(block_size && block_kmers)
cmd_print_usage("Cannot use --block-kmers and --block-size together");
const char *ctx_path = argv[optind];
//
// Open Graph file
//
GraphFileReader gfile;
memset(&gfile, 0, sizeof(GraphFileReader));
graph_file_open2(&gfile, ctx_path, "r+", true, 0);
if(!file_filter_is_direct(&gfile.fltr))
die("Cannot open graph file with a filter ('in.ctx:blah' syntax)");
// Open output file
FILE *fout = out_path ? futil_fopen_create(out_path, "w") : stdout;
// Start
size_t filencols = gfile.hdr.num_of_cols;
size_t kmer_size = gfile.hdr.kmer_size;
const char *path = file_filter_path(&gfile.fltr);
size_t ncols = file_filter_into_ncols(&gfile.fltr);
size_t kmer_mem = sizeof(BinaryKmer) + (sizeof(Edges)+sizeof(Covg))*filencols;
if(block_size) {
block_kmers = block_size / kmer_mem;
} else if(!block_size && !block_kmers) {
block_size = 4 * ONE_MEGABYTE;
block_kmers = block_size / kmer_mem;
}
// Update block-size
block_size = block_kmers * kmer_mem;
status("[index] block bytes: %zu kmers: %zu; kmer bytes: %zu, hdr: %zu",
block_size, block_kmers, kmer_mem, (size_t)gfile.hdr_size);
if(block_kmers == 0) die("Cannot set block_kmers to zero");
// Print header
fputs("#block_start\tnext_block\tfirst_kmer\tkmer_idx\tnext_kmer_idx\n", fout);
BinaryKmer bkmer = BINARY_KMER_ZERO_MACRO;
BinaryKmer prev_bkmer = BINARY_KMER_ZERO_MACRO;
Covg *covgs = ctx_malloc(ncols * sizeof(Covg));
Edges *edges = ctx_malloc(ncols * sizeof(Edges));
char bkmerstr[MAX_KMER_SIZE+1];
size_t rem_block = block_size - kmer_mem; // block after first kmer
char *tmp_mem = ctx_malloc(rem_block);
// Read in file, print index
size_t nblocks = 0;
size_t bl_bytes = 0, bl_kmers = 0;
size_t bl_byte_offset = gfile.hdr_size, bl_kmer_offset = 0;
while(1)
{
if(!graph_file_read(&gfile, &bkmer, covgs, edges)) {
status("Read kmer failed"); break; }
binary_kmer_to_str(bkmer, kmer_size, bkmerstr);
if(nblocks > 0 && !binary_kmer_less_than(prev_bkmer,bkmer))
die("File is not sorted: %s [%s]", bkmerstr, path);
// We've already read one kmer entry, read rest of block
bl_bytes = kmer_mem + gfr_fread_bytes(&gfile, tmp_mem, rem_block);
bl_kmers = 1 + bl_bytes / kmer_mem;
fprintf(fout, "%zu\t%zu\t%s\t%zu\t%zu\n",
bl_byte_offset, bl_byte_offset+bl_bytes, bkmerstr,
bl_kmer_offset, bl_kmer_offset+bl_kmers);
bl_byte_offset += bl_bytes;
bl_kmer_offset += bl_kmers;
nblocks++;
if(bl_kmers < block_kmers) {
status("last block %zu < %zu; %zu vs %zu",
bl_kmers, block_kmers, bl_bytes, block_size);
break;
}
prev_bkmer = bkmer;
}
ctx_free(covgs);
ctx_free(edges);
ctx_free(tmp_mem);
// done
char num_kmers_str[50], num_blocks_str[50];
char block_mem_str[50], block_kmers_str[50];
ulong_to_str(bl_kmer_offset, num_kmers_str);
ulong_to_str(nblocks, num_blocks_str);
bytes_to_str(block_size, 1, block_mem_str);
ulong_to_str(block_kmers, block_kmers_str);
status("Read %s kmers in %s block%s (block size %s / %s kmers)",
num_kmers_str, num_blocks_str, util_plural_str(nblocks),
block_mem_str, block_kmers_str);
if(fout != stdout) status("Saved to %s", out_path);
graph_file_close(&gfile);
fclose(fout);
return EXIT_SUCCESS;
}