void sort_block_q(uint64_t* buffer, int count) {
if ( count <= 1 ) return;
if ( count <= 32 ) {
sort_block(buffer,count);
return;
};
uint64_t z[2] = {buffer[0], buffer[1]};
int nel = -1;
bool alleq = true;
for ( int i = 1; i < count; i++ ) {
uint64_t a[2] = {buffer[i*2], buffer[i*2+1]};
if ( !compareeq (a,z) ) {
alleq = false;
nel = i;
break;
}
}
if ( alleq ) return;
if ( nel >= 0 ) {
swap(buffer,0,nel);
}
z[0] = buffer[0];
z[1] = buffer[1];
int lc = 1;
for ( int i = 1; i < count; i++ ) {
uint64_t a[2] = {buffer[i*2], buffer[i*2+1]};
if ( compare (a,z) ) {
swap(buffer, i,lc);
lc++;
}
}
swap(buffer,0,lc-1);
sort_block_q(buffer, lc);
sort_block_q(buffer+(lc*2), count-lc);
if ( count < SORT_BLOCK_SIZE ) return;
if ( !check_sorted(buffer, count) ) {
printf( "Block sort has errors!\n" );
}
}
int ctx_sort(int argc, char **argv)
{
const char *out_path = NULL;
struct MemArgs memargs = MEM_ARGS_INIT;
// 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 'f': cmd_check(!futil_get_force(), cmd); futil_set_force(true); break;
case 'm': cmd_mem_args_set_memory(&memargs, optarg); break;
case 'n': cmd_mem_args_set_nkmers(&memargs, optarg); break;
case 'o': cmd_check(!out_path, cmd); out_path = optarg; break;
case ':': /* BADARG */
case '?': /* BADCH getopt_long has already printed error */
// cmd_print_usage(NULL);
die("`"CMD" sort -h` for help. Bad option: %s", argv[optind-1]);
default: die("Bad option: [%c]: %s", c, cmd);
}
}
if(optind+1 != argc)
cmd_print_usage("Require exactly one input graph file (.ctx)");
const char *ctx_path = argv[optind];
//
// Open Graph file
//
GraphFileReader gfile;
memset(&gfile, 0, sizeof(GraphFileReader));
graph_file_open2(&gfile, ctx_path, out_path ? "r" : "r+", true, 0);
if(!file_filter_is_direct(&gfile.fltr))
die("Cannot open graph file with a filter ('in.ctx:blah' syntax)");
size_t num_kmers, memory;
// Reading from a stream
if(gfile.num_of_kmers < 0) {
if(!memargs.num_kmers_set)
die("If reading from a stream, must give -n <num_kmers>");
num_kmers = memargs.num_kmers;
}
else num_kmers = gfile.num_of_kmers;
// Open output path (if given)
FILE *fout = out_path ? futil_fopen_create(out_path, "w") : NULL;
size_t i;
size_t ncols = gfile.hdr.num_of_cols;
size_t kmer_mem = sizeof(BinaryKmer) + (sizeof(Edges)+sizeof(Covg))*ncols;
memory = (sizeof(char*) + kmer_mem) * num_kmers;
char mem_str[50];
bytes_to_str(memory, 1, mem_str);
if(memory > memargs.mem_to_use)
die("Require at least %s memory", mem_str);
status("[memory] Total: %s", mem_str);
char *mem = ctx_malloc(kmer_mem * num_kmers);
char **kmers = ctx_malloc(num_kmers*sizeof(char*));
// Read in whole file
// if(graph_file_fseek(gfile, gfile.hdr_size, SEEK_SET) != 0) die("fseek failed");
size_t nkread = gfr_fread_bytes(&gfile, mem, num_kmers*kmer_mem);
if(nkread != num_kmers*kmer_mem)
die("Could only read %zu bytes [<%zu]", nkread, num_kmers*kmer_mem);
// check we are at the end of the file
char tmpc;
if(gfr_fread_bytes(&gfile, &tmpc, 1) != 0) {
die("More kmers in file than believed (kmers: %zu ncols: %zu).",
num_kmers, ncols);
}
status("Read %zu kmers with %zu colour%s", num_kmers,
ncols, util_plural_str(ncols));
for(i = 0; i < num_kmers; i++)
kmers[i] = mem + kmer_mem*i;
sort_block(kmers, num_kmers);
// Print
if(out_path != NULL) {
// saving to a different destination - write header
graph_write_header(fout, &gfile.hdr);
}
else {
// Directly manipulating gfile.fh here, using it to write later
// Not doing any more reading
if(fseek(gfile.fh, gfile.hdr_size, SEEK_SET) != 0) die("fseek failed");
fout = gfile.fh;
}
for(i = 0; i < num_kmers; i++)
if(fwrite(kmers[i], 1, kmer_mem, fout) != kmer_mem)
die("Cannot write to file");
if(out_path) fclose(fout);
graph_file_close(&gfile);
ctx_free(kmers);
ctx_free(mem);
return EXIT_SUCCESS;
}
