// Using file so can call fseek and don't need to load whole graph
static size_t inferedges_on_file(const dBGraph *db_graph, bool add_all_edges,
GraphFileReader *file, FILE *fout)
{
ctx_assert(db_graph->num_of_cols == file->hdr.num_of_cols);
ctx_assert(file_filter_is_direct(&file->fltr));
ctx_assert2(!isatty(fileno(file->fh)), "Use inferedges_on_stream() instead");
ctx_assert(fout != NULL);
ctx_assert(fileno(file->fh) != fileno(fout));
status("[inferedges] Processing file: %s", file_filter_path(&file->fltr));
// Print header
graph_write_header(fout, &file->hdr);
// Read the input file again
if(fseek(file->fh, file->hdr_size, SEEK_SET) != 0)
die("fseek failed: %s", strerror(errno));
const size_t ncols = file->hdr.num_of_cols;
BinaryKmer bkmer;
Edges edges[ncols];
Covg covgs[ncols];
size_t num_kmers_edited = 0;
bool updated;
while(graph_file_read_reset(file, ncols, &bkmer, covgs, edges))
{
updated = (add_all_edges ? infer_all_edges(bkmer, edges, covgs, db_graph)
: infer_pop_edges(bkmer, edges, covgs, db_graph));
graph_write_kmer(fout, file->hdr.num_of_bitfields, file->hdr.num_of_cols,
bkmer, covgs, edges);
num_kmers_edited += updated;
}
return num_kmers_edited;
}
int ctx_view(int argc, char **argv)
{
// Arg parsing
char cmd[100];
char shortopts[300];
cmd_long_opts_to_short(longopts, shortopts, sizeof(shortopts));
int c;
// TODO:
// print_action actions[argc];
// bool read_kmers = false;
// 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 ':': /* BADARG */
case '?': /* BADCH getopt_long has already printed error */
// cmd_print_usage(NULL);
cmd_print_usage("`"CMD" "SUBCMD" -h` for help. Bad option: %s", argv[optind-1]);
default:
cmd_print_usage("Programmer fail. Tell Isaac.");
}
}
if(print_kmers) parse_kmers = 1;
bool no_flags = (!print_info && !parse_kmers && !print_kmers);
if(no_flags) { print_info = parse_kmers = 1; }
if(optind+1 != argc) cmd_print_usage("Require one input graph file (.ctx)");
char *path = argv[optind];
size_t num_errors = 0, num_warnings = 0;
GraphFileReader gfile;
memset(&gfile, 0, sizeof(gfile));
int ret = graph_file_open(&gfile, path);
if(ret == 0) die("Cannot open file: %s", path);
if(print_info)
{
char fsize_str[50];
bytes_to_str((size_t)gfile.file_size, 0, fsize_str);
printf("Loading file: %s\n", file_filter_path(&gfile.fltr));
printf("File size: %s\n", fsize_str);
printf("----\n");
}
size_t i, col, ncols = file_filter_into_ncols(&gfile.fltr);
size_t kmer_size = gfile.hdr.kmer_size;
ctx_assert(ncols > 0);
GraphFileHeader hdr;
memset(&hdr, 0, sizeof(hdr));
graph_file_merge_header(&hdr, &gfile);
uint64_t nkmers_read = 0, nkmers_loaded = 0;
uint64_t num_all_zero_kmers = 0, num_zero_covg_kmers = 0;
uint64_t *col_nkmers, *col_sum_covgs;
col_nkmers = ctx_calloc(ncols, sizeof(col_nkmers[0]));
col_sum_covgs = ctx_calloc(ncols, sizeof(col_sum_covgs[0]));
// Print header
if(print_info) print_header(&hdr, gfile.num_of_kmers);
BinaryKmer bkmer;
Covg covgs[ncols], keep_kmer;
Edges edges[ncols];
bool direct_read = file_filter_is_direct(&gfile.fltr);
if(parse_kmers || print_kmers)
{
if(print_info && print_kmers) printf("----\n");
for(; graph_file_read_reset(&gfile, &bkmer, covgs, edges); nkmers_read++)
{
// If kmer has no covg in any samples -> don't load
keep_kmer = 0;
for(col = 0; col < ncols; col++) {
col_nkmers[col] += (covgs[col] > 0);
col_sum_covgs[col] += covgs[col];
keep_kmer |= covgs[col];
}
if(!direct_read && !keep_kmer) continue;
nkmers_loaded++;
/* Kmer Checks */
// graph_file_read_reset() already checks for:
// 1. oversized kmers
// 2. kmers with covg 0 in all colours
// 3. edges without coverage in a colour
// Check for all-zeros (i.e. all As kmer: AAAAAA)
uint64_t kmer_words_or = 0;
for(i = 0; i < hdr.num_of_bitfields; i++)
kmer_words_or |= bkmer.b[i];
if(kmer_words_or == 0)
{
if(num_all_zero_kmers == 1)
{
loading_error("more than one all 'A's kmers seen [index: %"PRIu64"]\n",
nkmers_read);
}
num_all_zero_kmers++;
}
// Check covg is 0 for all colours
for(i = 0; i < ncols && covgs[i] == 0; i++);
num_zero_covg_kmers += (i == ncols);
// Print
if(print_kmers)
db_graph_print_kmer2(bkmer, covgs, edges, ncols, kmer_size, stdout);
}
}
// check for various reading errors
// if(errno != 0)
// loading_error("errno set [%i]: %s\n", (int)errno, strerror(errno));
int err = ferror(gfile.fh);
if(err != 0)
loading_error("occurred after file reading [%i]\n", err);
char nstr[50];
if(print_kmers || parse_kmers)
{
// file_size is set to -1 if we are reading from a stream,
// therefore won't be able to check number of kmers read
if(gfile.file_size != -1 && nkmers_read != (uint64_t)gfile.num_of_kmers) {
loading_warning("Expected %zu kmers, read %zu\n",
(size_t)gfile.num_of_kmers, (size_t)nkmers_read);
}
if(num_all_zero_kmers > 1)
{
loading_error("%s all-zero-kmers seen\n",
ulong_to_str(num_all_zero_kmers, nstr));
}
if(num_zero_covg_kmers > 0)
{
loading_warning("%s kmers have no coverage in any colour\n",
ulong_to_str(num_zero_covg_kmers, nstr));
}
}
// Count warnings printed by graph_file_reader.c
num_warnings += gfile.error_zero_covg;
num_warnings += gfile.error_missing_covg;
// Can only print these stats if we're read in the kmers
if((print_kmers || parse_kmers) && print_info)
{
// print kmer coverage per sample
printf("\n---- Per colour stats\n");
printf("num. kmers:");
for(col = 0; col < ncols; col++)
printf("\t%s", ulong_to_str(col_nkmers[col], nstr));
printf("\n");
printf("sum coverage:");
for(col = 0; col < ncols; col++)
printf("\t%s", ulong_to_str(col_sum_covgs[col], nstr));
printf("\n");
printf("kmer coverage:");
for(col = 0; col < ncols; col++)
printf("\t%.2f", safe_frac(col_sum_covgs[col], col_nkmers[col]));
printf("\n");
// Overall stats
uint64_t sum_covgs = 0;
double mean_kmer_covg = 0.0;
for(col = 0; col < ncols; col++) sum_covgs += col_sum_covgs[col];
mean_kmer_covg = nkmers_loaded ? (double)sum_covgs / nkmers_loaded : 0.0;
printf("\n---- Overall stats\n");
printf("Total kmers: %s\n", ulong_to_str(nkmers_loaded, nstr));
printf("Total coverage: %s\n", ulong_to_str(sum_covgs, nstr));
printf("Mean coverage: %s\n", double_to_str(mean_kmer_covg, 2, nstr));
}
if(print_info)
{
// Print memory stats
uint64_t mem, capacity, num_buckets, req_capacity;
uint8_t bucket_size;
req_capacity = (size_t)(gfile.num_of_kmers / IDEAL_OCCUPANCY);
capacity = hash_table_cap(req_capacity, &num_buckets, &bucket_size);
mem = ht_mem(bucket_size, num_buckets,
sizeof(BinaryKmer)*8 + ncols*(sizeof(Covg)+sizeof(Edges))*8);
char memstr[100], capacitystr[100], bucket_size_str[100], num_buckets_str[100];
bytes_to_str(mem, 1, memstr);
ulong_to_str(capacity, capacitystr);
ulong_to_str(bucket_size, bucket_size_str);
ulong_to_str(num_buckets, num_buckets_str);
size_t mem_height = (size_t)__builtin_ctzl(num_buckets);
printf("\n---- Memory\n");
printf("memory required: %s [capacity: %s]\n", memstr, capacitystr);
printf(" bucket size: %s; number of buckets: %s\n",
bucket_size_str, num_buckets_str);
printf(" --kmer_size %zu --mem_height %zu --mem_width %i\n",
kmer_size, mem_height, bucket_size);
}
if((print_kmers || parse_kmers) && print_info)
{
printf("\n----\n");
if(num_warnings > 0 || num_errors > 0) {
printf("Warnings: %zu; Errors: %zu\n",
(size_t)num_warnings, (size_t)num_errors);
}
if(num_errors == 0)
printf(num_warnings ? "Graph may be ok\n" : "Graph is valid\n");
}
ctx_free(col_nkmers);
ctx_free(col_sum_covgs);
// Close file (which zeros it)
graph_file_close(&gfile);
graph_header_dealloc(&hdr);
return num_errors ? EXIT_FAILURE : EXIT_SUCCESS;
}