static void parse_cmdline_args(int argc, char **argv)
{
// 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 'f': cmd_check(!futil_get_force(), cmd); futil_set_force(true); break;
case 'F': cmd_check(!sam_path,cmd); sam_path = optarg; break;
case 'Q': cmd_check(min_mapq == SIZE_MAX,cmd); min_mapq = cmd_uint32(cmd, optarg); break;
case 'A': cmd_check(max_align_len == SIZE_MAX,cmd); max_align_len = cmd_uint32(cmd, optarg); break;
case 'L': cmd_check(max_allele_len == SIZE_MAX,cmd); max_allele_len = cmd_uint32(cmd, optarg); break;
case 'D': cmd_check(max_path_diff == SIZE_MAX, cmd); max_path_diff = cmd_uint32(cmd, optarg); break;
case 'm': nwmatch = cmd_int32(cmd, optarg); break;
case 'M': nwmismatch = cmd_int32(cmd, optarg); break;
case 'g': nwgapopen = cmd_int32(cmd, optarg); break;
case 'G': nwgapextend = cmd_int32(cmd, optarg); break;
case ':': /* BADARG */
case '?': /* BADCH getopt_long has already printed error */
die("`"CMD" calls2vcf -h` for help. Bad option: %s", argv[optind-1]);
default: ctx_assert2(0, "shouldn't reach here: %c", c);
}
}
// Defaults for unset values
if(out_path == NULL) out_path = default_out_path;
if(min_mapq == SIZE_MAX) min_mapq = DEFAULT_MIN_MAPQ;
if(max_align_len == SIZE_MAX) max_align_len = DEFAULT_MAX_ALIGN;
if(max_allele_len == SIZE_MAX) max_allele_len = DEFAULT_MAX_ALLELE;
if(max_path_diff == SIZE_MAX) max_path_diff = DEFAULT_MAX_PDIFF;
if(optind+2 > argc)
cmd_print_usage("Require <in.txt.gz> and at least one reference");
input_path = argv[optind++];
ref_paths = argv + optind;
num_ref_paths = argc - optind;
}
// if one of the files is reading from stdin, sum_kmers_ptr is set to 0
// `max_cols_ptr` is used to return the most colours being loaded from a single file
// returns the number of colours being loaded in total
size_t graph_files_open(char **graph_paths,
GraphFileReader *gfiles, size_t num_gfiles,
size_t *max_kmers_ptr, size_t *sum_kmers_ptr)
{
size_t i, ctx_max_kmers = 0, ctx_sum_kmers = 0;
bool ctx_uses_stdin = false;
size_t ncols = 0;
for(i = 0; i < num_gfiles; i++)
{
memset(&gfiles[i], 0, sizeof(GraphFileReader));
graph_file_open2(&gfiles[i], graph_paths[i], "r", ncols);
if(gfiles[0].hdr.kmer_size != gfiles[i].hdr.kmer_size) {
cmd_print_usage("Kmer sizes don't match [%u vs %u]",
gfiles[0].hdr.kmer_size, gfiles[i].hdr.kmer_size);
}
ncols = MAX2(ncols, file_filter_into_ncols(&gfiles[i].fltr));
ctx_max_kmers = MAX2(ctx_max_kmers, graph_file_nkmers(&gfiles[i]));
ctx_sum_kmers += graph_file_nkmers(&gfiles[i]);
ctx_uses_stdin |= file_filter_isstdin(&gfiles[i].fltr);
}
if(ctx_uses_stdin) ctx_sum_kmers = SIZE_MAX;
*max_kmers_ptr = ctx_max_kmers;
*sum_kmers_ptr = ctx_sum_kmers;
return ncols;
}
static void flanks_sam_open()
{
if(!futil_path_has_extension(sam_path, ".bam") &&
!futil_path_has_extension(sam_path, ".sam"))
{
cmd_print_usage("Mapped flanks is not .sam or .bam file: %s", sam_path);
}
bool isbam = futil_path_has_extension(sam_path, ".bam");
samfh = sam_open(sam_path, isbam ? "rb" : "rs");
if(samfh == NULL) die("Cannot open SAM/BAM %s", sam_path);
// Load BAM header
bam_header = sam_hdr_read(samfh);
bamentry = bam_init1();
}
int ctx_calls2vcf(int argc, char **argv)
{
parse_cmdline_args(argc, argv);
size_t i;
// These functions call die() on error
gzFile gzin = futil_gzopen(input_path, "r");
nw_aligner_setup();
// Read file header
cJSON *json = read_input_header(gzin);
// Get format (bubble or breakpoint file)
cJSON *json_fmt = json_hdr_get(json, "file_format", cJSON_String, input_path);
if(strcmp(json_fmt->valuestring,"CtxBreakpoints") == 0) input_bubble_format = false;
else if(strcmp(json_fmt->valuestring,"CtxBubbles") == 0) input_bubble_format = true;
else die("Unknown format: '%s'", json_fmt->valuestring);
status("Reading %s in %s format", futil_inpath_str(input_path),
input_bubble_format ? "bubble" : "breakpoint");
if(input_bubble_format && sam_path == NULL)
cmd_print_usage("Require -F <flanks.sam> with bubble file");
// Open flank file if it exists
if(sam_path) flanks_sam_open();
// Open output file
FILE *fout = futil_fopen_create(out_path, "w");
// Load reference genome
read_buf_alloc(&chroms, 1024);
genome = kh_init(ChromHash);
seq_reader_load_ref_genome(ref_paths, num_ref_paths, &chroms, genome);
// convert to upper case
char *s;
for(i = 0; i < chroms.len; i++)
for(s = chroms.b[i].seq.b; *s; s++) *s = toupper(*s);
if(!input_bubble_format) brkpnt_check_refs_match(json, input_path);
// Output VCF has 0 samples if bubbles file, otherwise has N where N is
// number of samples/colours in the breakpoint graph
size_t num_graph_samples = json_hdr_get_ncols(json, input_path);
size_t num_graph_nonref = json_hdr_get_nonref_ncols(json, input_path);
num_samples = 0;
if(!input_bubble_format) {
// If last colour has "is_ref", drop number of samples by one
num_samples = num_graph_nonref < num_graph_samples ? num_graph_samples-1
: num_graph_samples;
}
print_vcf_header(json, !input_bubble_format, fout);
status("Reading %s call file with %zu samples",
input_bubble_format ? "Bubble" : "Breakpoint", num_graph_samples);
status("Writing a VCF with %zu samples", num_samples);
parse_entries(gzin, fout);
// Print stats
char num_entries_read_str[50];
char num_vars_printed_str[50];
ulong_to_str(num_entries_read, num_entries_read_str);
ulong_to_str(num_vars_printed, num_vars_printed_str);
status("Read %s entries, printed %s vcf entries to: %s",
num_entries_read_str, num_vars_printed_str, futil_outpath_str(out_path));
if(input_bubble_format) {
char msg[200];
// Bubble caller specific
print_stat(num_flank5p_unmapped, num_entries_read, "flank 5p unmapped");
sprintf(msg, "flank 5p low mapq (<%zu)", min_mapq);
print_stat(num_flank5p_lowqual, num_entries_read, msg);
print_stat(num_flank3p_not_found, num_entries_read, "flank 3p not found");
print_stat(num_flank3p_multihits, num_entries_read, "flank 3p multiple hits");
print_stat(num_flank3p_approx_match,num_entries_read, "flank 3p approx match used");
print_stat(num_flank3p_exact_match, num_entries_read, "flank 3p exact match");
} else {
// Breakpoint caller specific
print_stat(num_flanks_not_uniquely_mapped, num_entries_read, "flank pairs contain one flank not mapped uniquely");
print_stat(num_flanks_diff_chroms, num_entries_read, "flank pairs map to diff chroms");
print_stat(num_flanks_diff_strands, num_entries_read, "flank pairs map to diff strands");
}
print_stat(num_flanks_too_far_apart, num_entries_read, "flank pairs too far apart");
print_stat(num_flanks_overlap_too_large, num_entries_read, "flank pairs overlap too much");
print_stat(num_entries_well_mapped, num_entries_read, "flank pairs map well");
status("Aligned %zu allele pairs and %zu flanks", num_nw_allele, num_nw_flank);
// Finished - clean up
cJSON_Delete(json);
gzclose(gzin);
fclose(fout);
for(i = 0; i < chroms.len; i++) seq_read_dealloc(&chroms.b[i]);
read_buf_dealloc(&chroms);
kh_destroy_ChromHash(genome);
nw_aligner_destroy();
if(sam_path) flanks_sam_close();
// hide unused method warnings
(void)kh_del_ChromHash;
(void)kh_put_ChromHash;
(void)kh_get_ChromHash;
(void)kh_clear_ChromHash;
(void)kh_destroy_ChromHash;
(void)kh_init_ChromHash;
return EXIT_SUCCESS;
}
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;
}
void cmd_parse(const char * str)
{
int name_len;
name_len=0;
char cmd_name[MAX_LEN_NAME];
int arg_len;
arg_len=0;
char cmd_arg[MAX_LEN_ARG];
while(*str && *str != ' ')
{
cmd_name[name_len] = *str;
name_len++;
str++;
}
cmd_name[name_len] = '\0';
while(*str && *str == ' ')
str++;
while(*str && *str != ' ')
{
cmd_arg[arg_len] = *str;
arg_len++;
str++;
}
cmd_arg[arg_len] = '\0';
if (console_streq(cmd_name, led_cmd.name))
{
int arg_value;
led_cfg_set(1);
if(arg_len == 0)
led_dat_set(!led_dat_get_state());
else if (arg_len == 1)
{
arg_value = atoi(cmd_arg);
if(arg_value == 1 || arg_value == 0)
led_dat_set(arg_value);
else
{
console_print("Bad argument : Not 0 or 1.\r\n");
cmd_print_usage(led_cmd);
}
}
else
{
console_print("Bad number of arguments\r\n");
cmd_print_usage(led_cmd);
}
console_prompt();
}
else if (console_streq(cmd_name, gpio_cmd.name))
{
gpio_output_set(9);
gpio_activate(9);
console_prompt();
}
else
{
console_print("Unknown command : ");
console_print(cmd_name);
console_print("\r\n");
console_prompt();
}
}
int ctx_exp_abc(int argc, char **argv)
{
size_t i, nthreads = 0, num_repeats = 0, max_AB_dist = 0;
struct MemArgs memargs = MEM_ARGS_INIT;
bool print_failed_contigs = false;
GPathReader tmp_gpfile;
GPathFileBuffer gpfiles;
gpfile_buf_alloc(&gpfiles, 8);
// 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 't': cmd_check(!nthreads,cmd); nthreads = cmd_uint32_nonzero(cmd, optarg); break;
case 'm': cmd_mem_args_set_memory(&memargs, optarg); break;
case 'n': cmd_mem_args_set_nkmers(&memargs, optarg); break;
case 'p':
memset(&tmp_gpfile, 0, sizeof(GPathReader));
gpath_reader_open(&tmp_gpfile, optarg);
gpfile_buf_push(&gpfiles, &tmp_gpfile, 1);
break;
case 'N': cmd_check(!num_repeats,cmd); num_repeats = cmd_uint32_nonzero(cmd, optarg); break;
case 'M': cmd_check(!max_AB_dist,cmd); max_AB_dist = cmd_uint32_nonzero(cmd, optarg); break;
case 'P': cmd_check(!print_failed_contigs,cmd); print_failed_contigs = true; break;
case ':': /* BADARG */
case '?': /* BADCH getopt_long has already printed error */
// cmd_print_usage(NULL);
die("`"CMD" exp_abc -h` for help. Bad option: %s", argv[optind-1]);
default: abort();
}
}
// Defaults
if(nthreads == 0) nthreads = DEFAULT_NTHREADS;
if(num_repeats == 0) num_repeats = DEFAULT_NUM_REPEATS;
if(max_AB_dist == 0) max_AB_dist = DEFAULT_MAX_AB_DIST;
if(print_failed_contigs && nthreads != 1) {
warn("--print forces nthreads to be one. soz.");
nthreads = 1;
}
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_open(&gfile, ctx_path);
size_t ncols = file_filter_into_ncols(&gfile.fltr);
// Check only loading one colour
if(ncols > 1) die("Only implemented for one colour currently");
// Check graph + paths are compatible
graphs_gpaths_compatible(&gfile, 1, gpfiles.b, gpfiles.len, -1);
//
// Decide on memory
//
size_t bits_per_kmer, kmers_in_hash, graph_mem, path_mem, total_mem;
// 1 bit needed per kmer if we need to keep track of kmer usage
bits_per_kmer = sizeof(BinaryKmer)*8 + sizeof(Edges)*8 + sizeof(GPath*)*8 +
ncols;
kmers_in_hash = cmd_get_kmers_in_hash(memargs.mem_to_use,
memargs.mem_to_use_set,
memargs.num_kmers,
memargs.num_kmers_set,
bits_per_kmer,
gfile.num_of_kmers, gfile.num_of_kmers,
false, &graph_mem);
// Paths memory
size_t rem_mem = memargs.mem_to_use - MIN2(memargs.mem_to_use, graph_mem);
path_mem = gpath_reader_mem_req(gpfiles.b, gpfiles.len, ncols, rem_mem, false,
kmers_in_hash, false);
// Shift path store memory from graphs->paths
graph_mem -= sizeof(GPath*)*kmers_in_hash;
path_mem += sizeof(GPath*)*kmers_in_hash;
cmd_print_mem(path_mem, "paths");
total_mem = graph_mem + path_mem;
cmd_check_mem_limit(memargs.mem_to_use, total_mem);
//
// Allocate memory
//
dBGraph db_graph;
db_graph_alloc(&db_graph, gfile.hdr.kmer_size, 1, 1, kmers_in_hash,
DBG_ALLOC_EDGES | DBG_ALLOC_NODE_IN_COL);
// Paths
gpath_reader_alloc_gpstore(gpfiles.b, gpfiles.len, path_mem, false, &db_graph);
// Load the graph
GraphLoadingPrefs gprefs = graph_loading_prefs(&db_graph);
gprefs.empty_colours = true;
graph_load(&gfile, gprefs, NULL);
graph_file_close(&gfile);
hash_table_print_stats(&db_graph.ht);
// Load link files
for(i = 0; i < gpfiles.len; i++) {
gpath_reader_load(&gpfiles.b[i], GPATH_DIE_MISSING_KMERS, &db_graph);
gpath_reader_close(&gpfiles.b[i]);
}
gpfile_buf_dealloc(&gpfiles);
status("\n");
status("Test 1: Priming region A->B (n: %zu max_AB_dist: %zu)",
num_repeats, max_AB_dist);
run_exp_abc(&db_graph, true, nthreads, num_repeats,
max_AB_dist, print_failed_contigs);
status("\n");
status("Test 2: Trying to traverse A->B (n: %zu max_AB_dist: %zu)",
num_repeats, max_AB_dist);
run_exp_abc(&db_graph, false, nthreads, num_repeats,
max_AB_dist, print_failed_contigs);
db_graph_dealloc(&db_graph);
return EXIT_SUCCESS;
}
int ctx_pop_bubbles(int argc, char **argv)
{
size_t nthreads = 0;
struct MemArgs memargs = MEM_ARGS_INIT;
const char *out_path = NULL;
int32_t max_covg = -1; // max mean coverage to remove <=0 => ignore
int32_t max_klen = -1; // max length (kmers) to remove <=0 => ignore
int32_t max_kdiff = -1; // max diff between bubble branch lengths <0 => ignore
// 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 'f': cmd_check(!futil_get_force(), cmd); futil_set_force(true); break;
case 't': cmd_check(!nthreads, cmd); nthreads = cmd_uint32_nonzero(cmd, optarg); break;
case 'm': cmd_mem_args_set_memory(&memargs, optarg); break;
case 'n': cmd_mem_args_set_nkmers(&memargs, optarg); break;
case 'C': cmd_check(max_covg<0, cmd); max_covg = cmd_uint32(cmd, optarg); break;
case 'L': cmd_check(max_klen<0, cmd); max_klen = cmd_uint32(cmd, optarg); break;
case 'D': cmd_check(max_kdiff<0, cmd); max_kdiff = cmd_uint32(cmd, optarg); break;
case ':': /* BADARG */
case '?': /* BADCH getopt_long has already printed error */
// cmd_print_usage(NULL);
die("`"CMD" pop -h` for help. Bad option: %s", argv[optind-1]);
default: abort();
}
}
// Defaults for unset values
if(out_path == NULL) out_path = "-";
if(nthreads == 0) nthreads = DEFAULT_NTHREADS;
if(optind >= argc) cmd_print_usage("Require input graph files (.ctx)");
//
// Open graph files
//
const size_t num_gfiles = argc - optind;
char **graph_paths = argv + optind;
ctx_assert(num_gfiles > 0);
GraphFileReader *gfiles = ctx_calloc(num_gfiles, sizeof(GraphFileReader));
size_t i, ncols, ctx_max_kmers = 0, ctx_sum_kmers = 0;
ncols = graph_files_open(graph_paths, gfiles, num_gfiles,
&ctx_max_kmers, &ctx_sum_kmers);
bool reread_graph_to_filter = (num_gfiles == 1 &&
strcmp(file_filter_path(&gfiles[0].fltr),"-") != 0);
if(reread_graph_to_filter) {
file_filter_flatten(&gfiles[0].fltr, 0);
ncols = 1;
}
// Check graphs are compatible
graphs_gpaths_compatible(gfiles, num_gfiles, NULL, 0, -1);
//
// Decide on memory
//
size_t bits_per_kmer, kmers_in_hash, graph_mem;
bits_per_kmer = sizeof(BinaryKmer)*8 +
sizeof(Covg)*8*ncols +
sizeof(Edges)*8*ncols +
2; // 1 bit for visited, 1 for removed
kmers_in_hash = cmd_get_kmers_in_hash(memargs.mem_to_use,
memargs.mem_to_use_set,
memargs.num_kmers,
memargs.num_kmers_set,
bits_per_kmer,
ctx_max_kmers, ctx_sum_kmers,
false, &graph_mem);
cmd_check_mem_limit(memargs.mem_to_use, graph_mem);
// Check out_path is writable
futil_create_output(out_path);
// Allocate memory
dBGraph db_graph;
db_graph_alloc(&db_graph, gfiles[0].hdr.kmer_size, ncols, ncols,
kmers_in_hash, DBG_ALLOC_EDGES | DBG_ALLOC_COVGS);
size_t nkwords = roundup_bits2bytes(db_graph.ht.capacity);
uint8_t *visited = ctx_calloc(1, nkwords);
uint8_t *rmvbits = ctx_calloc(1, nkwords);
//
// Load graphs
//
GraphLoadingPrefs gprefs = graph_loading_prefs(&db_graph);
gprefs.empty_colours = true;
for(i = 0; i < num_gfiles; i++) {
graph_load(&gfiles[i], gprefs, NULL);
graph_file_close(&gfiles[i]);
gprefs.empty_colours = false;
}
ctx_free(gfiles);
hash_table_print_stats(&db_graph.ht);
PopBubblesPrefs prefs = {.max_rmv_covg = max_covg,
.max_rmv_klen = max_klen,
.max_rmv_kdiff = max_kdiff};
size_t npopped = 0;
char npopped_str[50];
status("Popping bubbles...");
npopped = pop_bubbles(&db_graph, nthreads, prefs, visited, rmvbits);
ulong_to_str(npopped, npopped_str);
status("Popped %s bubbles", npopped_str);
size_t nkmers0 = db_graph.ht.num_kmers;
status("Removing nodes...");
for(i = 0; i < nkwords; i++) rmvbits[i] = ~rmvbits[i];
prune_nodes_lacking_flag(nthreads, rmvbits, &db_graph);
size_t nkmers1 = db_graph.ht.num_kmers;
ctx_assert(nkmers1 <= nkmers0);
char nkmers0str[50], nkmers1str[50], ndiffstr[50];
ulong_to_str(nkmers0, nkmers0str);
ulong_to_str(nkmers1, nkmers1str);
ulong_to_str(nkmers0-nkmers1, ndiffstr);
status("Number of kmers %s -> %s (-%s)", nkmers0str, nkmers1str, ndiffstr);
if(reread_graph_to_filter)
{
status("Streaming filtered file to: %s\n", out_path);
GraphFileReader gfile;
memset(&gfile, 0, sizeof(GraphFileReader));
graph_file_open(&gfile, graph_paths[0]);
graph_writer_stream_mkhdr(out_path, &gfile, &db_graph,
db_graph.col_edges, NULL);
graph_file_close(&gfile);
}
else
{
status("Saving to: %s\n", out_path);
graph_writer_save_mkhdr(out_path, &db_graph, CTX_GRAPH_FILEFORMAT, NULL,
0, ncols);
}
ctx_free(visited);
ctx_free(rmvbits);
db_graph_dealloc(&db_graph);
return EXIT_SUCCESS;
}
int ctx_contigs(int argc, char **argv)
{
size_t nthreads = 0;
struct MemArgs memargs = MEM_ARGS_INIT;
const char *out_path = NULL;
size_t i, contig_limit = 0, colour = 0;
bool cmd_reseed = false, cmd_no_reseed = false; // -r, -R
const char *conf_table_path = NULL; // save confidence table to here
bool use_missing_info_check = true, seed_with_unused_paths = false;
double min_step_confid = -1.0, min_cumul_confid = -1.0; // < 0 => no min
// Read length and expected depth for calculating confidences
size_t genome_size = 0;
seq_file_t *tmp_seed_file = NULL;
SeqFilePtrBuffer seed_buf;
seq_file_ptr_buf_alloc(&seed_buf, 16);
GPathReader tmp_gpfile;
GPathFileBuffer gpfiles;
gpfile_buf_alloc(&gpfiles, 8);
// Arg parsing
char cmd[100], 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 'o': cmd_check(!out_path,cmd); out_path = optarg; break;
case 't': cmd_check(!nthreads,cmd); nthreads = cmd_uint32_nonzero(cmd, optarg); break;
case 'm': cmd_mem_args_set_memory(&memargs, optarg); break;
case 'n': cmd_mem_args_set_nkmers(&memargs, optarg); break;
case 'p':
memset(&tmp_gpfile, 0, sizeof(GPathReader));
gpath_reader_open(&tmp_gpfile, optarg);
gpfile_buf_push(&gpfiles, &tmp_gpfile, 1);
break;
case '1':
case 's': // --seed <in.fa>
if((tmp_seed_file = seq_open(optarg)) == NULL)
die("Cannot read --seed file: %s", optarg);
seq_file_ptr_buf_add(&seed_buf, tmp_seed_file);
break;
case 'r': cmd_check(!cmd_reseed,cmd); cmd_reseed = true; break;
case 'R': cmd_check(!cmd_no_reseed,cmd); cmd_no_reseed = true; break;
case 'N':
cmd_check(!contig_limit,cmd);
contig_limit = cmd_uint32_nonzero(cmd, optarg);
break;
case 'c': cmd_check(!colour,cmd); colour = cmd_uint32(cmd, optarg); break;
case 'G': cmd_check(!genome_size,cmd); genome_size = cmd_bases(cmd, optarg); break;
case 'S': cmd_check(!conf_table_path,cmd); conf_table_path = optarg; break;
case 'M': cmd_check(use_missing_info_check,cmd); use_missing_info_check = false; break;
case 'P': cmd_check(!seed_with_unused_paths,cmd); seed_with_unused_paths = true; break;
case 'C':
cmd_check(min_cumul_confid < 0,cmd);
min_cumul_confid = cmd_udouble(cmd,optarg);
if(min_cumul_confid > 1) die("%s must be 0 <= x <= 1", cmd);
break;
case 'T':
cmd_check(min_step_confid < 0,cmd);
min_step_confid = cmd_udouble(cmd,optarg);
if(min_step_confid > 1) die("%s must be 0 <= x <= 1", cmd);
break;
case ':': /* BADARG */
case '?': /* BADCH getopt_long has already printed error */
die("`"CMD" contigs -h` for help. Bad option: %s", argv[optind-1]);
default: abort();
}
}
if(cmd_no_reseed && cmd_reseed)
cmd_print_usage("Cannot specify both -r and -R");
if(contig_limit && seed_with_unused_paths)
cmd_print_usage("Cannot combine --ncontigs with --use-seed-paths");
bool sample_with_replacement = cmd_reseed;
// Defaults
if(nthreads == 0) nthreads = DEFAULT_NTHREADS;
if(!seed_buf.len && !contig_limit && sample_with_replacement) {
cmd_print_usage("Please specify one or more of: "
"--no-reseed | --ncontigs | --seed <in.fa>");
}
if(optind >= argc) cmd_print_usage("Require input graph files (.ctx)");
//
// Open graph files
//
const size_t num_gfiles = argc - optind;
char **graph_paths = argv + optind;
ctx_assert(num_gfiles > 0);
GraphFileReader *gfiles = ctx_calloc(num_gfiles, sizeof(GraphFileReader));
size_t ncols, ctx_max_kmers = 0, ctx_sum_kmers = 0;
graph_files_open(graph_paths, gfiles, num_gfiles,
&ctx_max_kmers, &ctx_sum_kmers);
// char *ctx_path = argv[optind];
//
// Open Graph file
//
// GraphFileReader gfile;
// memset(&gfile, 0, sizeof(GraphFileReader));
// graph_file_open(&gfile, ctx_path);
// Update colours in graph file - sample in 0, all others in 1
// never need more than two colours
ncols = gpath_load_sample_pop(gfiles, num_gfiles,
gpfiles.b, gpfiles.len, colour);
// Check for compatibility between graph files and path files
// pop_colour is colour 1
graphs_gpaths_compatible(gfiles, num_gfiles, gpfiles.b, gpfiles.len, 1);
if(!genome_size)
{
char nk_str[50];
if(ctx_max_kmers <= 0) die("Please pass --genome <G> if streaming");
genome_size = ctx_max_kmers;
ulong_to_str(genome_size, nk_str);
status("Taking number of kmers as genome size: %s", nk_str);
}
//
// Decide on memory
//
size_t bits_per_kmer, kmers_in_hash, graph_mem, path_mem, total_mem;
// 1 bit needed per kmer if we need to keep track of kmer usage
bits_per_kmer = sizeof(BinaryKmer)*8 + sizeof(Edges)*8 + sizeof(GPath*)*8 +
ncols + !sample_with_replacement;
kmers_in_hash = cmd_get_kmers_in_hash(memargs.mem_to_use,
memargs.mem_to_use_set,
memargs.num_kmers,
memargs.num_kmers_set,
bits_per_kmer,
ctx_max_kmers, ctx_sum_kmers,
false, &graph_mem);
// Paths memory
size_t rem_mem = memargs.mem_to_use - MIN2(memargs.mem_to_use, graph_mem);
path_mem = gpath_reader_mem_req(gpfiles.b, gpfiles.len, ncols, rem_mem, false);
// Shift path store memory from graphs->paths
graph_mem -= sizeof(GPath*)*kmers_in_hash;
path_mem += sizeof(GPath*)*kmers_in_hash;
cmd_print_mem(path_mem, "paths");
// Total memory
total_mem = graph_mem + path_mem;
cmd_check_mem_limit(memargs.mem_to_use, total_mem);
// Load contig hist distribution from ctp files
ZeroSizeBuffer contig_hist;
memset(&contig_hist, 0, sizeof(contig_hist));
for(i = 0; i < gpfiles.len; i++) {
gpath_reader_load_contig_hist(gpfiles.b[i].json,
gpfiles.b[i].fltr.path.b,
file_filter_fromcol(&gpfiles.b[i].fltr, 0),
&contig_hist);
}
// Calculate confidences, only for one colour
ContigConfidenceTable conf_table;
conf_table_alloc(&conf_table, 1);
conf_table_update_hist(&conf_table, 0, genome_size,
contig_hist.b, contig_hist.len);
if(conf_table_path != NULL) {
conf_table_save(&conf_table, conf_table_path);
}
zsize_buf_dealloc(&contig_hist);
//
// Output file if printing
//
FILE *fout = out_path ? futil_fopen_create(out_path, "w") : NULL;
// Allocate
dBGraph db_graph;
db_graph_alloc(&db_graph, gfiles[0].hdr.kmer_size, ncols, 1, kmers_in_hash,
DBG_ALLOC_EDGES | DBG_ALLOC_NODE_IN_COL);
// Paths
gpath_reader_alloc_gpstore(gpfiles.b, gpfiles.len, path_mem,
false, &db_graph);
uint8_t *visited = NULL;
if(!sample_with_replacement)
visited = ctx_calloc(roundup_bits2bytes(db_graph.ht.capacity), 1);
// Load graph
LoadingStats stats = LOAD_STATS_INIT_MACRO;
GraphLoadingPrefs gprefs = {.db_graph = &db_graph,
.boolean_covgs = false,
.must_exist_in_graph = false,
.empty_colours = true};
for(i = 0; i < num_gfiles; i++) {
graph_load(&gfiles[i], gprefs, &stats);
graph_file_close(&gfiles[i]);
gprefs.empty_colours = false;
}
ctx_free(gfiles);
hash_table_print_stats(&db_graph.ht);
// Load path files
for(i = 0; i < gpfiles.len; i++) {
gpath_reader_load(&gpfiles.b[i], GPATH_DIE_MISSING_KMERS, &db_graph);
gpath_reader_close(&gpfiles.b[i]);
}
gpfile_buf_dealloc(&gpfiles);
AssembleContigStats assem_stats;
assemble_contigs_stats_init(&assem_stats);
assemble_contigs(nthreads, seed_buf.b, seed_buf.len,
contig_limit, visited,
use_missing_info_check, seed_with_unused_paths,
min_step_confid, min_cumul_confid,
fout, out_path, &assem_stats, &conf_table,
&db_graph, 0); // Sample always loaded into colour zero
if(fout && fout != stdout) fclose(fout);
assemble_contigs_stats_print(&assem_stats);
assemble_contigs_stats_destroy(&assem_stats);
conf_table_dealloc(&conf_table);
for(i = 0; i < seed_buf.len; i++)
seq_close(seed_buf.b[i]);
seq_file_ptr_buf_dealloc(&seed_buf);
ctx_free(visited);
db_graph_dealloc(&db_graph);
return EXIT_SUCCESS;
}
int ctx_thread(int argc, char **argv)
{
struct ReadThreadCmdArgs args;
read_thread_args_alloc(&args);
read_thread_args_parse(&args, argc, argv, longopts, false);
GraphFileReader *gfile = &args.gfile;
GPathFileBuffer *gpfiles = &args.gpfiles;
CorrectAlnInputBuffer *inputs = &args.inputs;
size_t i;
if(args.zero_link_counts && gpfiles->len == 0)
cmd_print_usage("-0,--zero-paths without -p,--paths <in.ctp> has no meaning");
// Check each path file only loads one colour
gpaths_only_for_colour(gpfiles->b, gpfiles->len, 0);
//
// Decide on memory
//
size_t bits_per_kmer, kmers_in_hash, graph_mem, total_mem;
size_t path_hash_mem, path_store_mem, path_mem;
bool sep_path_list = (!args.use_new_paths && gpfiles->len > 0);
bits_per_kmer = sizeof(BinaryKmer)*8 + sizeof(Edges)*8 + sizeof(GPath*)*8 +
2 * args.nthreads; // Have traversed
// false -> don't use mem_to_use to decide how many kmers to store in hash
// since we need some of that memory for storing paths
kmers_in_hash = cmd_get_kmers_in_hash(args.memargs.mem_to_use,
args.memargs.mem_to_use_set,
args.memargs.num_kmers,
args.memargs.num_kmers_set,
bits_per_kmer,
gfile->num_of_kmers,
gfile->num_of_kmers,
false, &graph_mem);
// Paths memory
size_t min_path_mem = 0;
gpath_reader_sum_mem(gpfiles->b, gpfiles->len, 1, true, true, &min_path_mem);
if(graph_mem + min_path_mem > args.memargs.mem_to_use) {
char buf[50];
die("Require at least %s memory", bytes_to_str(graph_mem+min_path_mem, 1, buf));
}
path_mem = args.memargs.mem_to_use - graph_mem;
size_t pentry_hash_mem = sizeof(GPEntry)/0.7;
size_t pentry_store_mem = sizeof(GPath) + 8 + // struct + sequence
1 + // in colour
sizeof(uint8_t) + // counts
sizeof(uint32_t); // kmer length
size_t max_paths = path_mem / (pentry_store_mem + pentry_hash_mem);
path_store_mem = max_paths * pentry_store_mem;
path_hash_mem = max_paths * pentry_hash_mem;
cmd_print_mem(path_hash_mem, "paths hash");
cmd_print_mem(path_store_mem, "paths store");
total_mem = graph_mem + path_mem;
cmd_check_mem_limit(args.memargs.mem_to_use, total_mem);
//
// Open output file
//
gzFile gzout = futil_gzopen_create(args.out_ctp_path, "w");
status("Creating paths file: %s", futil_outpath_str(args.out_ctp_path));
//
// Allocate memory
//
dBGraph db_graph;
size_t kmer_size = gfile->hdr.kmer_size;
db_graph_alloc(&db_graph, kmer_size, 1, 1, kmers_in_hash,
DBG_ALLOC_EDGES | DBG_ALLOC_NODE_IN_COL);
// Split path memory 2:1 between store and hash
// Create a path store that tracks path counts
gpath_store_alloc(&db_graph.gpstore,
db_graph.num_of_cols, db_graph.ht.capacity,
0, path_store_mem, true, sep_path_list);
// Create path hash table for fast lookup
gpath_hash_alloc(&db_graph.gphash, &db_graph.gpstore, path_hash_mem);
if(args.use_new_paths) {
status("Using paths as they are added (risky)");
} else {
status("Not using new paths as they are added (safe)");
}
//
// Start up workers to add paths to the graph
//
GenPathWorker *workers;
workers = gen_paths_workers_alloc(args.nthreads, &db_graph);
// Setup for loading graphs graph
LoadingStats gstats;
loading_stats_init(&gstats);
// Path statistics
LoadingStats *load_stats = gen_paths_get_stats(workers);
CorrectAlnStats *aln_stats = gen_paths_get_aln_stats(workers);
// Load contig hist distribution
for(i = 0; i < gpfiles->len; i++) {
gpath_reader_load_contig_hist(gpfiles->b[i].json,
gpfiles->b[i].fltr.path.b,
file_filter_fromcol(&gpfiles->b[i].fltr, 0),
&aln_stats->contig_histgrm);
}
GraphLoadingPrefs gprefs = {.db_graph = &db_graph,
.boolean_covgs = false,
.must_exist_in_graph = false,
.must_exist_in_edges = NULL,
.empty_colours = false}; // already loaded paths
// Load graph, print stats, close file
graph_load(gfile, gprefs, &gstats);
hash_table_print_stats_brief(&db_graph.ht);
graph_file_close(gfile);
// Load existing paths
for(i = 0; i < gpfiles->len; i++)
gpath_reader_load(&gpfiles->b[i], GPATH_DIE_MISSING_KMERS, &db_graph);
// zero link counts of already loaded links
if(args.zero_link_counts) {
status("Zeroing link counts for loaded links");
gpath_set_zero_nseen(&db_graph.gpstore.gpset);
}
if(!args.use_new_paths)
gpath_store_split_read_write(&db_graph.gpstore);
// Deal with a set of files at once
// Can have different numbers of inputs vs threads
size_t start, end;
for(start = 0; start < inputs->len; start += MAX_IO_THREADS)
{
end = MIN2(inputs->len, start+MAX_IO_THREADS);
generate_paths(inputs->b+start, end-start, workers, args.nthreads);
}
// Print memory statistics
gpath_hash_print_stats(&db_graph.gphash);
gpath_store_print_stats(&db_graph.gpstore);
correct_aln_dump_stats(aln_stats, load_stats,
args.dump_seq_sizes,
args.dump_frag_sizes,
db_graph.ht.num_kmers);
// Don't need GPathHash anymore
gpath_hash_dealloc(&db_graph.gphash);
cJSON **hdrs = ctx_malloc(gpfiles->len * sizeof(cJSON*));
for(i = 0; i < gpfiles->len; i++) hdrs[i] = gpfiles->b[i].json;
size_t output_threads = MIN2(args.nthreads, MAX_IO_THREADS);
// Generate a cJSON header for all inputs
cJSON *thread_hdr = cJSON_CreateObject();
cJSON *inputs_hdr = cJSON_CreateArray();
cJSON_AddItemToObject(thread_hdr, "inputs", inputs_hdr);
for(i = 0; i < inputs->len; i++)
cJSON_AddItemToArray(inputs_hdr, correct_aln_input_json_hdr(&inputs->b[i]));
// Write output file
gpath_save(gzout, args.out_ctp_path, output_threads, true,
"thread", thread_hdr, hdrs, gpfiles->len,
&aln_stats->contig_histgrm, 1,
&db_graph);
gzclose(gzout);
ctx_free(hdrs);
// Optionally run path checks for debugging
// gpath_checks_all_paths(&db_graph, args.nthreads);
// ins_gap, err_gap no longer allocated after this line
gen_paths_workers_dealloc(workers, args.nthreads);
// Close and free input files etc.
read_thread_args_dealloc(&args);
db_graph_dealloc(&db_graph);
return EXIT_SUCCESS;
}
// Returns 0 on success, otherwise != 0
int ctx_unitigs(int argc, char **argv)
{
size_t nthreads = 0;
struct MemArgs memargs = MEM_ARGS_INIT;
const char *out_path = NULL;
UnitigSyntax syntax = PRINT_FASTA;
bool dot_use_points = false;
// 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 'o': cmd_check(!out_path, cmd); out_path = optarg; break;
case 't': cmd_check(!nthreads, cmd); nthreads = cmd_uint32_nonzero(cmd, optarg); break;
case 'm': cmd_mem_args_set_memory(&memargs, optarg); break;
case 'n': cmd_mem_args_set_nkmers(&memargs, optarg); break;
case 'F': cmd_check(!syntax, cmd); syntax = PRINT_FASTA; break;
case 'g': cmd_check(!syntax, cmd); syntax = PRINT_GFA; break;
case 'd': cmd_check(!syntax, cmd); syntax = PRINT_DOT; break;
case 'P': cmd_check(!dot_use_points, cmd); dot_use_points = true; break;
case ':': /* BADARG */
case '?': /* BADCH getopt_long has already printed error */
die("`"CMD" unitigs -h` for help. Bad option: %s", argv[optind-1]);
default: abort();
}
}
if(dot_use_points && syntax == PRINT_FASTA)
cmd_print_usage("--point is only for use with --dot");
// Defaults for unset values
if(out_path == NULL) out_path = "-";
if(nthreads == 0) nthreads = DEFAULT_NTHREADS;
if(optind >= argc) cmd_print_usage(NULL);
size_t i, num_gfiles = (size_t)(argc - optind);
char **gfile_paths = argv + optind;
if(dot_use_points && syntax != PRINT_DOT)
cmd_print_usage("--points only valid with --graphviz / --dot");
ctx_assert(num_gfiles > 0);
// Open graph files
GraphFileReader *gfiles = ctx_calloc(num_gfiles, sizeof(GraphFileReader));
size_t ctx_max_kmers = 0, ctx_sum_kmers = 0;
graph_files_open(gfile_paths, gfiles, num_gfiles,
&ctx_max_kmers, &ctx_sum_kmers);
//
// Decide on memory
//
size_t bits_per_kmer, kmers_in_hash, graph_mem;
bits_per_kmer = sizeof(BinaryKmer)*8 + sizeof(Edges)*8 + 1;
if(syntax != PRINT_FASTA) bits_per_kmer += sizeof(UnitigEnd) * 8;
kmers_in_hash = cmd_get_kmers_in_hash(memargs.mem_to_use,
memargs.mem_to_use_set,
memargs.num_kmers,
memargs.num_kmers_set,
bits_per_kmer,
ctx_max_kmers, ctx_sum_kmers,
true, &graph_mem);
cmd_check_mem_limit(memargs.mem_to_use, graph_mem);
status("Output in %s format to %s\n", syntax_strs[syntax],
futil_outpath_str(out_path));
//
// Open output file
//
// Print to stdout unless --out <out> is specified
FILE *fout = futil_fopen_create(out_path, "w");
//
// Allocate memory
//
dBGraph db_graph;
db_graph_alloc(&db_graph, gfiles[0].hdr.kmer_size, 1, 1, kmers_in_hash,
DBG_ALLOC_EDGES);
UnitigPrinter printer;
unitig_printer_init(&printer, &db_graph, nthreads, syntax, fout);
if(syntax == PRINT_DOT || syntax == PRINT_GFA)
unitig_graph_alloc(&printer.ugraph, &db_graph);
// Load graphs
GraphLoadingPrefs gprefs = {.db_graph = &db_graph,
.boolean_covgs = false,
.must_exist_in_graph = false,
.empty_colours = false};
for(i = 0; i < num_gfiles; i++) {
file_filter_flatten(&gfiles[i].fltr, 0);
graph_load(&gfiles[i], gprefs, NULL);
graph_file_close(&gfiles[i]);
}
ctx_free(gfiles);
hash_table_print_stats(&db_graph.ht);
switch(syntax)
{
case PRINT_FASTA:
status("Printing unitgs in FASTA using %zu threads", nthreads);
supernodes_iterate(nthreads, printer.visited, &db_graph,
print_unitig_fasta, &printer);
break;
case PRINT_GFA:
print_gfa_syntax(&printer);
break;
case PRINT_DOT:
print_dot_syntax(&printer, dot_use_points);
break;
default:
die("Invalid print syntax: %i", syntax);
}
char num_unitigs_str[50];
ulong_to_str(printer.num_unitigs, num_unitigs_str);
status("Dumped %s unitigs\n", num_unitigs_str);
fclose(fout);
unitig_printer_destroy(&printer);
db_graph_dealloc(&db_graph);
return EXIT_SUCCESS;
}
int ctx_correct(int argc, char **argv)
{
size_t i, j;
struct ReadThreadCmdArgs args = READ_THREAD_CMD_ARGS_INIT;
read_thread_args_alloc(&args);
read_thread_args_parse(&args, argc, argv, longopts, true);
GraphFileReader *gfile = &args.gfile;
PathFileBuffer *pfiles = &args.pfiles;
CorrectAlnInputBuffer *inputs = &args.inputs;
size_t ctx_total_cols = gfile->hdr.num_of_cols;
size_t ctx_num_kmers = gfile->num_of_kmers;
if(args.colour > ctx_total_cols)
cmd_print_usage("-c %zu is too big [> %zu]", args.colour, ctx_total_cols);
size_t ctp_usedcols = 0;
for(i = 0; i < pfiles->len; i++) {
if(!file_filter_iscolloaded(&pfiles->data[i].fltr, args.colour)) {
cmd_print_usage("Path file doesn't load into colour %zu: %s",
args.colour, pfiles->data[i].fltr.orig_path.buff);
}
ctp_usedcols = MAX2(ctp_usedcols, path_file_usedcols(&pfiles->data[i]));
}
//
// Decide on memory
//
size_t bits_per_kmer, kmers_in_hash, graph_mem, path_mem, total_mem;
// 1 bit needed per kmer if we need to keep track of noreseed
bits_per_kmer = sizeof(Edges)*8 + ctx_num_kmers + sizeof(uint64_t)*8;
kmers_in_hash = cmd_get_kmers_in_hash2(args.memargs.mem_to_use,
args.memargs.mem_to_use_set,
args.memargs.num_kmers,
args.memargs.num_kmers_set,
bits_per_kmer,
ctx_num_kmers, ctx_num_kmers,
false, &graph_mem);
// Paths memory
path_mem = path_files_mem_required(pfiles->data, pfiles->len, false, false,
ctp_usedcols, 0);
cmd_print_mem(path_mem, "paths");
// Total memory
total_mem = graph_mem + path_mem;
cmd_check_mem_limit(args.memargs.mem_to_use, total_mem);
//
// Check we can read all output files
//
// Open output files
SeqOutput *outputs = ctx_calloc(inputs->len, sizeof(SeqOutput));
bool output_files_exist = false;
for(i = 0; i < inputs->len; i++)
{
CorrectAlnInput *input = &inputs->data[i];
input->crt_params.ctxcol = input->crt_params.ctpcol = args.colour;
SeqOutput *output = &outputs[i];
seq_output_alloc(output);
seq_output_set_paths(output, input->out_base,
async_task_pe_output(&input->files));
input->output = output;
// output check prints warnings and returns true if errors
output_files_exist |= seq_output_files_exist_check(output);
}
// Abandon if some of the output files already exist
if(output_files_exist) die("Output files already exist");
// Attempt to open all files
for(i = 0; i < inputs->len && seq_output_open(&outputs[i]); i++) {}
// Check if something went wrong - if so remove all output files
if(i < inputs->len) {
for(j = 0; j < i; j++) seq_output_delete(&outputs[i]);
die("Couldn't open output files");
}
//
// Allocate memory
//
dBGraph db_graph;
db_graph_alloc(&db_graph, gfile->hdr.kmer_size, ctx_total_cols, 1, kmers_in_hash);
size_t bytes_per_col = roundup_bits2bytes(db_graph.ht.capacity);
db_graph.col_edges = ctx_calloc(db_graph.ht.capacity, sizeof(Edges));
db_graph.node_in_cols = ctx_calloc(bytes_per_col * ctx_total_cols, 1);
// Paths
path_store_alloc(&db_graph.pstore, path_mem, false,
db_graph.ht.capacity, ctp_usedcols);
//
// Load Graph and Path files
//
LoadingStats gstats = LOAD_STATS_INIT_MACRO;
GraphLoadingPrefs gprefs = {.db_graph = &db_graph,
.boolean_covgs = false,
.must_exist_in_graph = false,
.must_exist_in_edges = NULL,
.empty_colours = true};
// Load graph, print stats, close file
graph_load(gfile, gprefs, &gstats);
hash_table_print_stats_brief(&db_graph.ht);
graph_file_close(gfile);
// Load path files (does nothing if num_fpiles == 0)
paths_format_merge(pfiles->data, pfiles->len, false, false,
args.num_of_threads, &db_graph);
//
// Run alignment
//
correct_reads(args.num_of_threads, MAX_IO_THREADS,
inputs->data, inputs->len,
&db_graph);
// Close and free output files
for(i = 0; i < inputs->len; i++) seq_output_dealloc(&outputs[i]);
ctx_free(outputs);
read_thread_args_dealloc(&args);
db_graph_dealloc(&db_graph);
return EXIT_SUCCESS;
}
int ctx_infer_edges(int argc, char **argv)
{
size_t num_of_threads = DEFAULT_NTHREADS;
struct MemArgs memargs = MEM_ARGS_INIT;
char *out_ctx_path = NULL;
bool add_pop_edges = false, add_all_edges = false;
// Arg parsing
char cmd[100];
char shortopts[100];
cmd_long_opts_to_short(longopts, shortopts, sizeof(shortopts));
int c;
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 'o': cmd_check(!out_ctx_path,cmd); out_ctx_path = optarg; break;
case 't': num_of_threads = cmd_uint32_nonzero(cmd, optarg); break;
case 'm': cmd_mem_args_set_memory(&memargs, optarg); break;
case 'n': cmd_mem_args_set_nkmers(&memargs, optarg); break;
case 'A': add_all_edges = true; break;
case 'P': add_pop_edges = true; break;
case ':': /* BADARG */
case '?': /* BADCH getopt_long has already printed error */
// cmd_print_usage(NULL);
die("`"CMD" inferedges -h` for help. Bad option: %s", argv[optind-1]);
default: abort();
}
}
// Default to adding all edges
if(!add_pop_edges && !add_all_edges) add_all_edges = true;
// Can only specify one of --pop --all
if(add_pop_edges && add_all_edges)
cmd_print_usage("Please specify only one of --all --pop");
// Check that optind+1 == argc
if(optind+1 > argc)
cmd_print_usage("Expected exactly one graph file");
else if(optind+1 < argc)
cmd_print_usage("Expected only one graph file. What is this: '%s'", argv[optind]);
//
// Open graph file
//
char *graph_path = argv[optind];
status("Reading graph: %s", graph_path);
if(strchr(graph_path,':') != NULL)
cmd_print_usage("Cannot use ':' in input graph for `"CMD" inferedges`");
GraphFileReader file;
memset(&file, 0, sizeof(file));
file_filter_open(&file.fltr, graph_path);
// Use stat to detect if we are reading from a stream
struct stat st;
bool reading_stream = (stat(file.fltr.path.b, &st) != 0);
// Mode r+ means open (not create) for update (read & write)
graph_file_open2(&file, graph_path, reading_stream ? "r" : "r+", 0);
if(!file_filter_is_direct(&file.fltr))
cmd_print_usage("Inferedges with filter not implemented - sorry");
bool editing_file = !(out_ctx_path || reading_stream);
FILE *fout = NULL;
// Editing input file or writing a new file
if(!editing_file)
fout = futil_fopen_create(out_ctx_path ? out_ctx_path : "-", "w");
// Print output status
if(fout == stdout) status("Writing to STDOUT");
else if(fout != NULL) status("Writing to: %s", out_ctx_path);
else status("Editing file in place: %s", graph_path);
status("Inferring all missing %sedges", add_pop_edges ? "population " : "");
//
// Decide on memory
//
const size_t ncols = file.hdr.num_of_cols;
size_t kmers_in_hash, graph_mem, bits_per_kmer;
// reading stream: all covgs + edges
// reading file: one bit per kmer per colour for 'in colour'
bits_per_kmer = sizeof(BinaryKmer)*8;
if(reading_stream) {
bits_per_kmer += ncols * 8 * (sizeof(Edges) + sizeof(Covg));
} else {
bits_per_kmer += ncols; // in colour
}
kmers_in_hash = cmd_get_kmers_in_hash(memargs.mem_to_use,
memargs.mem_to_use_set,
memargs.num_kmers,
memargs.num_kmers_set,
bits_per_kmer,
file.num_of_kmers, file.num_of_kmers,
memargs.mem_to_use_set, &graph_mem);
cmd_check_mem_limit(memargs.mem_to_use, graph_mem);
//
// Allocate memory
//
int alloc_flags = reading_stream ? DBG_ALLOC_EDGES | DBG_ALLOC_COVGS
: DBG_ALLOC_NODE_IN_COL;
dBGraph db_graph;
db_graph_alloc(&db_graph, file.hdr.kmer_size,
ncols, reading_stream ? ncols : 1,
kmers_in_hash, alloc_flags);
LoadingStats stats = LOAD_STATS_INIT_MACRO;
GraphLoadingPrefs gprefs = {.db_graph = &db_graph,
.boolean_covgs = false,
.must_exist_in_graph = false,
.must_exist_in_edges = NULL,
.empty_colours = false};
// We need to load the graph for both --pop and --all since we need to check
// if the next kmer is in each of the colours
graph_load(&file, gprefs, &stats);
if(add_pop_edges) status("Inferring edges from population...\n");
else status("Inferring all missing edges...\n");
size_t num_kmers_edited;
if(reading_stream)
{
ctx_assert(fout != NULL);
num_kmers_edited = infer_edges(num_of_threads, add_all_edges, &db_graph);
graph_write_header(fout, &file.hdr);
graph_write_all_kmers(fout, &db_graph);
}
else if(fout == NULL) {
num_kmers_edited = inferedges_on_mmap(&db_graph, add_all_edges, &file);
} else {
num_kmers_edited = inferedges_on_file(&db_graph, add_all_edges, &file, fout);
}
if(fout != NULL && fout != stdout) fclose(fout);
char modified_str[100], kmers_str[100];
ulong_to_str(num_kmers_edited, modified_str);
ulong_to_str(db_graph.ht.num_kmers, kmers_str);
double modified_rate = 0;
if(db_graph.ht.num_kmers)
modified_rate = (100.0 * num_kmers_edited) / db_graph.ht.num_kmers;
status("%s of %s (%.2f%%) nodes modified\n",
modified_str, kmers_str, modified_rate);
if(editing_file)
{
// Close and re-open
fclose(file.fh);
file.fh = NULL;
futil_update_timestamp(file.fltr.path.b);
}
graph_file_close(&file);
db_graph_dealloc(&db_graph);
return EXIT_SUCCESS;
}
static void parse_args(int argc, char **argv)
{
seq_format fmt = SEQ_FMT_FASTQ;
bool invert = false;
size_t i;
aln_reads_buf_alloc(&inputs, 8);
asyncio_buf_alloc(&files, 8);
AlignReadsData input;
AsyncIOInput seqfiles;
// Arg parsing
char cmd[100], shortopts[100];
cmd_long_opts_to_short(longopts, shortopts, sizeof(shortopts));
int c;
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 't': cmd_check(!nthreads,cmd); nthreads = cmd_uint32_nonzero(cmd, optarg); break;
case 'm': cmd_mem_args_set_memory(&memargs, optarg); break;
case 'n': cmd_mem_args_set_nkmers(&memargs, optarg); break;
case 'F': cmd_check(fmt==SEQ_FMT_FASTQ, cmd); fmt = cmd_parse_format(cmd, optarg); break;
case 'v': cmd_check(!invert,cmd); invert = true; break;
case '1':
case '2':
case 'i':
memset(&input, 0, sizeof(input));
memset(&seqfiles, 0, sizeof(seqfiles));
asyncio_task_parse(&seqfiles, c, optarg, 0, &input.out_base);
aln_reads_buf_push(&inputs, &input, 1);
asyncio_buf_push(&files, &seqfiles, 1);
break;
case ':': /* BADARG */
case '?': /* BADCH getopt_long has already printed error */
// cmd_print_usage(NULL);
die("`"CMD" reads -h` for help. Bad option: %s", argv[optind-1]);
default: abort();
}
}
ctx_assert(inputs.len == files.len);
// Defaults
if(!nthreads) nthreads = DEFAULT_NTHREADS;
if(inputs.len == 0)
cmd_print_usage("Please specify at least one sequence file (-1, -2 or -i)");
if(optind >= argc)
cmd_print_usage("Please specify input graph file(s)");
num_gfiles = (size_t)(argc - optind);
gfile_paths = argv + optind;
for(i = 0; i < inputs.len; i++) {
inputs.b[i].invert = invert;
inputs.b[i].fmt = fmt;
files.b[i].ptr = &inputs.b[i];
}
}
int ctx_links(int argc, char **argv)
{
size_t limit = 0;
const char *link_out_path = NULL, *csv_out_path = NULL, *plot_out_path = NULL;
const char *thresh_path = NULL, *hist_path = NULL;
size_t hist_distsize = 0, hist_covgsize = 0;
size_t cutoff = 0;
bool clean = false;
// Arg parsing
char cmd[100];
char shortopts[300];
cmd_long_opts_to_short(longopts, shortopts, sizeof(shortopts));
int c;
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(!link_out_path, cmd); link_out_path = optarg; break;
case 'f': cmd_check(!futil_get_force(), cmd); futil_set_force(true); break;
case 'l': cmd_check(!csv_out_path, cmd); csv_out_path = optarg; break;
case 'c': cmd_check(!cutoff, cmd); cutoff = cmd_size(cmd, optarg); clean = true; break;
case 'L': cmd_check(!limit, cmd); limit = cmd_size(cmd, optarg); break;
case 'P': cmd_check(!plot_out_path, cmd); plot_out_path = optarg; break;
case 'T': cmd_check(!thresh_path, cmd); thresh_path = optarg; break;
case 'H': cmd_check(!hist_path, cmd); hist_path = optarg; break;
case 'C': cmd_check(!hist_covgsize, cmd); hist_covgsize = cmd_size(cmd, optarg); break;
case 'D': cmd_check(!hist_distsize, cmd); hist_distsize = cmd_size(cmd, optarg); break;
case ':': /* BADARG */
case '?': /* BADCH getopt_long has already printed error */
// cmd_print_usage(NULL);
die("`"CMD" links -h` for help. Bad option: %s", argv[optind-1]);
default: ctx_assert2(0, "shouldn't reach here: %c", c);
}
}
if(hist_distsize && !hist_path) cmd_print_usage("--max-dist without --covg-hist");
if(hist_covgsize && !hist_path) cmd_print_usage("--max-covg without --covg-hist");
// Defaults
if(!hist_distsize) hist_distsize = DEFAULT_MAX_DIST;
if(!hist_covgsize) hist_covgsize = DEFAULT_MAX_COVG;
if(optind + 1 != argc) cmd_print_usage("Wrong number of arguments");
const char *ctp_path = argv[optind];
bool list = (csv_out_path != NULL);
bool plot = (plot_out_path != NULL);
bool save = (link_out_path != NULL);
bool hist_covg = (thresh_path != NULL || hist_path != NULL);
size_t plot_kmer_idx = (limit == 0 ? 0 : limit - 1);
if(clean && !save)
cmd_print_usage("Need to give --out <out.ctp.gz> with --clean");
if(!save && !list && !plot && !hist_covg)
cmd_print_usage("Please specify one of --plot, --list or --clean");
if(link_out_path && hist_covg && strcmp(link_out_path,"-") == 0)
cmd_print_usage("Outputing both cleaning threshold (-T) and links (-o) to STDOUT!");
// Open input file
FILE *list_fh = NULL, *plot_fh = NULL, *link_tmp_fh = NULL;
FILE *thresh_fh = NULL, *hist_fh = NULL;
gzFile link_gz = NULL;
// Check file don't exist or that we can overwrite
// Will ignore if path is null
bool err = false;
err |= futil_check_outfile(csv_out_path);
err |= futil_check_outfile(plot_out_path);
err |= futil_check_outfile(link_out_path);
err |= futil_check_outfile(thresh_path);
err |= futil_check_outfile(hist_path);
if(err) die("Use -f,--force to overwrite files");
StrBuf link_tmp_path;
strbuf_alloc(&link_tmp_path, 1024);
GPathReader ctpin;
memset(&ctpin, 0, sizeof(ctpin));
gpath_reader_open(&ctpin, ctp_path);
size_t ncols = file_filter_into_ncols(&ctpin.fltr);
size_t kmer_size = gpath_reader_get_kmer_size(&ctpin);
cJSON *newhdr = cJSON_Duplicate(ctpin.json, 1);
if(ncols != 1) die("Can only clean a single colour at a time. Sorry.");
uint64_t (*hists)[hist_covgsize] = NULL;
if(hist_covg) {
hists = ctx_calloc(hist_distsize, sizeof(hists[0]));
}
if(hist_path && (hist_fh = futil_fopen_create(hist_path, "w")) == NULL)
die("Cannot open file: %s", hist_path);
if(thresh_path && (thresh_fh = futil_fopen_create(thresh_path, "w")) == NULL)
die("Cannot open file: %s", thresh_path);
if(limit)
status("Limiting to the first %zu kmers", limit);
if(clean)
{
timestamp();
message(" Cleaning coverage below %zu", cutoff);
message("\n");
}
if(save)
{
// Check we can find the fields we need
cJSON *links_json = json_hdr_get(newhdr, "paths", cJSON_Object, link_out_path);
cJSON *nkmers_json = json_hdr_get(links_json, "num_kmers_with_paths", cJSON_Number, link_out_path);
cJSON *nlinks_json = json_hdr_get(links_json, "num_paths", cJSON_Number, link_out_path);
cJSON *nbytes_json = json_hdr_get(links_json, "path_bytes", cJSON_Number, link_out_path);
if(!nkmers_json || !nlinks_json || !nbytes_json)
die("Cannot find required header entries");
// Create a random temporary file
link_tmp_fh = create_tmp_file(&link_tmp_path, link_out_path);
status("Saving output to: %s", link_out_path);
status("Temporary output: %s", link_tmp_path.b);
// Open output file
if((link_gz = futil_gzopen_create(link_out_path, "w")) == NULL)
die("Cannot open output link file: %s", link_out_path);
// Need to open output file first so we can get absolute path
// Update the header to include this command
json_hdr_add_curr_cmd(newhdr, link_out_path);
}
if(list)
{
status("Listing to %s", csv_out_path);
if((list_fh = futil_fopen_create(csv_out_path, "w")) == NULL)
die("Cannot open output CSV file %s", csv_out_path);
// Print csv header
fprintf(list_fh, "SeqLen,Covg\n");
}
if(plot)
{
status("Plotting kmer %zu to %s", plot_kmer_idx, plot_out_path);
if((plot_fh = futil_fopen_create(plot_out_path, "w")) == NULL)
die("Cannot open output .dot file %s", plot_out_path);
}
SizeBuffer countbuf, jposbuf;
size_buf_alloc(&countbuf, 16);
size_buf_alloc(&jposbuf, 1024);
StrBuf kmerbuf, juncsbuf, seqbuf, outbuf;
strbuf_alloc(&kmerbuf, 1024);
strbuf_alloc(&juncsbuf, 1024);
strbuf_alloc(&seqbuf, 1024);
strbuf_alloc(&outbuf, 1024);
bool link_fw;
size_t njuncs;
size_t knum, nlinks, num_links_exp = 0;
LinkTree ltree;
ltree_alloc(<ree, kmer_size);
LinkTreeStats tree_stats;
memset(&tree_stats, 0, sizeof(tree_stats));
size_t init_num_links = 0, num_links = 0;
for(knum = 0; !limit || knum < limit; knum++)
{
ltree_reset(<ree);
if(!gpath_reader_read_kmer(&ctpin, &kmerbuf, &num_links_exp)) break;
ctx_assert2(kmerbuf.end == kmer_size, "Kmer incorrect length %zu != %zu",
kmerbuf.end, kmer_size);
// status("kmer: %s", kmerbuf.b);
for(nlinks = 0;
gpath_reader_read_link(&ctpin, &link_fw, &njuncs,
&countbuf, &juncsbuf,
&seqbuf, &jposbuf);
nlinks++)
{
ltree_add(<ree, link_fw, countbuf.b[0], jposbuf.b,
juncsbuf.b, seqbuf.b);
}
if(nlinks != num_links_exp)
warn("Links count mismatch %zu != %zu", nlinks, num_links_exp);
if(hist_covg)
{
ltree_update_covg_hists(<ree, (uint64_t*)hists,
hist_distsize, hist_covgsize);
}
if(clean)
{
ltree_clean(<ree, cutoff);
}
// Accumulate statistics
ltree_get_stats(<ree, &tree_stats);
num_links = tree_stats.num_links - init_num_links;
init_num_links = tree_stats.num_links;
if(list)
{
ltree_write_list(<ree, &outbuf);
if(fwrite(outbuf.b, 1, outbuf.end, list_fh) != outbuf.end)
die("Cannot write CSV file to: %s", csv_out_path);
strbuf_reset(&outbuf);
}
if(save && num_links)
{
ltree_write_ctp(<ree, kmerbuf.b, num_links, &outbuf);
if(fwrite(outbuf.b, 1, outbuf.end, link_tmp_fh) != outbuf.end)
die("Cannot write ctp file to: %s", link_tmp_path.b);
strbuf_reset(&outbuf);
}
if(plot && knum == plot_kmer_idx)
{
status("Plotting tree...");
ltree_write_dot(<ree, &outbuf);
if(fwrite(outbuf.b, 1, outbuf.end, plot_fh) != outbuf.end)
die("Cannot write plot DOT file to: %s", plot_out_path);
strbuf_reset(&outbuf);
}
}
gpath_reader_close(&ctpin);
cJSON *links_json = json_hdr_get(newhdr, "paths", cJSON_Object, link_out_path);
cJSON *nkmers_json = json_hdr_get(links_json, "num_kmers_with_paths", cJSON_Number, link_out_path);
cJSON *nlinks_json = json_hdr_get(links_json, "num_paths", cJSON_Number, link_out_path);
cJSON *nbytes_json = json_hdr_get(links_json, "path_bytes", cJSON_Number, link_out_path);
status("Number of kmers with links %li -> %zu", nkmers_json->valueint, tree_stats.num_trees_with_links);
status("Number of links %li -> %zu", nlinks_json->valueint, tree_stats.num_links);
status("Number of bytes %li -> %zu", nbytes_json->valueint, tree_stats.num_link_bytes);
if(save)
{
// Update JSON
nkmers_json->valuedouble = nkmers_json->valueint = tree_stats.num_trees_with_links;
nlinks_json->valuedouble = nlinks_json->valueint = tree_stats.num_links;
nbytes_json->valuedouble = nbytes_json->valueint = tree_stats.num_link_bytes;
char *json_str = cJSON_Print(newhdr);
if(gzputs(link_gz, json_str) != (int)strlen(json_str))
die("Cannot write ctp file to: %s", link_out_path);
free(json_str);
gzputs(link_gz, "\n\n");
gzputs(link_gz, ctp_explanation_comment);
gzputs(link_gz, "\n");
fseek(link_tmp_fh, 0, SEEK_SET);
char *tmp = ctx_malloc(4*ONE_MEGABYTE);
size_t s;
while((s = fread(tmp, 1, 4*ONE_MEGABYTE, link_tmp_fh)) > 0) {
if(gzwrite(link_gz, tmp, s) != (int)s)
die("Cannot write to output: %s", link_out_path);
}
ctx_free(tmp);
gzclose(link_gz);
fclose(link_tmp_fh);
}
// Write histogram to file
if(hist_fh)
{
size_t i, j;
fprintf(hist_fh, " ");
for(j = 1; j < hist_covgsize; j++) fprintf(hist_fh, ",covg.%02zu", j);
fprintf(hist_fh, "\n");
for(i = 1; i < hist_distsize; i++) {
fprintf(hist_fh, "dist.%02zu", i);
for(j = 1; j < hist_covgsize; j++) {
fprintf(hist_fh, ",%"PRIu64, hists[i][j]);
}
fprintf(hist_fh, "\n");
}
}
if(thresh_fh)
{
// Use median of first five cutoffs
print_suggest_cutoff(6, hist_covgsize, hists, thresh_fh);
}
if(hist_fh && hist_fh != stdout) fclose(hist_fh);
if(list)
{
fclose(list_fh);
}
if(plot)
{
fclose(plot_fh);
}
ctx_free(hists);
cJSON_Delete(newhdr);
strbuf_dealloc(&link_tmp_path);
ltree_dealloc(<ree);
size_buf_dealloc(&countbuf);
size_buf_dealloc(&jposbuf);
strbuf_dealloc(&kmerbuf);
strbuf_dealloc(&juncsbuf);
strbuf_dealloc(&seqbuf);
strbuf_dealloc(&outbuf);
return EXIT_SUCCESS;
}
void read_thread_args_parse(struct ReadThreadCmdArgs *args,
int argc, char **argv,
const struct option *longopts, bool correct_cmd)
{
size_t i;
CorrectAlnInput task = CORRECT_ALN_INPUT_INIT;
uint8_t fq_offset = 0;
GPathReader tmp_gpfile;
CorrectAlnInputBuffer *inputs = &args->inputs;
args->memargs = (struct MemArgs)MEM_ARGS_INIT;
args->fmt = SEQ_FMT_FASTQ;
// Arg parsing
char cmd[100];
char shortopts[300];
cmd_long_opts_to_short(longopts, shortopts, sizeof(shortopts));
int used = 1, c;
char *tmp_path;
// 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 'o': cmd_check(!args->out_ctp_path,cmd); args->out_ctp_path = optarg; break;
case 'p':
memset(&tmp_gpfile, 0, sizeof(GPathReader));
gpath_reader_open(&tmp_gpfile, optarg);
gpfile_buf_push(&args->gpfiles, &tmp_gpfile, 1);
break;
case 't':
cmd_check(!args->nthreads, cmd);
args->nthreads = cmd_uint32_nonzero(cmd, optarg);
break;
case 'm': cmd_mem_args_set_memory(&args->memargs, optarg); break;
case 'n': cmd_mem_args_set_nkmers(&args->memargs, optarg); break;
case 'c': args->colour = cmd_uint32(cmd, optarg); break;
case 'F':
cmd_check(args->fmt == SEQ_FMT_FASTQ, cmd);
args->fmt = cmd_parse_format(cmd, optarg);
break;
case '1':
case '2':
case 'i':
used = 1;
correct_aln_input_buf_push(inputs, &task, 1);
asyncio_task_parse(&inputs->b[inputs->len-1].files, c, optarg,
fq_offset, correct_cmd ? &tmp_path : NULL);
if(correct_cmd) inputs->b[inputs->len-1].out_base = tmp_path;
break;
case 'M':
if(!strcmp(optarg,"FF")) task.matedir = READPAIR_FF;
else if(!strcmp(optarg,"FR")) task.matedir = READPAIR_FR;
else if(!strcmp(optarg,"RF")) task.matedir = READPAIR_RF;
else if(!strcmp(optarg,"RR")) task.matedir = READPAIR_RR;
else die("-M,--matepair <orient> must be one of: FF,FR,RF,RR");
used = 0; break;
case 'O': fq_offset = cmd_uint8(cmd, optarg); used = 0; break;
case 'Q': task.fq_cutoff = cmd_uint8(cmd, optarg); used = 0; break;
case 'H': task.hp_cutoff = cmd_uint8(cmd, optarg); used = 0; break;
case 'l': task.crt_params.frag_len_min = cmd_uint32(cmd, optarg); used = 0; break;
case 'L': task.crt_params.frag_len_max = cmd_uint32(cmd, optarg); used = 0; break;
case 'w': task.crt_params.one_way_gap_traverse = true; used = 0; break;
case 'W': task.crt_params.one_way_gap_traverse = false; used = 0; break;
case 'd': task.crt_params.gap_wiggle = cmd_udouble(cmd, optarg); used = 0; break;
case 'D': task.crt_params.gap_variance = cmd_udouble(cmd, optarg); used = 0; break;
case 'X': task.crt_params.max_context = cmd_uint32(cmd, optarg); used = 0; break;
case 'e': task.crt_params.use_end_check = true; used = 0; break;
case 'E': task.crt_params.use_end_check = false; used = 0; break;
case 'g': cmd_check(!args->dump_seq_sizes, cmd); args->dump_seq_sizes = optarg; break;
case 'G': cmd_check(!args->dump_frag_sizes, cmd); args->dump_frag_sizes = optarg; break;
case 'u': args->use_new_paths = true; break;
case 'x': gen_paths_print_contigs = true; break;
case 'y': gen_paths_print_paths = true; break;
case 'z': gen_paths_print_reads = true; break;
case 'Z':
cmd_check(!args->fq_zero, cmd);
if(strlen(optarg) != 1)
cmd_print_usage("--fq-zero <c> requires a single char");
args->fq_zero = optarg[0];
break;
case 'P': cmd_check(!args->append_orig_seq,cmd); args->append_orig_seq = true; break;
case ':': /* BADARG */
case '?': /* BADCH getopt_long has already printed error */
// cmd_print_usage(NULL);
die("`"CMD" thread/correct -h` for help. Bad option: %s", argv[optind-1]);
default: abort();
}
}
if(args->nthreads == 0) args->nthreads = DEFAULT_NTHREADS;
// Check that optind+1 == argc
if(optind+1 > argc)
cmd_print_usage("Expected exactly one graph file");
else if(optind+1 < argc)
cmd_print_usage("Expected only one graph file. What is this: '%s'", argv[optind]);
char *graph_path = argv[optind];
status("Reading graph: %s", graph_path);
if(!used) cmd_print_usage("Ignored arguments after last --seq");
// ctx_thread requires output file
if(!correct_cmd && !args->out_ctp_path)
cmd_print_usage("--out <out.ctp> is required");
//
// Open graph graph file
//
GraphFileReader *gfile = &args->gfile;
graph_file_open(gfile, graph_path);
if(!correct_cmd && file_filter_into_ncols(&gfile->fltr) > 1)
die("Please specify a single colour e.g. %s:0", file_filter_path(&gfile->fltr));
//
// Open path files
//
size_t path_max_usedcols = 0;
for(i = 0; i < args->gpfiles.len; i++) {
// file_filter_update_intocol(&args->pfiles.b[i].fltr, 0);
if(!correct_cmd && file_filter_into_ncols(&args->gpfiles.b[i].fltr) > 1) {
die("Please specify a single colour e.g. %s:0",
file_filter_path(&args->gpfiles.b[i].fltr));
}
path_max_usedcols = MAX2(path_max_usedcols,
file_filter_into_ncols(&args->gpfiles.b[i].fltr));
}
args->path_max_usedcols = path_max_usedcols;
// Check for compatibility between graph files and path files
graphs_gpaths_compatible(gfile, 1, args->gpfiles.b, args->gpfiles.len, -1);
// if no paths loaded, set all max_context values to 1, since >1 kmer only
// useful if can pickup paths
if(args->gpfiles.len == 0) {
for(i = 0; i < inputs->len; i++)
inputs->b[i].crt_params.max_context = 1;
}
// Check frag_len_min < frag_len_max
for(i = 0; i < inputs->len; i++)
{
CorrectAlnInput *t = &inputs->b[i];
t->files.ptr = t;
if(t->crt_params.frag_len_min > t->crt_params.frag_len_max) {
die("--min-ins %u is greater than --max-ins %u",
t->crt_params.frag_len_min, t->crt_params.frag_len_max);
}
correct_aln_input_print(&inputs->b[i]);
args->max_gap_limit = MAX2(args->max_gap_limit, t->crt_params.frag_len_max);
}
futil_create_output(args->dump_seq_sizes);
futil_create_output(args->dump_frag_sizes);
}
void read_thread_args_parse(struct ReadThreadCmdArgs *args,
int argc, char **argv,
const struct option *longopts, bool correct_cmd)
{
size_t i;
int tmp_thresh; // 0 => no calling, -1 => auto
CorrectAlnInput task = CORRECT_ALN_INPUT_INIT;
uint8_t fq_offset = 0;
size_t dump_seq_n = 0, dump_mp_n = 0; // how many times are -g -G specified
PathFileReader tmp_pfile;
CorrectAlnInputBuffer *inputs = &args->inputs;
// Arg parsing
char cmd[100];
char shortopts[300];
cmd_long_opts_to_short(longopts, shortopts, sizeof(shortopts));
int used = 1, c;
char *tmp_path;
// 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':
if(args->out_ctp_path != NULL) cmd_print_usage(NULL);
args->out_ctp_path = optarg;
break;
case 'p':
tmp_pfile = INIT_PATH_READER;
path_file_open(&tmp_pfile, optarg, true);
pfile_buf_add(&args->pfiles, tmp_pfile);
break;
case 't':
if(args->num_of_threads != 0) die("%s set twice", cmd);
args->num_of_threads = cmd_parse_arg_uint32_nonzero(cmd, optarg);
break;
case 'm': cmd_mem_args_set_memory(&args->memargs, optarg); break;
case 'n': cmd_mem_args_set_nkmers(&args->memargs, optarg); break;
case 'c': args->colour = cmd_parse_arg_uint32(cmd, optarg); break;
case '1':
case '2':
case 'i':
used = 1;
correct_aln_input_buf_add(inputs, task);
asyncio_task_parse(&inputs->data[inputs->len-1].files, c, optarg,
fq_offset, correct_cmd ? &tmp_path : NULL);
if(correct_cmd) inputs->data[inputs->len-1].out_base = tmp_path;
break;
case 'f': task.matedir = READPAIR_FR; used = 0; break;
case 'F': task.matedir = READPAIR_FF; used = 0; break;
case 'r': task.matedir = READPAIR_RF; used = 0; break;
case 'R': task.matedir = READPAIR_RR; used = 0; break;
case 'w': task.crt_params.one_way_gap_traverse = true; used = 0; break;
case 'W': task.crt_params.one_way_gap_traverse = false; used = 0; break;
case 'q': fq_offset = cmd_parse_arg_uint8(cmd, optarg); used = 0; break;
case 'Q': task.fq_cutoff = cmd_parse_arg_uint8(cmd, optarg); used = 0; break;
case 'H': task.hp_cutoff = cmd_parse_arg_uint8(cmd, optarg); used = 0; break;
case 'e': task.crt_params.use_end_check = true; used = 0; break;
case 'E': task.crt_params.use_end_check = false; used = 0; break;
case 'g': task.crt_params.ins_gap_min = cmd_parse_arg_uint32(cmd, optarg); used = 0; break;
case 'G': task.crt_params.ins_gap_max = cmd_parse_arg_uint32(cmd, optarg); used = 0; break;
case 'S': args->dump_seq_sizes = optarg; dump_seq_n++; break;
case 'M': args->dump_mp_sizes = optarg; dump_mp_n++; break;
case 'u': args->use_new_paths = true; break;
case 'C':
if(optarg == NULL || strcmp(optarg,"auto")) args->clean_threshold = -1;
else if(parse_entire_int(optarg,&tmp_thresh) && tmp_thresh >= -1) {
if(tmp_thresh != -1 && tmp_thresh < 2)
warn("Ignoring --clean %u (too small < 2)", tmp_thresh);
else if(tmp_thresh > 255)
warn("Ignoring --clean %u (too big > 255)", tmp_thresh);
else
args->clean_threshold = tmp_thresh;
}
else die("Bad argument for %s <auto|N> where N > 1", cmd);
args->clean_paths = (args->clean_threshold != 0);
break;
case 'X': gen_paths_print_contigs = true; break;
case 'Y': gen_paths_print_paths = true; break;
case 'Z': gen_paths_print_reads = true; break;
case ':': /* BADARG */
case '?': /* BADCH getopt_long has already printed error */
// cmd_print_usage(NULL);
die("`"CMD" thread -h` for help. Bad option: %s", argv[optind-1]);
default: abort();
}
}
if(args->num_of_threads == 0) args->num_of_threads = DEFAULT_NTHREADS;
// Check that optind+1 == argc
if(optind+1 > argc)
cmd_print_usage("Expected exactly one graph file");
else if(optind+1 < argc)
cmd_print_usage("Expected only one graph file. What is this: '%s'", argv[optind]);
char *graph_path = argv[optind];
status("Reading graph: %s", graph_path);
if(!used) cmd_print_usage("Ignored arguments after last --seq");
if(dump_seq_n > 1) die("Cannot specify --seq-gaps <out> more than once");
if(dump_mp_n > 1) die("Cannot specify --mp-gaps <out> more than once");
//
// Open graph graph file
//
GraphFileReader *gfile = &args->gfile;
graph_file_open(gfile, graph_path, true);
file_filter_update_intocol(&gfile->fltr, 0);
if(!correct_cmd && graph_file_usedcols(gfile) > 1)
die("Please specify a single colour e.g. %s:0", gfile->fltr.file_path.buff);
//
// Open path files
//
size_t path_max_usedcols = 0;
for(i = 0; i < args->pfiles.len; i++) {
// file_filter_update_intocol(&args->pfiles.data[i].fltr, 0);
if(!correct_cmd && path_file_usedcols(&args->pfiles.data[i]) > 1) {
die("Please specify a single colour e.g. %s:0",
args->pfiles.data[i].fltr.file_path.buff);
}
path_max_usedcols = MAX2(path_max_usedcols,
path_file_usedcols(&args->pfiles.data[i]));
}
args->path_max_usedcols = path_max_usedcols;
// Check for compatibility between graph files and path files
graphs_paths_compatible(gfile, 1, args->pfiles.data, args->pfiles.len);
// Check ins_gap_min < ins_gap_max
for(i = 0; i < inputs->len; i++)
{
CorrectAlnInput *t = &inputs->data[i];
t->files.ptr = t;
if(t->crt_params.ins_gap_min > t->crt_params.ins_gap_max) {
die("--min-ins %u is greater than --max-ins %u",
t->crt_params.ins_gap_min, t->crt_params.ins_gap_max);
}
correct_aln_input_print(&inputs->data[i]);
args->max_gap_limit = MAX2(args->max_gap_limit, t->crt_params.ins_gap_max);
}
}
int ctx_bubbles(int argc, char **argv)
{
size_t nthreads = 0;
struct MemArgs memargs = MEM_ARGS_INIT;
const char *out_path = NULL;
size_t max_allele_len = 0, max_flank_len = 0;
bool remove_serial_bubbles = true;
// List of haploid colours
size_t *hapcols = NULL;
int nhapcols = 0;
char *hapcols_arg = NULL;
GPathReader tmp_gpfile;
GPathFileBuffer gpfiles;
gpfile_buf_alloc(&gpfiles, 8);
// 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 'f': cmd_check(!futil_get_force(), cmd); futil_set_force(true); break;
case 'p':
memset(&tmp_gpfile, 0, sizeof(GPathReader));
gpath_reader_open(&tmp_gpfile, optarg);
gpfile_buf_push(&gpfiles, &tmp_gpfile, 1);
break;
case 't': cmd_check(!nthreads, cmd); nthreads = cmd_uint32_nonzero(cmd, optarg); break;
case 'm': cmd_mem_args_set_memory(&memargs, optarg); break;
case 'n': cmd_mem_args_set_nkmers(&memargs, optarg); break;
case 'H': cmd_check(!hapcols_arg, cmd); hapcols_arg = optarg; break;
case 'A': cmd_check(!max_allele_len, cmd); max_allele_len = cmd_uint32_nonzero(cmd, optarg); break;
case 'F': cmd_check(!max_flank_len, cmd); max_flank_len = cmd_uint32_nonzero(cmd, optarg); break;
case 'S': cmd_check(remove_serial_bubbles,cmd); remove_serial_bubbles = false; break;
case ':': /* BADARG */
case '?': /* BADCH getopt_long has already printed error */
// cmd_print_usage(NULL);
die("`"CMD" "SUBCMD" -h` for help. Bad option: %s", argv[optind-1]);
default: abort();
}
}
// Defaults for unset values
if(out_path == NULL) out_path = "-";
if(nthreads == 0) nthreads = DEFAULT_NTHREADS;
if(max_allele_len == 0) max_allele_len = DEFAULT_MAX_ALLELE;
if(max_flank_len == 0) max_flank_len = DEFAULT_MAX_FLANK;
if(optind >= argc) cmd_print_usage("Require input graph files (.ctx)");
//
// Open graph files
//
const size_t num_gfiles = argc - optind;
char **graph_paths = argv + optind;
ctx_assert(num_gfiles > 0);
GraphFileReader *gfiles = ctx_calloc(num_gfiles, sizeof(GraphFileReader));
size_t i, ncols, ctx_max_kmers = 0, ctx_sum_kmers = 0;
ncols = graph_files_open(graph_paths, gfiles, num_gfiles,
&ctx_max_kmers, &ctx_sum_kmers);
// Check graph + paths are compatible
graphs_gpaths_compatible(gfiles, num_gfiles, gpfiles.b, gpfiles.len, -1);
//
// Check haploid colours are valid
//
if(hapcols_arg != NULL) {
if((nhapcols = range_get_num(hapcols_arg, ncols)) < 0)
die("Invalid haploid colour list: %s", hapcols_arg);
hapcols = ctx_calloc(nhapcols, sizeof(hapcols[0]));
if(range_parse_array(hapcols_arg, hapcols, ncols) < 0)
die("Invalid haploid colour list: %s", hapcols_arg);
}
//
// Decide on memory
//
size_t bits_per_kmer, kmers_in_hash, graph_mem, path_mem, thread_mem;
char thread_mem_str[100];
// edges(1bytes) + kmer_paths(8bytes) + in_colour(1bit/col) +
// visitedfw/rv(2bits/thread)
bits_per_kmer = sizeof(BinaryKmer)*8 + sizeof(Edges)*8 +
(gpfiles.len > 0 ? sizeof(GPath*)*8 : 0) +
ncols + 2*nthreads;
kmers_in_hash = cmd_get_kmers_in_hash(memargs.mem_to_use,
memargs.mem_to_use_set,
memargs.num_kmers,
memargs.num_kmers_set,
bits_per_kmer,
ctx_max_kmers, ctx_sum_kmers,
false, &graph_mem);
// Thread memory
thread_mem = roundup_bits2bytes(kmers_in_hash) * 2;
bytes_to_str(thread_mem * nthreads, 1, thread_mem_str);
status("[memory] (of which threads: %zu x %zu = %s)\n",
nthreads, thread_mem, thread_mem_str);
// Paths memory
size_t rem_mem = memargs.mem_to_use - MIN2(memargs.mem_to_use, graph_mem+thread_mem);
path_mem = gpath_reader_mem_req(gpfiles.b, gpfiles.len, ncols, rem_mem, false,
kmers_in_hash, false);
// Shift path store memory from graphs->paths
graph_mem -= sizeof(GPath*)*kmers_in_hash;
path_mem += sizeof(GPath*)*kmers_in_hash;
cmd_print_mem(path_mem, "paths");
size_t total_mem = graph_mem + thread_mem + path_mem;
cmd_check_mem_limit(memargs.mem_to_use, total_mem);
//
// Open output file
//
gzFile gzout = futil_gzopen_create(out_path, "w");
// Allocate memory
dBGraph db_graph;
db_graph_alloc(&db_graph, gfiles[0].hdr.kmer_size, ncols, 1, kmers_in_hash,
DBG_ALLOC_EDGES | DBG_ALLOC_NODE_IN_COL);
// Paths
gpath_reader_alloc_gpstore(gpfiles.b, gpfiles.len, path_mem, false, &db_graph);
//
// Load graphs
//
GraphLoadingPrefs gprefs = graph_loading_prefs(&db_graph);
gprefs.empty_colours = true;
for(i = 0; i < num_gfiles; i++) {
graph_load(&gfiles[i], gprefs, NULL);
graph_file_close(&gfiles[i]);
gprefs.empty_colours = false;
}
ctx_free(gfiles);
hash_table_print_stats(&db_graph.ht);
// Load link files
for(i = 0; i < gpfiles.len; i++)
gpath_reader_load(&gpfiles.b[i], GPATH_DIE_MISSING_KMERS, &db_graph);
// Create array of cJSON** from input files
cJSON **hdrs = ctx_malloc(gpfiles.len * sizeof(cJSON*));
for(i = 0; i < gpfiles.len; i++) hdrs[i] = gpfiles.b[i].json;
// Now call variants
BubbleCallingPrefs call_prefs = {.max_allele_len = max_allele_len,
.max_flank_len = max_flank_len,
.haploid_cols = hapcols,
.nhaploid_cols = nhapcols,
.remove_serial_bubbles = remove_serial_bubbles};
invoke_bubble_caller(nthreads, &call_prefs,
gzout, out_path,
hdrs, gpfiles.len,
&db_graph);
status(" saved to: %s\n", out_path);
gzclose(gzout);
ctx_free(hdrs);
// Close input link files
for(i = 0; i < gpfiles.len; i++)
gpath_reader_close(&gpfiles.b[i]);
gpfile_buf_dealloc(&gpfiles);
ctx_free(hapcols);
db_graph_dealloc(&db_graph);
return EXIT_SUCCESS;
}
int ctx_calls2vcf(int argc, char **argv)
{
const char *in_path = NULL, *out_path = NULL, *out_type = NULL;
// Filtering parameters
int32_t min_mapq = -1, max_align_len = -1, max_allele_len = -1;
// Alignment parameters
int nwmatch = 1, nwmismatch = -2, nwgapopen = -4, nwgapextend = -1;
// ref paths
char const*const* ref_paths = NULL;
size_t nref_paths = 0;
// flank file
const char *sam_path = NULL;
//
// Things we figure out by looking at the input
//
bool isbubble = false;
// samples in VCF, (0 for bubble, does not include ref in breakpoint calls)
size_t i, kmer_size, num_samples;
//
// Reference genome
//
// Hash map of chromosome name -> sequence
ChromHash *genome;
ReadBuffer chroms;
// 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 'O': cmd_check(!out_type, cmd); out_type = optarg; break;
case 'f': cmd_check(!futil_get_force(), cmd); futil_set_force(true); break;
case 'F': cmd_check(!sam_path,cmd); sam_path = optarg; break;
case 'Q': cmd_check(min_mapq < 0,cmd); min_mapq = cmd_uint32(cmd, optarg); break;
case 'A': cmd_check(max_align_len < 0,cmd); max_align_len = cmd_uint32(cmd, optarg); break;
case 'L': cmd_check(max_allele_len < 0,cmd); max_allele_len = cmd_uint32(cmd, optarg); break;
case 'm': nwmatch = cmd_int32(cmd, optarg); break;
case 'M': nwmismatch = cmd_int32(cmd, optarg); break;
case 'g': nwgapopen = cmd_int32(cmd, optarg); break;
case 'G': nwgapextend = cmd_int32(cmd, optarg); break;
case ':': /* BADARG */
case '?': /* BADCH getopt_long has already printed error */
die("`"CMD" "SUBCMD" -h` for help. Bad option: %s", argv[optind-1]);
default: ctx_assert2(0, "shouldn't reach here: %c", c);
}
}
// Defaults for unset values
if(out_path == NULL) out_path = "-";
if(max_align_len < 0) max_align_len = DEFAULT_MAX_ALIGN;
if(max_allele_len < 0) max_allele_len = DEFAULT_MAX_ALLELE;
if(optind+2 > argc)
cmd_print_usage("Require <in.txt.gz> and at least one reference");
in_path = argv[optind++];
ref_paths = (char const*const*)argv + optind;
nref_paths = argc - optind;
// These functions call die() on error
gzFile gzin = futil_gzopen(in_path, "r");
// Read call file header
cJSON *json = json_hdr_load(gzin, in_path);
// Check we can handle the kmer size
kmer_size = json_hdr_get_kmer_size(json, in_path);
db_graph_check_kmer_size(kmer_size, in_path);
// Get format (bubble or breakpoint file)
cJSON *json_fmt = json_hdr_get(json, "file_format", cJSON_String, in_path);
if(strcmp(json_fmt->valuestring,"CtxBreakpoints") == 0) isbubble = false;
else if(strcmp(json_fmt->valuestring,"CtxBubbles") == 0) isbubble = true;
else die("Unknown format: '%s'", json_fmt->valuestring);
status("Reading %s in %s format", futil_inpath_str(in_path),
isbubble ? "bubble" : "breakpoint");
if(isbubble) {
// bubble specific
if(sam_path == NULL)
cmd_print_usage("Require -F <flanks.sam> with bubble file");
if(min_mapq < 0) min_mapq = DEFAULT_MIN_MAPQ;
}
else {
// breakpoint specific
if(min_mapq >= 0)
cmd_print_usage("-Q,--min-mapq <Q> only valid with bubble calls");
}
// Open flank file if it exists
htsFile *samfh = NULL;
bam_hdr_t *bam_hdr = NULL;
bam1_t *mflank = NULL;
if(sam_path)
{
if((samfh = hts_open(sam_path, "r")) == NULL)
die("Cannot open SAM/BAM %s", sam_path);
// Load BAM header
bam_hdr = sam_hdr_read(samfh);
if(bam_hdr == NULL) die("Cannot load BAM header: %s", sam_path);
mflank = bam_init1();
}
// Output VCF has 0 samples if bubbles file, otherwise has N where N is
// number of samples/colours in the breakpoint graph
size_t num_graph_samples = json_hdr_get_ncols(json, in_path);
size_t num_graph_nonref = json_hdr_get_nonref_ncols(json, in_path);
num_samples = 0;
if(!isbubble) {
// If last colour has "is_ref", drop number of samples by one
num_samples = num_graph_nonref < num_graph_samples ? num_graph_samples-1
: num_graph_samples;
}
//
// Open output file
//
if(!out_path) out_path = "-";
int mode = vcf_misc_get_outtype(out_type, out_path);
futil_create_output(out_path);
htsFile *vcffh = hts_open(out_path, modes_htslib[mode]);
status("[calls2vcf] Reading %s call file with %zu samples",
isbubble ? "Bubble" : "Breakpoint", num_graph_samples);
status("[calls2vcf] %zu sample output to: %s format: %s",
num_samples, futil_outpath_str(out_path), hsmodes_htslib[mode]);
if(isbubble) status("[calls2vcf] min. MAPQ: %i", min_mapq);
status("[calls2vcf] max alignment length: %i", max_align_len);
status("[calls2vcf] max VCF allele length: %i", max_allele_len);
status("[calls2vcf] alignment match:%i mismatch:%i gap open:%i extend:%i",
nwmatch, nwmismatch, nwgapopen, nwgapextend);
// Load reference genome
read_buf_alloc(&chroms, 1024);
genome = chrom_hash_init();
chrom_hash_load(ref_paths, nref_paths, &chroms, genome);
// convert to upper case
char *s;
for(i = 0; i < chroms.len; i++)
for(s = chroms.b[i].seq.b; *s; s++) *s = toupper(*s);
if(!isbubble) brkpnt_check_refs_match(json, genome, in_path);
bcf_hdr_t *vcfhdr = make_vcf_hdr(json, in_path, !isbubble, kmer_size,
ref_paths, nref_paths,
chroms.b, chroms.len);
if(bcf_hdr_write(vcffh, vcfhdr) != 0) die("Cannot write VCF header");
AlignedCall *call = acall_init();
CallDecomp *aligner = call_decomp_init(vcffh, vcfhdr);
scoring_t *scoring = call_decomp_get_scoring(aligner);
scoring_init(scoring, nwmatch, nwmismatch, nwgapopen, nwgapextend,
false, false, 0, 0, 0, 0);
CallFileEntry centry;
call_file_entry_alloc(¢ry);
char kmer_str[50];
sprintf(kmer_str, ";K%zu", kmer_size);
if(isbubble)
{
// Bubble calls
DecompBubble *bubbles = decomp_bubble_init();
// Set scoring for aligning 3' flank
scoring = decomp_bubble_get_scoring(bubbles);
scoring_init(scoring, nwmatch, nwmismatch, nwgapopen, nwgapextend,
true, true, 0, 0, 0, 0);
while(call_file_read(gzin, in_path, ¢ry)) {
do {
if(sam_read1(samfh, bam_hdr, mflank) < 0)
die("We've run out of SAM entries!");
} while(mflank->core.flag & (BAM_FSECONDARY | BAM_FSUPPLEMENTARY));
// Align call
strbuf_reset(&call->info);
decomp_bubble_call(bubbles, genome, kmer_size, min_mapq,
¢ry, mflank, bam_hdr, call);
strbuf_append_str(&call->info, kmer_str);
acall_decompose(aligner, call, max_align_len, max_allele_len);
}
// print bubble stats
DecompBubbleStats *bub_stats = ctx_calloc(1, sizeof(*bub_stats));
decomp_bubble_cpy_stats(bub_stats, bubbles);
print_bubble_stats(bub_stats);
ctx_free(bub_stats);
decomp_bubble_destroy(bubbles);
}
else
{
// Breakpoint calls
DecompBreakpoint *breakpoints = decomp_brkpt_init();
while(call_file_read(gzin, in_path, ¢ry)) {
strbuf_reset(&call->info);
decomp_brkpt_call(breakpoints, genome, num_samples, ¢ry, call);
strbuf_append_str(&call->info, kmer_str);
acall_decompose(aligner, call, max_align_len, max_allele_len);
}
// print bubble stats
DecompBreakpointStats *brk_stats = ctx_calloc(1, sizeof(*brk_stats));
decomp_brkpt_cpy_stats(brk_stats, breakpoints);
print_breakpoint_stats(brk_stats);
ctx_free(brk_stats);
decomp_brkpt_destroy(breakpoints);
}
// Print stats
DecomposeStats *astats = ctx_calloc(1, sizeof(*astats));
call_decomp_cpy_stats(astats, aligner);
print_acall_stats(astats);
ctx_free(astats);
call_file_entry_dealloc(¢ry);
call_decomp_destroy(aligner);
acall_destroy(call);
// Finished - clean up
cJSON_Delete(json);
gzclose(gzin);
bcf_hdr_destroy(vcfhdr);
hts_close(vcffh);
for(i = 0; i < chroms.len; i++) seq_read_dealloc(&chroms.b[i]);
read_buf_dealloc(&chroms);
chrom_hash_destroy(genome);
if(sam_path) {
hts_close(samfh);
bam_hdr_destroy(bam_hdr);
bam_destroy1(mflank);
}
return EXIT_SUCCESS;
}
static void parse_args(int argc, char **argv)
{
BuildGraphTask task;
memset(&task, 0, sizeof(task));
task.prefs = SEQ_LOADING_PREFS_INIT;
task.stats = SEQ_LOADING_STATS_INIT;
uint8_t fq_offset = 0;
int intocolour = -1;
GraphFileReader tmp_gfile;
// Arg parsing
char cmd[100], shortopts[100];
cmd_long_opts_to_short(longopts, shortopts, sizeof(shortopts));
int c;
bool sample_named = false, pref_unused = false;
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 't': cmd_check(!nthreads,cmd); nthreads = cmd_uint32_nonzero(cmd, optarg); break;
case 'm': cmd_mem_args_set_memory(&memargs, optarg); break;
case 'n': cmd_mem_args_set_nkmers(&memargs, optarg); break;
case 'f': cmd_check(!futil_get_force(), cmd); futil_set_force(true); break;
case 'k': cmd_check(!kmer_size,cmd); kmer_size = cmd_kmer_size(cmd, optarg); break;
case 's':
intocolour++;
check_sample_name(optarg);
sample_name_buf_add(&snamebuf, (SampleName){.colour = intocolour,
.name = optarg});
sample_named = true;
break;
case '1':
case '2':
case 'i':
pref_unused = false;
if(!sample_named)
cmd_print_usage("Please give sample name first [-s,--sample <name>]");
asyncio_task_parse(&task.files, c, optarg, fq_offset, NULL);
task.prefs.colour = intocolour;
add_task(&task);
break;
case 'M':
if(!strcmp(optarg,"FF")) task.prefs.matedir = READPAIR_FF;
else if(!strcmp(optarg,"FR")) task.prefs.matedir = READPAIR_FR;
else if(!strcmp(optarg,"RF")) task.prefs.matedir = READPAIR_RF;
else if(!strcmp(optarg,"RR")) task.prefs.matedir = READPAIR_RR;
else die("-M,--matepair <orient> must be one of: FF,FR,RF,RR");
pref_unused = true; break;
case 'O': fq_offset = cmd_uint8(cmd, optarg); pref_unused = true; break;
case 'Q': task.prefs.fq_cutoff = cmd_uint8(cmd, optarg); pref_unused = true; break;
case 'H': task.prefs.hp_cutoff = cmd_uint8(cmd, optarg); pref_unused = true; break;
case 'p': task.prefs.remove_pcr_dups = true; pref_unused = true; break;
case 'P': task.prefs.remove_pcr_dups = false; pref_unused = true; break;
case 'g':
if(intocolour == -1) intocolour = 0;
graph_file_reset(&tmp_gfile);
graph_file_open2(&tmp_gfile, optarg, "r", true, intocolour);
intocolour = MAX2((size_t)intocolour, file_filter_into_ncols(&tmp_gfile.fltr)-1);
gfile_buf_push(&gfilebuf, &tmp_gfile, 1);
sample_named = false;
break;
case 'I':
graph_file_reset(&tmp_gfile);
graph_file_open(&tmp_gfile, optarg);
if(file_filter_into_ncols(&tmp_gfile.fltr) > 1)
warn("Flattening intersection graph into colour 0: %s", optarg);
file_filter_flatten(&tmp_gfile.fltr, 0);
gfile_buf_push(&gisecbuf, &tmp_gfile, 1);
break;
case ':': /* BADARG */
case '?': /* BADCH getopt_long has already printed error */
// cmd_print_usage(NULL);
die("`"CMD" build -h` for help. Bad option: %s", argv[optind-1]);
default: die("Bad option: %s", cmd);
}
}
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;
}
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;
}
int ctx_clean(int argc, char **argv)
{
size_t nthreads = 0, use_ncols = 0;
struct MemArgs memargs = MEM_ARGS_INIT;
const char *out_ctx_path = NULL;
int min_keep_tip = -1, unitig_min = -1; // <0 => default, 0 => noclean
uint32_t fallback_thresh = 0;
const char *len_before_path = NULL, *len_after_path = NULL;
const char *covg_before_path = NULL, *covg_after_path = NULL;
// 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(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 'o':
if(out_ctx_path != NULL) cmd_print_usage(NULL);
out_ctx_path = optarg;
break;
case 'm': cmd_mem_args_set_memory(&memargs, optarg); break;
case 'n': cmd_mem_args_set_nkmers(&memargs, optarg); break;
case 'N': use_ncols = cmd_uint32_nonzero(cmd, optarg); break;
case 't': cmd_check(!nthreads, cmd); nthreads = cmd_uint32_nonzero(cmd, optarg); break;
case 'T':
cmd_check(min_keep_tip<0, cmd);
min_keep_tip = (optarg != NULL ? (int)cmd_uint32(cmd, optarg) : -1);
break;
case 'S':
case 'U':
cmd_check(unitig_min<0, cmd);
unitig_min = (optarg != NULL ? cmd_uint32(cmd, optarg) : -1);
break;
case 'B': cmd_check(!fallback_thresh, cmd); fallback_thresh = cmd_uint32_nonzero(cmd, optarg); break;
case 'l': cmd_check(!len_before_path, cmd); len_before_path = optarg; break;
case 'L': cmd_check(!len_after_path, cmd); len_after_path = optarg; break;
case 'c': cmd_check(!covg_before_path, cmd); covg_before_path = optarg; break;
case 'C': cmd_check(!covg_after_path, cmd); covg_after_path = optarg; break;
case ':': /* BADARG */
case '?': /* BADCH getopt_long has already printed error */
// cmd_print_usage(NULL);
die("`"CMD" clean -h` for help. Bad option: %s", argv[optind-1]);
default: abort();
}
}
if(nthreads == 0) nthreads = DEFAULT_NTHREADS;
if(optind >= argc) cmd_print_usage("Please give input graph files");
bool unitig_cleaning = (unitig_min != 0);
bool tip_cleaning = (min_keep_tip != 0);
bool doing_cleaning = (unitig_cleaning || tip_cleaning);
// If you ever want to estimate cleaning threshold without outputting
// a graph, change this to a warning
if(doing_cleaning && out_ctx_path == NULL) {
cmd_print_usage("Please specify --out <out.ctx> for cleaned graph");
// warn("No cleaning being done: you did not specify --out <out.ctx>");
}
if(!doing_cleaning && (covg_after_path || len_after_path)) {
warn("You gave --len-after <out> / --covg-after <out> without "
"any cleaning (set -U, --unitigs or -t, --tips)");
}
if(doing_cleaning && strcmp(out_ctx_path,"-") != 0 &&
!futil_get_force() && futil_file_exists(out_ctx_path))
{
cmd_print_usage("Output file already exists: %s", out_ctx_path);
}
if(fallback_thresh && !unitig_cleaning)
warn("-B, --fallback <T> without --unitigs");
// Use remaining args as graph files
char **gfile_paths = argv + optind;
size_t i, j, num_gfiles = (size_t)(argc - optind);
// Open graph files
GraphFileReader *gfiles = ctx_calloc(num_gfiles, sizeof(GraphFileReader));
size_t col, ncols, ctx_max_kmers = 0, ctx_sum_kmers = 0;
ncols = graph_files_open(gfile_paths, gfiles, num_gfiles,
&ctx_max_kmers, &ctx_sum_kmers);
size_t kmer_size = gfiles[0].hdr.kmer_size;
// default to one colour for now
if(use_ncols == 0) use_ncols = 1;
// Flatten if we don't have to remember colours / output a graph
if(out_ctx_path == NULL)
{
ncols = use_ncols = 1;
for(i = 0; i < num_gfiles; i++)
file_filter_flatten(&gfiles[i].fltr, 0);
}
if(ncols < use_ncols) {
warn("I only need %zu colour%s ('--ncols %zu' ignored)",
ncols, util_plural_str(ncols), use_ncols);
use_ncols = ncols;
}
char max_kmers_str[100];
ulong_to_str(ctx_max_kmers, max_kmers_str);
status("%zu input graph%s, max kmers: %s, using %zu colours",
num_gfiles, util_plural_str(num_gfiles), max_kmers_str, use_ncols);
// If no arguments given we default to removing tips < 2*kmer_size
if(min_keep_tip < 0)
min_keep_tip = 2 * kmer_size;
// Warn if any graph files already cleaned
size_t fromcol;
ErrorCleaning *cleaning;
for(i = 0; i < num_gfiles; i++) {
for(j = 0; j < file_filter_num(&gfiles[i].fltr); j++) {
fromcol = file_filter_fromcol(&gfiles[i].fltr, j);
cleaning = &gfiles[i].hdr.ginfo[fromcol].cleaning;
if(cleaning->cleaned_snodes && unitig_cleaning) {
warn("%s:%zu already has unitig cleaning with threshold: <%zu",
file_filter_path(&gfiles[i].fltr), fromcol,
(size_t)cleaning->clean_snodes_thresh);
}
if(cleaning->cleaned_tips && tip_cleaning) {
warn("%s:%zu already has had tip cleaned",
file_filter_path(&gfiles[i].fltr), fromcol);
}
}
}
// Print steps
size_t step = 0;
status("Actions:\n");
if(covg_before_path != NULL)
status("%zu. Saving kmer coverage distribution to: %s", step++, covg_before_path);
if(len_before_path != NULL)
status("%zu. Saving unitig length distribution to: %s", step++, len_before_path);
if(min_keep_tip > 0)
status("%zu. Cleaning tips shorter than %i nodes", step++, min_keep_tip);
if(unitig_min > 0)
status("%zu. Cleaning unitigs with coverage < %i", step++, unitig_min);
if(unitig_min < 0)
status("%zu. Cleaning unitigs with auto-detected threshold", step++);
if(covg_after_path != NULL)
status("%zu. Saving kmer coverage distribution to: %s", step++, covg_after_path);
if(len_after_path != NULL)
status("%zu. Saving unitig length distribution to: %s", step++, len_after_path);
//
// Decide memory usage
//
bool all_colours_loaded = (ncols <= use_ncols);
bool use_mem_limit = (memargs.mem_to_use_set && num_gfiles > 1) || !ctx_max_kmers;
size_t kmers_in_hash, bits_per_kmer, graph_mem;
size_t per_col_bits = (sizeof(Covg)+sizeof(Edges)) * 8;
size_t extra_edge_bits = (all_colours_loaded ? 0 : sizeof(Edges) * 8);
bits_per_kmer = sizeof(BinaryKmer)*8 +
per_col_bits * use_ncols +
extra_edge_bits;
kmers_in_hash = cmd_get_kmers_in_hash(memargs.mem_to_use,
memargs.mem_to_use_set,
memargs.num_kmers,
memargs.num_kmers_set,
bits_per_kmer,
ctx_max_kmers, ctx_sum_kmers,
use_mem_limit, &graph_mem);
// Maximise the number of colours we load to fill the mem
size_t max_usencols = (memargs.mem_to_use*8 -
sizeof(BinaryKmer)*8*kmers_in_hash +
extra_edge_bits*kmers_in_hash) /
(per_col_bits*kmers_in_hash);
use_ncols = MIN2(max_usencols, ncols);
cmd_check_mem_limit(memargs.mem_to_use, graph_mem);
//
// Check output files are writable
//
futil_create_output(out_ctx_path);
// Does nothing if arg is NULL
futil_create_output(covg_before_path);
futil_create_output(covg_after_path);
futil_create_output(len_before_path);
futil_create_output(len_after_path);
// Create db_graph
// Load as many colours as possible
// Use an extra set of edge to take intersections
dBGraph db_graph;
db_graph_alloc(&db_graph, gfiles[0].hdr.kmer_size, use_ncols, use_ncols,
kmers_in_hash, DBG_ALLOC_EDGES | DBG_ALLOC_COVGS);
// Extra edges required to hold union of kept edges
Edges *edges_union = NULL;
if(use_ncols < ncols)
edges_union = ctx_calloc(db_graph.ht.capacity, sizeof(Edges));
// Load graph into a single colour
GraphLoadingPrefs gprefs = graph_loading_prefs(&db_graph);
// Construct cleaned graph header
GraphFileHeader outhdr;
memset(&outhdr, 0, sizeof(GraphFileHeader));
for(i = 0; i < num_gfiles; i++)
graph_file_merge_header(&outhdr, &gfiles[i]);
if(ncols > use_ncols)
{
db_graph.num_of_cols = db_graph.num_edge_cols = 1;
SWAP(edges_union, db_graph.col_edges);
graphs_load_files_flat(gfiles, num_gfiles, gprefs, NULL);
SWAP(edges_union, db_graph.col_edges);
db_graph.num_of_cols = db_graph.num_edge_cols = use_ncols;
}
else {
for(i = 0; i < num_gfiles; i++)
graph_load(&gfiles[i], gprefs, NULL);
}
char num_kmers_str[100];
ulong_to_str(db_graph.ht.num_kmers, num_kmers_str);
status("Total kmers loaded: %s\n", num_kmers_str);
size_t initial_nkmers = db_graph.ht.num_kmers;
hash_table_print_stats(&db_graph.ht);
uint8_t *visited = ctx_calloc(roundup_bits2bytes(db_graph.ht.capacity), 1);
uint8_t *keep = ctx_calloc(roundup_bits2bytes(db_graph.ht.capacity), 1);
// Always estimate cleaning threshold
// if(unitig_min <= 0 || covg_before_path || len_before_path)
// {
// Get coverage distribution and estimate cleaning threshold
int est_min_covg = cleaning_get_threshold(nthreads,
covg_before_path,
len_before_path,
visited, &db_graph);
if(est_min_covg < 0) status("Cannot find recommended cleaning threshold");
else status("Recommended cleaning threshold is: %i", est_min_covg);
// Use estimated threshold if threshold not set
if(unitig_min < 0) {
if(fallback_thresh > 0 && est_min_covg < (int)fallback_thresh) {
status("Using fallback threshold: %i", fallback_thresh);
unitig_min = fallback_thresh;
}
else if(est_min_covg >= 0) unitig_min = est_min_covg;
}
// }
// Die if we failed to find suitable cleaning threshold
if(unitig_min < 0)
die("Need cleaning threshold (--unitigs=<D> or --fallback <D>)");
// Cleaning parameters should now be set (>0) or turned off (==0)
ctx_assert(unitig_min >= 0);
ctx_assert(min_keep_tip >= 0);
if(unitig_min || min_keep_tip)
{
// Clean graph of tips (if min_keep_tip > 0) and unitigs (if threshold > 0)
clean_graph(nthreads, unitig_min, min_keep_tip,
covg_after_path, len_after_path,
visited, keep, &db_graph);
}
ctx_free(visited);
ctx_free(keep);
if(out_ctx_path != NULL)
{
// Set output header ginfo cleaned
for(col = 0; col < ncols; col++)
{
cleaning = &outhdr.ginfo[col].cleaning;
cleaning->cleaned_snodes |= unitig_cleaning;
cleaning->cleaned_tips |= tip_cleaning;
// if(tip_cleaning) {
// strbuf_append_str(&outhdr.ginfo[col].sample_name, ".tipclean");
// }
if(unitig_cleaning) {
size_t thresh = cleaning->clean_snodes_thresh;
thresh = cleaning->cleaned_snodes ? MAX2(thresh, (uint32_t)unitig_min)
: (uint32_t)unitig_min;
cleaning->clean_snodes_thresh = thresh;
// char name_append[200];
// sprintf(name_append, ".supclean%zu", thresh);
// strbuf_append_str(&outhdr.ginfo[col].sample_name, name_append);
}
}
// Print stats on removed kmers
size_t removed_nkmers = initial_nkmers - db_graph.ht.num_kmers;
double removed_pct = (100.0 * removed_nkmers) / initial_nkmers;
char removed_str[100], init_str[100];
ulong_to_str(removed_nkmers, removed_str);
ulong_to_str(initial_nkmers, init_str);
status("Removed %s of %s (%.2f%%) kmers", removed_str, init_str, removed_pct);
// kmers_loaded=true
graph_writer_merge(out_ctx_path, gfiles, num_gfiles,
true, all_colours_loaded,
edges_union, &outhdr, &db_graph);
}
ctx_check(db_graph.ht.num_kmers == hash_table_count_kmers(&db_graph.ht));
// TODO: report kmer coverage for each sample
graph_header_dealloc(&outhdr);
for(i = 0; i < num_gfiles; i++) graph_file_close(&gfiles[i]);
ctx_free(gfiles);
ctx_free(edges_union);
db_graph_dealloc(&db_graph);
return EXIT_SUCCESS;
}
int ctx_rmsubstr(int argc, char **argv)
{
struct MemArgs memargs = MEM_ARGS_INIT;
size_t kmer_size = 0, nthreads = 0;
const char *output_file = NULL;
seq_format fmt = SEQ_FMT_FASTA;
bool invert = false;
// Arg parsing
char cmd[100], shortopts[100];
cmd_long_opts_to_short(longopts, shortopts, sizeof(shortopts));
int c;
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 'o': cmd_check(!output_file, cmd); output_file = optarg; break;
case 't': cmd_check(!nthreads, cmd); nthreads = cmd_uint32_nonzero(cmd, optarg); break;
case 'm': cmd_mem_args_set_memory(&memargs, optarg); break;
case 'n': cmd_mem_args_set_nkmers(&memargs, optarg); break;
case 'k': cmd_check(!kmer_size,cmd); kmer_size = cmd_uint32(cmd, optarg); break;
case 'F': cmd_check(fmt==SEQ_FMT_FASTA, cmd); fmt = cmd_parse_format(cmd, optarg); break;
case 'v': cmd_check(!invert,cmd); invert = true; break;
case ':': /* BADARG */
case '?': /* BADCH getopt_long has already printed error */
// cmd_print_usage(NULL);
cmd_print_usage("`"CMD" rmsubstr -h` for help. Bad option: %s", argv[optind-1]);
default: abort();
}
}
// Defaults
if(!nthreads) nthreads = DEFAULT_NTHREADS;
if(!kmer_size) kmer_size = DEFAULT_KMER;
if(!(kmer_size&1)) cmd_print_usage("Kmer size must be odd");
if(kmer_size < MIN_KMER_SIZE) cmd_print_usage("Kmer size too small (recompile)");
if(kmer_size > MAX_KMER_SIZE) cmd_print_usage("Kmer size too large (recompile?)");
if(optind >= argc)
cmd_print_usage("Please specify at least one input sequence file (.fq, .fq etc.)");
size_t i, num_seq_files = argc - optind;
char **seq_paths = argv + optind;
seq_file_t **seq_files = ctx_calloc(num_seq_files, sizeof(seq_file_t*));
for(i = 0; i < num_seq_files; i++)
if((seq_files[i] = seq_open(seq_paths[i])) == NULL)
die("Cannot read sequence file %s", seq_paths[i]);
// Estimate number of bases
// set to -1 if we cannot calc
int64_t est_num_bases = seq_est_seq_bases(seq_files, num_seq_files);
if(est_num_bases < 0) {
warn("Cannot get file sizes, using pipes");
est_num_bases = memargs.num_kmers * IDEAL_OCCUPANCY;
}
status("[memory] Estimated number of bases: %li", (long)est_num_bases);
// Use file sizes to decide on memory
//
// Decide on memory
//
size_t bits_per_kmer, kmers_in_hash, graph_mem;
bits_per_kmer = sizeof(BinaryKmer)*8 +
sizeof(KONodeList) + sizeof(KOccur) + // see kmer_occur.h
8; // 1 byte per kmer for each base to load sequence files
kmers_in_hash = cmd_get_kmers_in_hash(memargs.mem_to_use,
memargs.mem_to_use_set,
memargs.num_kmers,
memargs.num_kmers_set,
bits_per_kmer,
est_num_bases, est_num_bases,
false, &graph_mem);
cmd_check_mem_limit(memargs.mem_to_use, graph_mem);
//
// Open output file
//
if(output_file == NULL) output_file = "-";
FILE *fout = futil_fopen_create(output_file, "w");
//
// Set up memory
//
dBGraph db_graph;
db_graph_alloc(&db_graph, kmer_size, 1, 0, kmers_in_hash, DBG_ALLOC_BKTLOCKS);
//
// Load reference sequence into a read buffer
//
ReadBuffer rbuf;
read_buf_alloc(&rbuf, 1024);
seq_load_all_reads(seq_files, num_seq_files, &rbuf);
// Check for reads too short
for(i = 0; i < rbuf.len && rbuf.b[i].seq.end >= kmer_size; i++) {}
if(i < rbuf.len)
warn("Reads shorter than kmer size (%zu) will not be filtered", kmer_size);
KOGraph kograph = kograph_create(rbuf.b, rbuf.len, true, 0,
nthreads, &db_graph);
size_t num_reads = rbuf.len, num_reads_printed = 0, num_bad_reads = 0;
// Loop over reads printing those that are not substrings
int ret;
for(i = 0; i < rbuf.len; i++) {
ret = _is_substr(&rbuf, i, &kograph, &db_graph);
if(ret == -1) num_bad_reads++;
else if((ret && invert) || (!ret && !invert)) {
seqout_print_read(&rbuf.b[i], fmt, fout);
num_reads_printed++;
}
}
char num_reads_str[100], num_reads_printed_str[100], num_bad_reads_str[100];
ulong_to_str(num_reads, num_reads_str);
ulong_to_str(num_reads_printed, num_reads_printed_str);
ulong_to_str(num_bad_reads, num_bad_reads_str);
status("Printed %s / %s (%.1f%%) to %s",
num_reads_printed_str, num_reads_str,
!num_reads ? 0.0 : (100.0 * num_reads_printed) / num_reads,
futil_outpath_str(output_file));
if(num_bad_reads > 0) {
status("Bad reads: %s / %s (%.1f%%) - no kmer {ACGT} of length %zu",
num_bad_reads_str, num_reads_str,
(100.0 * num_bad_reads) / num_reads,
kmer_size);
}
fclose(fout);
kograph_dealloc(&kograph);
// Free sequence memory
for(i = 0; i < rbuf.len; i++) seq_read_dealloc(&rbuf.b[i]);
read_buf_dealloc(&rbuf);
ctx_free(seq_files);
db_graph_dealloc(&db_graph);
return EXIT_SUCCESS;
}
int main(int argc, char **argv)
{
time_t start, end;
time(&start);
ctx_msg_out = stderr;
cortex_init();
cmd_init(argc, argv);
if(argc == 1) print_help(stderr, NULL);
const CtxCmd *cmd = ctx_get_command(argv[1]);
if(cmd == NULL) print_help(stderr, "Unrecognised command: %s", argv[1]);
// Once we have set cmd_usage, we can call cmd_print_usage() from anywhere
cmd_set_usage(cmd->usage);
// If no arguments after command, print help
if(argc == 2) cmd_print_usage(NULL);
// Look for -q, --quiet argument, if given silence output
int argi = 1;
while(argi < argc && !(!strcmp(argv[argi],"-q") || !strcmp(argv[argi],"--quiet")))
argi++;
if(argi < argc) {
// Found -q, --quiet argument
ctx_msg_out = NULL;
// Remove argument
for(--argc; argi < argc; argi++)
argv[argi] = argv[argi+1];
}
// Print status header
cmd_print_status_header();
SWAP(argv[1],argv[0]);
int ret = cmd->func(argc-1, argv+1);
time(&end);
cmd_destroy();
// Warn if more allocations than deallocations
size_t still_alloced = alloc_get_num_allocs() - alloc_get_num_frees();
if(still_alloced) warn("%zu allocates not free'd.", still_alloced);
char nallocs_str[50];
ulong_to_str(alloc_get_num_allocs(), nallocs_str);
status("[memory] We made %s allocs", nallocs_str);
status(ret == 0 ? "Done." : "Fail.");
// Print time taken
double diff = difftime(end,start);
if(diff < 60) status("[time] %.2lf seconds\n", diff);
else {
char timestr[100];
seconds_to_str((size_t)diff, timestr);
status("[time] %.2lf seconds (%s)\n", diff, timestr);
}
cortex_destroy();
return ret;
}
static a_uint32_t *
cmd_parse(char *cmd_str, int *cmd_index, int *cmd_index_sub)
{
int cmd_nr = 0;
a_uint32_t *arg_val = ioctl_argp;
char *tmp_str[CMDSTR_ARGS_MAX];
if (cmd_str == NULL)
return NULL;
memset(arg_val, 0, CMDSTR_ARGS_MAX * sizeof (a_uint32_t));
/* split string into array */
if ((tmp_str[cmd_nr] = (void *) strtok(cmd_str, " ")) == NULL)
return NULL;
/*handle help */
if (!strcasecmp(tmp_str[cmd_nr], "help"))
{
dprintf("input ? get help\n\n");
return NULL;
}
while (tmp_str[cmd_nr])
{
if (++cmd_nr == 3)
break;
tmp_str[cmd_nr] = (void *) strtok(NULL, " ");
}
/*commond string lookup */
int cmd_depth = cmd_lookup(tmp_str, cmd_index, cmd_index_sub);
if (*cmd_index == GCMD_DESC_NO_MATCH || *cmd_index_sub == GCMD_DESC_NO_MATCH)
{
dprintf("invalid or incomplete command.\n\n");
return NULL;
}
/*parse param */
cmd_nr = 0;
if (cmd_depth == 2)
{
tmp_str[cmd_nr] = tmp_str[2];
cmd_nr++;
}
tmp_str[cmd_nr] = (void *) strtok(NULL, " ");
while (tmp_str[cmd_nr])
{
if (++cmd_nr == CMDSTR_ARGS_MAX)
break;
tmp_str[cmd_nr] = (void *) strtok(NULL, " ");
}
arg_val[0] = GCMD_SUB_API(*cmd_index, *cmd_index_sub);
arg_val[1] = (a_uint32_t) ioctl_buf;
int rtn_code;
if (arg_val[0] < SW_API_MAX)
{
/*api command parse */
rtn_code = cmd_parse_api(tmp_str, arg_val);
}
else if (arg_val[0] > SW_API_MAX)
{
/*user command parse */
rtn_code = cmd_parse_sw(tmp_str, arg_val);
}
else
{
rtn_code = SW_BAD_PARAM;
}
if(rtn_code != SW_OK)
{
cmd_print_error(rtn_code);
if(rtn_code == SW_BAD_PARAM)
cmd_print_usage(*cmd_index, *cmd_index_sub);
return NULL;
}
return arg_val;
}
int ctx_join(int argc, char **argv)
{
struct MemArgs memargs = MEM_ARGS_INIT;
const char *out_path = NULL;
size_t use_ncols = 0;
GraphFileReader tmp_gfile;
GraphFileBuffer isec_gfiles_buf;
gfile_buf_alloc(&isec_gfiles_buf, 8);
// Arg parsing
char cmd[100], shortopts[100];
cmd_long_opts_to_short(longopts, shortopts, sizeof(shortopts));
int c;
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 '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 'N': cmd_check(!use_ncols, cmd); use_ncols = cmd_uint32_nonzero(cmd, optarg); break;
case 'i':
graph_file_reset(&tmp_gfile);
graph_file_open(&tmp_gfile, optarg);
if(file_filter_into_ncols(&tmp_gfile.fltr) > 1)
warn("Flattening intersection graph into colour 0: %s", optarg);
file_filter_flatten(&tmp_gfile.fltr, 0);
gfile_buf_push(&isec_gfiles_buf, &tmp_gfile, 1);
break;
case ':': /* BADARG */
case '?': /* BADCH getopt_long has already printed error */
// cmd_print_usage(NULL);
die("`"CMD" join -h` for help. Bad option: %s", argv[optind-1]);
default: abort();
}
}
GraphFileReader *igfiles = isec_gfiles_buf.b;
size_t num_igfiles = isec_gfiles_buf.len;
if(!out_path) cmd_print_usage("--out <out.ctx> required");
if(optind >= argc)
cmd_print_usage("Please specify at least one input graph file");
// optind .. argend-1 are graphs to load
size_t num_gfiles = (size_t)(argc - optind);
char **gfile_paths = argv + optind;
GraphFileReader *gfiles = ctx_calloc(num_gfiles, sizeof(GraphFileReader));
status("Probing %zu graph files and %zu intersect files", num_gfiles, num_igfiles);
// Check all binaries are valid binaries with matching kmer size
size_t i;
size_t ctx_max_cols = 0;
uint64_t min_intersect_num_kmers = 0, ctx_max_kmers = 0, ctx_sum_kmers = 0;
for(i = 0; i < num_gfiles; i++)
{
graph_file_open2(&gfiles[i], gfile_paths[i], "r", true, ctx_max_cols);
if(gfiles[0].hdr.kmer_size != gfiles[i].hdr.kmer_size) {
cmd_print_usage("Kmer sizes don't match [%u vs %u]",
gfiles[0].hdr.kmer_size, gfiles[i].hdr.kmer_size);
}
ctx_max_cols = MAX2(ctx_max_cols, file_filter_into_ncols(&gfiles[i].fltr));
ctx_max_kmers = MAX2(ctx_max_kmers, graph_file_nkmers(&gfiles[i]));
ctx_sum_kmers += graph_file_nkmers(&gfiles[i]);
}
// Probe intersection graph files
for(i = 0; i < num_igfiles; i++)
{
if(gfiles[0].hdr.kmer_size != igfiles[i].hdr.kmer_size) {
cmd_print_usage("Kmer sizes don't match [%u vs %u]",
gfiles[0].hdr.kmer_size, igfiles[i].hdr.kmer_size);
}
uint64_t nkmers = graph_file_nkmers(&igfiles[i]);
if(i == 0) min_intersect_num_kmers = nkmers;
else if(nkmers < min_intersect_num_kmers)
{
// Put smallest intersection binary first
SWAP(igfiles[i], igfiles[0]);
min_intersect_num_kmers = nkmers;
}
}
bool take_intersect = (num_igfiles > 0);
// If we are taking an intersection,
// all kmers intersection kmers will need to be loaded
if(take_intersect)
ctx_max_kmers = ctx_sum_kmers = min_intersect_num_kmers;
bool use_ncols_set = (use_ncols > 0);
bool output_to_stdout = (strcmp(out_path,"-") == 0);
// if(use_ncols == 0) use_ncols = 1;
if(use_ncols_set) {
if(use_ncols < ctx_max_cols && output_to_stdout)
die("I need %zu colours if outputting to STDOUT (--ncols)", ctx_max_cols);
if(use_ncols > ctx_max_cols) {
warn("I only need %zu colour%s ('--ncols %zu' ignored)",
ctx_max_cols, util_plural_str(ctx_max_cols), use_ncols);
use_ncols = ctx_max_cols;
}
}
else {
use_ncols = output_to_stdout ? ctx_max_cols : 1;
}
// Check out_path is writable
futil_create_output(out_path);
status("Output %zu cols; from %zu files; intersecting %zu graphs; ",
ctx_max_cols, num_gfiles, num_igfiles);
if(num_gfiles == 1 && num_igfiles == 0)
{
// Loading only one file with no intersection files
// Don't need to store a graph in memory, can filter as stream
// Don't actually store anything in the de Bruijn graph, but we need to
// pass it, so mock one up
dBGraph db_graph;
db_graph_alloc(&db_graph, gfiles[0].hdr.kmer_size,
file_filter_into_ncols(&gfiles[0].fltr), 0, 1024, 0);
graph_writer_stream_mkhdr(out_path, &gfiles[0], &db_graph, NULL, NULL);
graph_file_close(&gfiles[0]);
gfile_buf_dealloc(&isec_gfiles_buf);
ctx_free(gfiles);
db_graph_dealloc(&db_graph);
return EXIT_SUCCESS;
}
//
// Decide on memory
//
size_t bits_per_kmer, kmers_in_hash, graph_mem;
bits_per_kmer = sizeof(BinaryKmer)*8 +
(sizeof(Covg) + sizeof(Edges)) * 8 * use_ncols;
kmers_in_hash = cmd_get_kmers_in_hash(memargs.mem_to_use,
memargs.mem_to_use_set,
memargs.num_kmers,
memargs.num_kmers_set,
bits_per_kmer,
ctx_max_kmers, ctx_sum_kmers,
true, &graph_mem);
if(!use_ncols_set)
{
// Maximise use_ncols
size_t max_usencols = (memargs.mem_to_use*8) / bits_per_kmer;
use_ncols = MIN2(max_usencols, ctx_max_cols);
bits_per_kmer = sizeof(BinaryKmer)*8 +
(sizeof(Covg) + sizeof(Edges)) * 8 * use_ncols;
// Re-check memory used
kmers_in_hash = cmd_get_kmers_in_hash(memargs.mem_to_use,
memargs.mem_to_use_set,
memargs.num_kmers,
memargs.num_kmers_set,
bits_per_kmer,
ctx_max_kmers, ctx_sum_kmers,
true, &graph_mem);
}
status("Using %zu colour%s in memory", use_ncols, util_plural_str(use_ncols));
cmd_check_mem_limit(memargs.mem_to_use, graph_mem);
// Create db_graph
dBGraph db_graph;
Edges *intersect_edges = NULL;
size_t edge_cols = (use_ncols + take_intersect);
db_graph_alloc(&db_graph, gfiles[0].hdr.kmer_size, use_ncols, use_ncols,
kmers_in_hash, DBG_ALLOC_COVGS);
// We allocate edges ourself since it's a special case
db_graph.col_edges = ctx_calloc(db_graph.ht.capacity*edge_cols, sizeof(Edges));
// Load intersection binaries
char *intsct_gname_ptr = NULL;
StrBuf intersect_gname;
strbuf_alloc(&intersect_gname, 1024);
if(take_intersect)
{
GraphLoadingPrefs gprefs = graph_loading_prefs(&db_graph);
gprefs.boolean_covgs = true; // covg++ only
for(i = 0; i < num_igfiles; i++)
{
graph_load(&igfiles[i], gprefs, NULL);
// Update intersect header
// note: intersection graphs all load exactly one colour into colour 0
graph_info_make_intersect(&igfiles[i].hdr.ginfo[0], &intersect_gname);
gprefs.must_exist_in_graph = true;
gprefs.must_exist_in_edges = db_graph.col_edges;
}
if(num_igfiles > 1)
{
// Remove nodes where covg != num_igfiles
HASH_ITERATE_SAFE(&db_graph.ht, remove_non_intersect_nodes,
db_graph.col_covgs, (Covg)num_igfiles, &db_graph.ht);
}
status("Loaded intersection set\n");
intsct_gname_ptr = intersect_gname.b;
for(i = 0; i < num_igfiles; i++) graph_file_close(&igfiles[i]);
// Reset graph info
for(i = 0; i < db_graph.num_of_cols; i++)
graph_info_init(&db_graph.ginfo[i]);
// Zero covgs
memset(db_graph.col_covgs, 0, db_graph.ht.capacity * sizeof(Covg));
// Use union edges we loaded to intersect new edges
intersect_edges = db_graph.col_edges;
db_graph.col_edges += db_graph.ht.capacity;
}
bool kmers_loaded = take_intersect, colours_loaded = false;
graph_writer_merge_mkhdr(out_path, gfiles, num_gfiles,
kmers_loaded, colours_loaded, intersect_edges,
intsct_gname_ptr, &db_graph);
if(take_intersect)
db_graph.col_edges -= db_graph.ht.capacity;
for(i = 0; i < num_gfiles; i++) graph_file_close(&gfiles[i]);
strbuf_dealloc(&intersect_gname);
gfile_buf_dealloc(&isec_gfiles_buf);
ctx_free(gfiles);
db_graph_dealloc(&db_graph);
return EXIT_SUCCESS;
}
int ctx_clean(int argc, char **argv)
{
size_t nthreads = 0, use_ncols = 0;
struct MemArgs memargs = MEM_ARGS_INIT;
const char *out_ctx_path = NULL;
bool tip_cleaning = false, supernode_cleaning = false;
size_t min_keep_tip = 0;
Covg threshold = 0, fallback_thresh = 0;
const char *len_before_path = NULL, *len_after_path = NULL;
const char *covg_before_path = NULL, *covg_after_path = NULL;
// 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(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 'o':
if(out_ctx_path != NULL) cmd_print_usage(NULL);
out_ctx_path = optarg;
break;
case 'm': cmd_mem_args_set_memory(&memargs, optarg); break;
case 'n': cmd_mem_args_set_nkmers(&memargs, optarg); break;
case 'N': use_ncols = cmd_uint32_nonzero(cmd, optarg); break;
case 't': cmd_check(!nthreads, cmd); nthreads = cmd_uint32_nonzero(cmd, optarg); break;
case 'T':
cmd_check(!tip_cleaning, cmd);
min_keep_tip = cmd_uint32_nonzero(cmd, optarg);
tip_cleaning = true;
break;
case 'S':
cmd_check(!supernode_cleaning, cmd);
if(optarg != NULL) threshold = cmd_uint32_nonzero(cmd, optarg);
supernode_cleaning = true;
break;
case 'B': cmd_check(!fallback_thresh, cmd); fallback_thresh = cmd_uint32_nonzero(cmd, optarg); break;
case 'l': cmd_check(!len_before_path, cmd); len_before_path = optarg; break;
case 'L': cmd_check(!len_after_path, cmd); len_after_path = optarg; break;
case 'c': cmd_check(!covg_before_path, cmd); covg_before_path = optarg; break;
case 'C': cmd_check(!covg_after_path, cmd); covg_after_path = optarg; break;
case ':': /* BADARG */
case '?': /* BADCH getopt_long has already printed error */
// cmd_print_usage(NULL);
die("`"CMD" clean -h` for help. Bad option: %s", argv[optind-1]);
default: abort();
}
}
if(nthreads == 0) nthreads = DEFAULT_NTHREADS;
if(optind >= argc) cmd_print_usage("Please give input graph files");
// Default behaviour
if(!tip_cleaning && !supernode_cleaning) {
if(out_ctx_path != NULL)
supernode_cleaning = tip_cleaning = true; // do both
else
warn("No cleaning being done: you did not specify --out <out.ctx>");
}
bool doing_cleaning = (supernode_cleaning || tip_cleaning);
if(doing_cleaning && out_ctx_path == NULL) {
cmd_print_usage("Please specify --out <out.ctx> for cleaned graph");
}
if(!doing_cleaning && (covg_after_path || len_after_path)) {
cmd_print_usage("You gave --len-after <out> / --covg-after <out> without "
"any cleaning (set -s, --supernodes or -t, --tips)");
}
if(doing_cleaning && strcmp(out_ctx_path,"-") != 0 &&
!futil_get_force() && futil_file_exists(out_ctx_path))
{
cmd_print_usage("Output file already exists: %s", out_ctx_path);
}
if(fallback_thresh && !supernode_cleaning)
cmd_print_usage("-B, --fallback <T> without --supernodes");
// Use remaining args as graph files
char **gfile_paths = argv + optind;
size_t i, j, num_gfiles = (size_t)(argc - optind);
// Open graph files
GraphFileReader *gfiles = ctx_calloc(num_gfiles, sizeof(GraphFileReader));
size_t ncols, ctx_max_kmers = 0, ctx_sum_kmers = 0;
ncols = graph_files_open(gfile_paths, gfiles, num_gfiles,
&ctx_max_kmers, &ctx_sum_kmers);
size_t kmer_size = gfiles[0].hdr.kmer_size;
// default to one colour for now
if(use_ncols == 0) use_ncols = 1;
// Flatten if we don't have to remember colours / output a graph
if(!doing_cleaning)
{
ncols = use_ncols = 1;
for(i = 0; i < num_gfiles; i++)
file_filter_flatten(&gfiles[i].fltr, 0);
}
if(ncols < use_ncols) {
warn("I only need %zu colour%s ('--ncols %zu' ignored)",
ncols, util_plural_str(ncols), use_ncols);
use_ncols = ncols;
}
char max_kmers_str[100];
ulong_to_str(ctx_max_kmers, max_kmers_str);
status("%zu input graph%s, max kmers: %s, using %zu colours",
num_gfiles, util_plural_str(num_gfiles), max_kmers_str, use_ncols);
// If no arguments given we default to removing tips < 2*kmer_size
if(tip_cleaning && min_keep_tip == 0)
min_keep_tip = 2 * kmer_size;
// Warn if any graph files already cleaned
size_t fromcol, intocol;
ErrorCleaning *cleaning;
for(i = 0; i < num_gfiles; i++) {
for(j = 0; j < file_filter_num(&gfiles[i].fltr); j++) {
fromcol = file_filter_fromcol(&gfiles[i].fltr, j);
cleaning = &gfiles[i].hdr.ginfo[fromcol].cleaning;
if(cleaning->cleaned_snodes && supernode_cleaning) {
warn("%s:%zu already has supernode cleaning with threshold: <%zu",
file_filter_path(&gfiles[i].fltr), fromcol,
(size_t)cleaning->clean_snodes_thresh);
}
if(cleaning->cleaned_tips && tip_cleaning) {
warn("%s:%zu already has had tip cleaned",
file_filter_path(&gfiles[i].fltr), fromcol);
}
}
}
// Print steps
size_t step = 0;
status("Actions:\n");
if(covg_before_path != NULL)
status("%zu. Saving kmer coverage distribution to: %s", step++, covg_before_path);
if(len_before_path != NULL)
status("%zu. Saving supernode length distribution to: %s", step++, len_before_path);
if(tip_cleaning)
status("%zu. Cleaning tips shorter than %zu nodes", step++, min_keep_tip);
if(supernode_cleaning && threshold > 0)
status("%zu. Cleaning supernodes with coverage < %u", step++, threshold);
if(supernode_cleaning && threshold <= 0)
status("%zu. Cleaning supernodes with auto-detected threshold", step++);
if(covg_after_path != NULL)
status("%zu. Saving kmer coverage distribution to: %s", step++, covg_after_path);
if(len_after_path != NULL)
status("%zu. Saving supernode length distribution to: %s", step++, len_after_path);
//
// Decide memory usage
//
bool all_colours_loaded = (ncols <= use_ncols);
bool use_mem_limit = (memargs.mem_to_use_set && num_gfiles > 1) || !ctx_max_kmers;
size_t kmers_in_hash, bits_per_kmer, graph_mem;
size_t per_kmer_per_col_bits = (sizeof(BinaryKmer)+sizeof(Covg)+sizeof(Edges)) * 8;
size_t pop_edges_per_kmer_bits = (all_colours_loaded ? 0 : sizeof(Edges) * 8);
bits_per_kmer = per_kmer_per_col_bits * use_ncols + pop_edges_per_kmer_bits;
kmers_in_hash = cmd_get_kmers_in_hash(memargs.mem_to_use,
memargs.mem_to_use_set,
memargs.num_kmers,
memargs.num_kmers_set,
bits_per_kmer,
ctx_max_kmers, ctx_sum_kmers,
use_mem_limit, &graph_mem);
// Maximise the number of colours we load to fill the mem
size_t max_usencols = (memargs.mem_to_use*8 - pop_edges_per_kmer_bits * kmers_in_hash) /
(per_kmer_per_col_bits * kmers_in_hash);
use_ncols = MIN2(max_usencols, ncols);
cmd_check_mem_limit(memargs.mem_to_use, graph_mem);
//
// Check output files are writable
//
futil_create_output(out_ctx_path);
// Does nothing if arg is NULL
futil_create_output(covg_before_path);
futil_create_output(covg_after_path);
futil_create_output(len_before_path);
futil_create_output(len_after_path);
// Create db_graph
// Load as many colours as possible
// Use an extra set of edge to take intersections
dBGraph db_graph;
db_graph_alloc(&db_graph, gfiles[0].hdr.kmer_size, use_ncols, use_ncols,
kmers_in_hash, DBG_ALLOC_COVGS);
// Edges is a special case
size_t num_edges = db_graph.ht.capacity * (use_ncols + !all_colours_loaded);
db_graph.col_edges = ctx_calloc(num_edges, sizeof(Edges));
// Load graph into a single colour
LoadingStats stats = LOAD_STATS_INIT_MACRO;
GraphLoadingPrefs gprefs = {.db_graph = &db_graph,
.boolean_covgs = false,
.must_exist_in_graph = false,
.must_exist_in_edges = NULL,
.empty_colours = false};
// Construct cleaned graph header
GraphFileHeader outhdr;
memset(&outhdr, 0, sizeof(GraphFileHeader));
outhdr.version = CTX_GRAPH_FILEFORMAT;
outhdr.kmer_size = db_graph.kmer_size;
outhdr.num_of_cols = ncols;
outhdr.num_of_bitfields = (db_graph.kmer_size*2+63)/64;
graph_header_alloc(&outhdr, ncols);
// Merge info into header
size_t gcol = 0;
for(i = 0; i < num_gfiles; i++) {
for(j = 0; j < file_filter_num(&gfiles[i].fltr); j++, gcol++) {
fromcol = file_filter_fromcol(&gfiles[i].fltr, j);
intocol = file_filter_intocol(&gfiles[i].fltr, j);
graph_info_merge(&outhdr.ginfo[intocol], &gfiles[i].hdr.ginfo[fromcol]);
}
}
if(ncols > use_ncols) {
graph_files_load_flat(gfiles, num_gfiles, gprefs, &stats);
} else {
for(i = 0; i < num_gfiles; i++)
graph_load(&gfiles[i], gprefs, &stats);
}
char num_kmers_str[100];
ulong_to_str(db_graph.ht.num_kmers, num_kmers_str);
status("Total kmers loaded: %s\n", num_kmers_str);
size_t initial_nkmers = db_graph.ht.num_kmers;
hash_table_print_stats(&db_graph.ht);
uint8_t *visited = ctx_calloc(roundup_bits2bytes(db_graph.ht.capacity), 1);
uint8_t *keep = ctx_calloc(roundup_bits2bytes(db_graph.ht.capacity), 1);
if((supernode_cleaning && threshold <= 0) || covg_before_path || len_before_path)
{
// Get coverage distribution and estimate cleaning threshold
int est_threshold = cleaning_get_threshold(nthreads,
covg_before_path,
len_before_path,
visited, &db_graph);
if(est_threshold < 0) status("Cannot find recommended cleaning threshold");
else status("Recommended cleaning threshold is: %i", est_threshold);
// Use estimated threshold if threshold not set
if(threshold <= 0) {
if(fallback_thresh > 0 && est_threshold < (int)fallback_thresh) {
status("Using fallback threshold: %i", fallback_thresh);
threshold = fallback_thresh;
}
else if(est_threshold >= 0) threshold = est_threshold;
}
}
// Die if we failed to find suitable cleaning threshold
if(supernode_cleaning && threshold <= 0)
die("Need cleaning threshold (--supernodes=<D> or --fallback <D>)");
if(doing_cleaning) {
// Clean graph of tips (if min_keep_tip > 0) and supernodes (if threshold > 0)
clean_graph(nthreads, threshold, min_keep_tip,
covg_after_path, len_after_path,
visited, keep, &db_graph);
}
ctx_free(visited);
ctx_free(keep);
if(doing_cleaning)
{
// Output graph file
Edges *intersect_edges = NULL;
bool kmers_loaded = true;
size_t col, thresh;
// Set output header ginfo cleaned
for(col = 0; col < ncols; col++)
{
cleaning = &outhdr.ginfo[col].cleaning;
cleaning->cleaned_snodes |= supernode_cleaning;
cleaning->cleaned_tips |= tip_cleaning;
// if(tip_cleaning) {
// strbuf_append_str(&outhdr.ginfo[col].sample_name, ".tipclean");
// }
if(supernode_cleaning) {
thresh = cleaning->clean_snodes_thresh;
thresh = cleaning->cleaned_snodes ? MAX2(thresh, (uint32_t)threshold)
: (uint32_t)threshold;
cleaning->clean_snodes_thresh = thresh;
// char name_append[200];
// sprintf(name_append, ".supclean%zu", thresh);
// strbuf_append_str(&outhdr.ginfo[col].sample_name, name_append);
}
}
if(!all_colours_loaded)
{
// We haven't loaded all the colours
// intersect_edges are edges to mask with
// resets graph edges
intersect_edges = db_graph.col_edges;
db_graph.col_edges += db_graph.ht.capacity;
}
// Print stats on removed kmers
size_t removed_nkmers = initial_nkmers - db_graph.ht.num_kmers;
double removed_pct = (100.0 * removed_nkmers) / initial_nkmers;
char removed_str[100], init_str[100];
ulong_to_str(removed_nkmers, removed_str);
ulong_to_str(initial_nkmers, init_str);
status("Removed %s of %s (%.2f%%) kmers", removed_str, init_str, removed_pct);
graph_files_merge(out_ctx_path, gfiles, num_gfiles,
kmers_loaded, all_colours_loaded,
intersect_edges, &outhdr, &db_graph);
// Swap back
if(!all_colours_loaded)
db_graph.col_edges = intersect_edges;
}
ctx_check(db_graph.ht.num_kmers == hash_table_count_kmers(&db_graph.ht));
graph_header_dealloc(&outhdr);
for(i = 0; i < num_gfiles; i++) graph_file_close(&gfiles[i]);
ctx_free(gfiles);
db_graph_dealloc(&db_graph);
return EXIT_SUCCESS;
}
int ctx_vcfcov(int argc, char **argv)
{
struct MemArgs memargs = MEM_ARGS_INIT;
const char *out_path = NULL, *out_type = NULL;
uint32_t max_allele_len = 0, max_gt_vars = 0;
char *ref_path = NULL;
bool low_mem = false;
// Arg parsing
char cmd[100];
char shortopts[300];
cmd_long_opts_to_short(longopts, shortopts, sizeof(shortopts));
int c;
size_t i;
// 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 'O': cmd_check(!out_type, cmd); out_type = optarg; 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 'r': cmd_check(!ref_path, cmd); ref_path = optarg; break;
case 'L': cmd_check(!max_allele_len,cmd); max_allele_len = cmd_uint32(cmd,optarg); break;
case 'N': cmd_check(!max_gt_vars,cmd); max_gt_vars = cmd_uint32(cmd,optarg); break;
case 'M': cmd_check(!low_mem, cmd); low_mem = true; break;
case ':': /* BADARG */
case '?': /* BADCH getopt_long has already printed error */
// cmd_print_usage(NULL);
die("`"CMD" "SUBCMD" -h` for help. Bad option: %s", argv[optind-1]);
default: abort();
}
}
// Defaults for unset values
if(out_path == NULL) out_path = "-";
if(ref_path == NULL) cmd_print_usage("Require a reference (-r,--ref <ref.fa>)");
if(optind+2 > argc) cmd_print_usage("Require VCF and graph files");
if(!max_allele_len) max_allele_len = DEFAULT_MAX_ALLELE_LEN;
if(!max_gt_vars) max_gt_vars = DEFAULT_MAX_GT_VARS;
status("[vcfcov] max allele length: %u; max number of variants: %u",
max_allele_len, max_gt_vars);
// open ref
// index fasta with: samtools faidx ref.fa
faidx_t *fai = fai_load(ref_path);
if(fai == NULL) die("Cannot load ref index: %s / %s.fai", ref_path, ref_path);
// Open input VCF file
const char *vcf_path = argv[optind++];
htsFile *vcffh = hts_open(vcf_path, "r");
if(vcffh == NULL) die("Cannot open VCF file: %s", vcf_path);
bcf_hdr_t *vcfhdr = bcf_hdr_read(vcffh);
if(vcfhdr == NULL) die("Cannot read VCF header: %s", vcf_path);
// Test we can close and reopen files
if(low_mem) {
if((vcffh = hts_open(vcf_path, "r")) == NULL)
die("Cannot re-open VCF file: %s", vcf_path);
if((vcfhdr = bcf_hdr_read(vcffh)) == NULL)
die("Cannot re-read VCF header: %s", vcf_path);
}
//
// Open graph files
//
const size_t num_gfiles = argc - optind;
char **graph_paths = argv + optind;
ctx_assert(num_gfiles > 0);
GraphFileReader *gfiles = ctx_calloc(num_gfiles, sizeof(GraphFileReader));
size_t ncols, ctx_max_kmers = 0, ctx_sum_kmers = 0;
ncols = graph_files_open(graph_paths, gfiles, num_gfiles,
&ctx_max_kmers, &ctx_sum_kmers);
// Check graph + paths are compatible
graphs_gpaths_compatible(gfiles, num_gfiles, NULL, 0, -1);
//
// Decide on memory
//
size_t bits_per_kmer, kmers_in_hash, graph_mem;
bits_per_kmer = sizeof(BinaryKmer)*8 + sizeof(Covg)*8 * ncols;
kmers_in_hash = cmd_get_kmers_in_hash(memargs.mem_to_use,
memargs.mem_to_use_set,
memargs.num_kmers,
memargs.num_kmers_set,
bits_per_kmer,
low_mem ? -1 : (int64_t)ctx_max_kmers,
ctx_sum_kmers,
true, &graph_mem);
cmd_check_mem_limit(memargs.mem_to_use, graph_mem);
//
// Open output file
//
// v=>vcf, z=>compressed vcf, b=>bcf, bu=>uncompressed bcf
int mode = vcf_misc_get_outtype(out_type, out_path);
futil_create_output(out_path);
htsFile *outfh = hts_open(out_path, modes_htslib[mode]);
status("[vcfcov] Output format: %s", hsmodes_htslib[mode]);
// Allocate memory
dBGraph db_graph;
db_graph_alloc(&db_graph, gfiles[0].hdr.kmer_size, ncols, 1, kmers_in_hash,
DBG_ALLOC_COVGS);
//
// Set up tag names
//
// *R => ref, *A => alt
sprintf(kcov_ref_tag, "K%zuR", db_graph.kmer_size); // mean coverage
sprintf(kcov_alt_tag, "K%zuA", db_graph.kmer_size);
// #SAMPLE=<ID=...,K29KCOV=...,K29NK=...,K29RLK>
// - K29_kcov is empirical kmer coverage
// - K29_nkmers is the number of kmers in the sample
// - mean_read_length is the mean read length in bases
char sample_kcov_tag[20], sample_nk_tag[20], sample_rlk_tag[20];
sprintf(sample_kcov_tag, "K%zu_kcov", db_graph.kmer_size); // mean coverage
sprintf(sample_nk_tag, "K%zu_nkmers", db_graph.kmer_size);
sprintf(sample_rlk_tag, "mean_read_length");
//
// Load kmers if we are using --low-mem
//
VcfCovStats st;
memset(&st, 0, sizeof(st));
VcfCovPrefs prefs = {.kcov_ref_tag = kcov_ref_tag,
.kcov_alt_tag = kcov_alt_tag,
.max_allele_len = max_allele_len,
.max_gt_vars = max_gt_vars,
.load_kmers_only = false};
if(low_mem)
{
status("[vcfcov] Loading kmers from VCF+ref");
prefs.load_kmers_only = true;
vcfcov_file(vcffh, vcfhdr, NULL, NULL, vcf_path, fai,
NULL, &prefs, &st, &db_graph);
// Close files
hts_close(vcffh);
bcf_hdr_destroy(vcfhdr);
// Re-open files
if((vcffh = hts_open(vcf_path, "r")) == NULL)
die("Cannot re-open VCF file: %s", vcf_path);
if((vcfhdr = bcf_hdr_read(vcffh)) == NULL)
die("Cannot re-read VCF header: %s", vcf_path);
prefs.load_kmers_only = false;
}
//
// Load graphs
//
GraphLoadingStats gstats;
memset(&gstats, 0, sizeof(gstats));
GraphLoadingPrefs gprefs = graph_loading_prefs(&db_graph);
gprefs.must_exist_in_graph = low_mem;
for(i = 0; i < num_gfiles; i++) {
graph_load(&gfiles[i], gprefs, &gstats);
graph_file_close(&gfiles[i]);
}
ctx_free(gfiles);
hash_table_print_stats(&db_graph.ht);
//
// Set up VCF header / graph matchup
//
size_t *samplehdrids = ctx_malloc(db_graph.num_of_cols * sizeof(size_t));
// Add samples to vcf header
bcf_hdr_t *outhdr = bcf_hdr_dup(vcfhdr);
bcf_hrec_t *hrec;
int sid;
char hdrstr[200];
for(i = 0; i < db_graph.num_of_cols; i++) {
char *sname = db_graph.ginfo[i].sample_name.b;
if((sid = bcf_hdr_id2int(outhdr, BCF_DT_SAMPLE, sname)) < 0) {
bcf_hdr_add_sample(outhdr, sname);
sid = bcf_hdr_id2int(outhdr, BCF_DT_SAMPLE, sname);
}
samplehdrids[i] = sid;
// Add SAMPLE field
hrec = bcf_hdr_get_hrec(outhdr, BCF_HL_STR, "ID", sname, "SAMPLE");
if(hrec == NULL) {
sprintf(hdrstr, "##SAMPLE=<ID=%s,%s=%"PRIu64",%s=%"PRIu64",%s=%zu>", sname,
sample_kcov_tag,
gstats.nkmers[i] ? gstats.sumcov[i] / gstats.nkmers[i] : 0,
sample_nk_tag, gstats.nkmers[i],
sample_rlk_tag, (size_t)db_graph.ginfo[i].mean_read_length);
bcf_hdr_append(outhdr, hdrstr);
}
else {
// mean kcovg
sprintf(hdrstr, "%"PRIu64, gstats.sumcov[i] / gstats.nkmers[i]);
vcf_misc_add_update_hrec(hrec, sample_kcov_tag, hdrstr);
// num kmers
sprintf(hdrstr, "%"PRIu64, gstats.nkmers[i]);
vcf_misc_add_update_hrec(hrec, sample_nk_tag, hdrstr);
// mean read length in kmers
sprintf(hdrstr, "%zu", (size_t)db_graph.ginfo[i].mean_read_length);
vcf_misc_add_update_hrec(hrec, sample_rlk_tag, hdrstr);
}
status("[vcfcov] Colour %zu: %s [VCF column %zu]", i, sname, samplehdrids[i]);
}
// Add genotype format fields
// One field per alternative allele
sprintf(hdrstr, "##FORMAT=<ID=%s,Number=A,Type=Integer,"
"Description=\"Coverage on ref (k=%zu): sum(kmer_covs) / exp_num_kmers\">\n",
kcov_ref_tag, db_graph.kmer_size);
bcf_hdr_append(outhdr, hdrstr);
sprintf(hdrstr, "##FORMAT=<ID=%s,Number=A,Type=Integer,"
"Description=\"Coverage on alt (k=%zu): sum(kmer_covs) / exp_num_kmers\">\n",
kcov_alt_tag, db_graph.kmer_size);
bcf_hdr_append(outhdr, hdrstr);
bcf_hdr_set_version(outhdr, "VCFv4.2");
// Add command string to header
vcf_misc_hdr_add_cmd(outhdr, cmd_get_cmdline(), cmd_get_cwd());
if(bcf_hdr_write(outfh, outhdr) != 0)
die("Cannot write header to: %s", futil_outpath_str(out_path));
status("[vcfcov] Reading %s and adding coverage", vcf_path);
// Reset stats and get coverage
memset(&st, 0, sizeof(st));
vcfcov_file(vcffh, vcfhdr, outfh, outhdr, vcf_path, fai,
samplehdrids, &prefs, &st, &db_graph);
// Print statistics
char ns0[50], ns1[50];
status("[vcfcov] Read %s VCF lines", ulong_to_str(st.nvcf_lines, ns0));
status("[vcfcov] Read %s ALTs", ulong_to_str(st.nalts_read, ns0));
status("[vcfcov] Used %s kmers", ulong_to_str(st.ngt_kmers, ns0));
status("[vcfcov] ALTs used: %s / %s (%.2f%%)",
ulong_to_str(st.nalts_loaded, ns0), ulong_to_str(st.nalts_read, ns1),
st.nalts_read ? (100.0*st.nalts_loaded) / st.nalts_read : 0.0);
status("[vcfcov] ALTs too long (>%ubp): %s / %s (%.2f%%)", max_allele_len,
ulong_to_str(st.nalts_too_long, ns0), ulong_to_str(st.nalts_read, ns1),
st.nalts_read ? (100.0*st.nalts_too_long) / st.nalts_read : 0.0);
status("[vcfcov] ALTs too dense (>%u within %zubp): %s / %s (%.2f%%)",
max_gt_vars, db_graph.kmer_size,
ulong_to_str(st.nalts_no_covg, ns0), ulong_to_str(st.nalts_read, ns1),
st.nalts_read ? (100.0*st.nalts_no_covg) / st.nalts_read : 0.0);
status("[vcfcov] ALTs printed with coverage: %s / %s (%.2f%%)",
ulong_to_str(st.nalts_with_covg, ns0), ulong_to_str(st.nalts_read, ns1),
st.nalts_read ? (100.0*st.nalts_with_covg) / st.nalts_read : 0.0);
status("[vcfcov] Saved to: %s\n", out_path);
ctx_free(samplehdrids);
graph_loading_stats_destroy(&gstats);
bcf_hdr_destroy(vcfhdr);
bcf_hdr_destroy(outhdr);
hts_close(vcffh);
hts_close(outfh);
fai_destroy(fai);
db_graph_dealloc(&db_graph);
return EXIT_SUCCESS;
}