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_correct(int argc, char **argv)
{
size_t i;
struct ReadThreadCmdArgs args;
read_thread_args_alloc(&args);
read_thread_args_parse(&args, argc, argv, longopts, true);
GraphFileReader *gfile = &args.gfile;
GPathFileBuffer *gpfiles = &args.gpfiles;
CorrectAlnInputBuffer *inputs = &args.inputs;
// Update colours in graph file - sample in 0, all others in 1
size_t ncols = gpath_load_sample_pop(gfile, 1, gpfiles->b, gpfiles->len,
args.colour);
// Check for compatibility between graph files and link files
graphs_gpaths_compatible(gfile, 1, gpfiles->b, gpfiles->len, 1);
int64_t ctx_num_kmers = gfile->num_of_kmers;
//
// 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(BinaryKmer)*8 + sizeof(Edges)*8 +
(gpfiles->len > 0 ? sizeof(GPath*)*8 : 0) +
ncols; // in colour
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,
ctx_num_kmers, ctx_num_kmers,
false, &graph_mem);
// Paths memory
size_t rem_mem = args.memargs.mem_to_use - MIN2(args.memargs.mem_to_use, graph_mem);
path_mem = gpath_reader_mem_req(gpfiles->b, gpfiles->len, ncols, rem_mem, false,
kmers_in_hash, false);
cmd_print_mem(path_mem, "paths");
// Shift path store memory from graphs->paths
graph_mem -= sizeof(GPath*)*kmers_in_hash;
path_mem += sizeof(GPath*)*kmers_in_hash;
// Total memory
total_mem = graph_mem + path_mem;
cmd_check_mem_limit(args.memargs.mem_to_use, total_mem);
//
// Check we can write all output files
//
// Open output files
SeqOutput *outputs = ctx_calloc(inputs->len, sizeof(SeqOutput));
bool err_occurred = false;
for(i = 0; i < inputs->len && !err_occurred; i++)
{
CorrectAlnInput *input = &inputs->b[i];
// We loaded target colour into colour zero
input->crt_params.ctxcol = input->crt_params.ctpcol = 0;
bool is_pe = asyncio_task_is_pe(&input->files);
err_occurred = !seqout_open(&outputs[i], input->out_base, args.fmt, is_pe);
input->output = &outputs[i];
}
// Abandon if some of the output files already exist
if(err_occurred) {
for(i = 0; i < inputs->len; i++)
seqout_close(&outputs[i], true);
die("Error creating output files");
}
//
// Allocate memory
//
dBGraph db_graph;
db_graph_alloc(&db_graph, gfile->hdr.kmer_size, ncols, 1, kmers_in_hash,
DBG_ALLOC_EDGES | DBG_ALLOC_NODE_IN_COL);
// Create a path store that does not tracks path counts
gpath_reader_alloc_gpstore(gpfiles->b, gpfiles->len, path_mem, false, &db_graph);
//
// Load Graph and link files
//
GraphLoadingPrefs gprefs = graph_loading_prefs(&db_graph);
gprefs.empty_colours = true;
// Load graph, print stats, close file
graph_load(gfile, gprefs, NULL);
hash_table_print_stats_brief(&db_graph.ht);
graph_file_close(gfile);
// 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]);
}
//
// Run alignment
//
correct_reads(inputs->b, inputs->len,
args.dump_seq_sizes, args.dump_frag_sizes,
args.fq_zero, args.append_orig_seq,
args.nthreads, &db_graph);
// Close and free output files
for(i = 0; i < inputs->len; i++)
seqout_close(&outputs[i], false);
ctx_free(outputs);
// Closes input files
read_thread_args_dealloc(&args);
db_graph_dealloc(&db_graph);
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);
}
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_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_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_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;
}
