void seq_parse_pe(const char *path1, const char *path2, uint8_t ascii_fq_offset,
read_t *r1, read_t *r2,
void (*read_func)(read_t *_r1, read_t *_r2,
uint8_t _qoffset1, uint8_t _qoffset2,
void *_ptr),
void *reader_ptr)
{
seq_file_t *sf1, *sf2;
if((sf1 = seq_open(path1)) == NULL) die("Cannot open: %s", path1);
if((sf2 = seq_open(path2)) == NULL) die("Cannot open: %s", path2);
seq_parse_pe_sf(sf1, sf2, ascii_fq_offset, r1, r2, read_func, reader_ptr);
seq_close(sf1);
seq_close(sf2);
}
int load_seqs(const char *path, char ***seqs_ptr, int *cap_ptr)
{
int cap = 1024;
char **seqs = my_malloc(sizeof(char*) * cap,__FILE__,__LINE__);
read_t read;
seq_read_alloc(&read);
seq_file_t *file = seq_open(path);
if(file == NULL) die("Cannot open file: %s.", path);
int num = 0;
while(seq_read(file, &read))
{
if(num == cap) {
cap *= 2;
seqs = realloc(seqs, sizeof(char*) * cap);
}
seqs[num++] = strdup(read.seq.b);
}
seq_read_dealloc(&read);
seq_close(file);
*seqs_ptr = seqs;
*cap_ptr = cap;
return num;
}
int main (int argc, char** argv) {
int pitch;
float length;
char buf[16];
seq_opened = 0;
if (argc > 1) seq_client = atoi(argv[1]);
seq_open();
while (fgets(buf, 16, stdin) != NULL) {
if (sscanf (buf, "%d %f", &pitch, &length)) {
/* a single short note */
if (length <= 0) {
if ((pitch > 0) && (pitch == (pitch % 128))) {
//seq_open();
play_note (pitch, 0.1);
//seq_close();
}
}
else {
//seq_open();
if ((pitch > 0) && (pitch == (pitch % 128)))
play_note (pitch, length);
else
play_rest (length);
}
}
}
seq_close();
return 0;
}
void filelist_dealloc(FileList *flist)
{
size_t i;
for(i = 0; i < flist->num_files; i++) seq_close(flist->files[i]);
seq_read_dealloc(&flist->read);
free(flist->files);
free(flist->fqoffsets);
free(flist->errors);
}
int main(int argc, char **argv)
{
if(argc != 2) exit(EXIT_FAILURE);
seq_file_t *f = seq_open(argv[1]);
read_t *r = seq_read_alloc();
if(f == NULL) exit(EXIT_FAILURE);
while(seq_read(f,r) > 0)
printf("%s\t[%lu,%lu,%lu]\n", r->name.b, r->name.end, r->seq.end, r->qual.end);
seq_close(f);
seq_read_destroy(r);
return EXIT_SUCCESS;
}
void seq_parse_se(const char *path, uint8_t ascii_fq_offset,
read_t *r1,
void (*read_func)(read_t *_r1, read_t *_r2,
uint8_t _qoffset1, uint8_t _qoffset2,
void *_ptr),
void *reader_ptr)
{
seq_file_t *sf;
if((sf = seq_open(path)) == NULL) die("Cannot open: %s", path);
seq_parse_se_sf(sf, ascii_fq_offset, r1, read_func, reader_ptr);
seq_close(sf);
}
/**
* Performs simple tests for abstract types implementations
*
* @return void
*/
static void test(void)
{
char a = 'b';
stack_ptr stack = NULL;
seq_ptr seq = NULL;
seq_prepare(&seq, "sequence.test");
seq_write(&seq, 'o');
seq_init(&seq);
log_info("main", "Character written in sequence: %c", a = seq_read_first(&seq));
seq_close(&seq);
stack_create(&stack);
log_info("main", "Stack is: %s", stack_empty(&stack) ? "Empty" : "Not empty");
stack_push(&stack, a);
log_info("main", "Stack is: %s", stack_empty(&stack) ? "Empty" : "Not empty");
log_info("main", "First character in stack: %c", stack_pop(&stack));
log_info("main", "Stack is: %s", stack_empty(&stack) ? "Empty" : "Not empty");
}
read_t* filelist_read(FileList *flist)
{
read_t *r = &flist->read;
size_t i; // i is number of file changes
for(i = 0; seq_read(flist->files[flist->curr], r) <= 0 && i <= flist->num_files; i++)
{
flist->curr++;
if(flist->curr == flist->num_files) { flist->curr = flist->filesready = 0; }
if(!flist->filesready) {
char path[PATH_MAX+1];
assert(strlen(flist->files[flist->curr]->path) <= PATH_MAX);
strcpy(path, flist->files[flist->curr]->path);
seq_close(flist->files[flist->curr]);
flist->files[flist->curr] = seq_open(path);
}
}
if(i > flist->num_files) die("All seq files empty");
return r;
}
/**
* Solves the exrecise
*
* Exercise 10 from the 4th workbook
*
* @param seq Sequence pointer
* @param stack Stack pointer
* @return void
*/
static void solve_exercise(seq_ptr *seq, stack_ptr *stack)
{
char c; int aux = 0;
if( ! seq_end(seq)) c = seq_read_first(seq);
while( ! seq_end(seq) && ! stack_full(stack)) {
if( ! isdigit(c)) {
stack_push(stack, c);
} else {
aux = atoi(&c);
while(aux > 0 && ! stack_empty(stack)) {
stack_pop(stack);
aux--;
}
}
c = seq_read_next(seq);
}
seq_close(seq);
}
// Load all reads from files into a read buffer and close the seq_files
// Returns the number of reads loaded
size_t seq_load_all_reads(seq_file_t **seq_files, size_t num_files,
ReadBuffer *rbuf)
{
status("Loading sequences...");
size_t i, nreads = rbuf->len;
read_t r;
seq_read_alloc(&r);
for(i = 0; i < num_files; i++) {
status(" file: %s", seq_files[i]->path);
while(seq_read_primary(seq_files[i], &r) > 0) {
read_buf_push(rbuf, &r, 1); // copy read
seq_read_alloc(&r); // allocate new read
}
seq_close(seq_files[i]);
}
seq_read_dealloc(&r);
return rbuf->len - nreads;
}
// If seq2 is NULL, read pair of entries from first file
// Otherwise read an entry from each
void align_from_file(const char *path1, const char *path2,
void (align)(read_t *r1, read_t *r2),
bool use_zlib)
{
seq_file_t *sf1, *sf2;
if((sf1 = open_seq_file(path1, use_zlib)) == NULL)
{
fprintf(stderr, "Alignment Error: couldn't open file %s\n", path1);
fflush(stderr);
return;
}
if(path2 == NULL)
{
sf2 = sf1;
}
else if((sf2 = open_seq_file(path2, use_zlib)) == NULL)
{
fprintf(stderr, "Alignment Error: couldn't open file %s\n", path1);
fflush(stderr);
return;
}
// fprintf(stderr, "File buffer %zu zlib: %i\n", sf1->in.size, seq_use_gzip(sf1));
read_t read1, read2;
seq_read_alloc(&read1);
seq_read_alloc(&read2);
// Loop while we can read a sequence from the first file
unsigned long alignments;
for(alignments = 0; seq_read(sf1, &read1) > 0; alignments++)
{
if(seq_read(sf2, &read2) <= 0)
{
fprintf(stderr, "Alignment Error: Odd number of sequences - "
"I read in pairs!\n");
fflush(stderr);
break;
}
(align)(&read1, &read2);
}
// warn if no bases read
if(alignments == 0)
{
fprintf(stderr, "Alignment Warning: empty input\n");
fflush(stderr);
}
// Close files
seq_close(sf1);
if(path2 != NULL)
seq_close(sf2);
// Free memory
seq_read_dealloc(&read1);
seq_read_dealloc(&read2);
}
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 main(int argc, char **argv) {
SEQ *sf;
uchar *s;
FILE *f;
char chr_name[100], info[1000], dir;
int i = 0, j = 0, k = 0, B = 0, E = 0;
int max_len = 0;
char *cur_seq;
int seq_len = 0;
bool is_correct_splicing = false;
int num_genes = 0;
int num_exons = 0;
int num = 0;
struct g_list *genes;
struct exons_list *exons;
bool no_branchpoint = false;
if( argc == 5 ) {
}
else if( argc == 4 ) {
if( strcmp( argv[3], "NO_BRANCHPOINT") == 0 ) {
no_branchpoint = true;
}
else {
fatalf("args: fasta gff (NO_BRANCHPOINT)");
}
}
else if (argc != 3)
fatalf("args: fasta gff (NO_BRANCHPOINT)");
if((f = ckopen(argv[2], "r")) == NULL )
{
fatalf("Cannot open file %s\n", argv[1]);
}
else {
num_genes = count_genes_in_gff(f, &num_exons);
if( num_genes > 0 ) {
genes = (struct g_list *) ckalloc(num_genes * sizeof(struct g_list));
if( num_exons < num_genes ) num_exons = num_genes;
exons = (struct exons_list *) ckalloc(num_exons * sizeof(struct exons_list));
initialize_genes(genes, num_genes);
initialize_exons(exons, num_exons);
}
}
fseek(f, 0, SEEK_SET);
branchpoints = (char **) ckalloc(sizeof(char *) * NUM_BP_SEQ);
for( i = 0; i < NUM_BP_SEQ; i++ ) {
branchpoints[i] = (char *) ckalloc(sizeof(char) * 8);
}
strcpy(branchpoints[0], "AACTAAC");
strcpy(branchpoints[1], "AATTAAC");
strcpy(branchpoints[2], "CACTAAC");
strcpy(branchpoints[3], "GACTAAC");
strcpy(branchpoints[4], "TACTAAC");
strcpy(branchpoints[5], "TACTAAT");
strcpy(branchpoints[6], "TATTAAC");
strcpy(branchpoints[7], "TGCTAAC");
strcpy(branchpoints[8], "GATTAAC");
num = input_genes_in_gff(f, genes, exons);
if( num != num_genes ) {
fatalf("gene counter error in %s\n", argv[1]);
}
if( num_genes > 0 ) {
quick_sort_inc_genes(genes, 0, num_genes-1, POS_BASE);
}
i = 0;
while( i < num_genes ) {
j = 0;
while( ((i+j) < num_genes) && (genes[i].txStart == genes[i+j].txStart )) j++;
quick_sort_dec_genes(genes, i, i+j-1, LEN_BASE);
i = i+j;
}
fclose(f);
compl['a'] = compl['A'] = 'T';
compl['c'] = compl['C'] = 'G';
compl['g'] = compl['G'] = 'C';
compl['t'] = compl['T'] = 'A';
sf = seq_get(argv[1]);
s = SEQ_CHARS(sf) - 1;
seq_len = SEQ_LEN(sf);
for( i = 0; i < num_genes; i++ ) {
B = genes[i].txStart;
E = genes[i].txEnd;
if( E > seq_len ) {
fatalf("gene boundary [%d,%d] over the sequence length %d\n", B, E, seq_len);
}
if( (E - B + 1) > max_len ) {
max_len = E - B + 1;
}
}
cur_seq = (char *) ckalloc(sizeof(char) * (max_len+1));
for( i = 0; i < num_genes; i++ ) {
if( genes[i].exonCount >= 2 ) {
strcpy(chr_name, genes[i].sname);
B = genes[i].txStart;
E = genes[i].txEnd;
dir = genes[i].strand;
strcpy(info, genes[i].gname);
k = 0;
if( dir == '+' ) {
for (j = B; j <= E; j++) {
cur_seq[k] = s[j];
k++;
}
cur_seq[k] = '\0';
}
else {
k = 0;
for (j = E; j >= B; j--) {
cur_seq[k] = compl[s[j]];
k++;
}
cur_seq[k] = '\0';
}
is_correct_splicing = true;
is_correct_splicing = check_introns(genes, i, exons, cur_seq, k);
if( is_correct_splicing == false ) {
if( no_branchpoint == false ) {
genes[i].type = REDUN;
}
}
else {
if( no_branchpoint == true ) {
genes[i].type = REDUN;
}
}
}
}
num_genes = rm_redun_genes(genes, 0, num_genes-1);
write_in_gff(genes, num_genes, exons, num_exons);
free(cur_seq);
for( i = 0; i < NUM_BP_SEQ; i++ ) free(branchpoints[i]);
free(branchpoints);
seq_close(sf);
return EXIT_SUCCESS;
}
int main(int argc, char **argv)
{
if(argc < 3) print_usage(usage, NULL);
// Sample reads from ref
char *refpath = NULL;
// int optt = 0, tlen = 800; double tlen_stddev = 0.1;
int insert = 250, rlen = 250, single_ended = 0;
double depth = 1.0, insert_stddev_prop = 0.2; // stddev as proportion of insert
int optr = 0, opti = 0, optv = 0, optl = 0, optd = 0; // keeps track of values
uint64_t seed = generate_seed(); // default RNG seed
char *in0path = NULL, *in1path = NULL;
char *profile_paths[argc];
size_t num_profile_paths = 0, i, total_seq = 0;
float err_rate = -1;
int c;
while((c = getopt(argc, argv, "p:r:i:v:l:d:s1:2:e:g:")) >= 0) {
switch (c) {
case 'p': profile_paths[num_profile_paths++] = optarg; break;
case 'r': refpath = optarg; optr++; break;
// case 't': tlen = atoi(optarg); optt++; break;
// case 'v': tlen_stddev = atof(optarg); optv++; break;
case 'i': insert = atoi(optarg); opti++; break;
case 'v': insert_stddev_prop = atof(optarg); optv++; break;
case 'l': rlen = atoi(optarg); optl++; break;
case 'd': depth = atof(optarg); optd++; break;
case 's': single_ended = 1; break;
case '1': in0path = optarg; break;
case '2': in1path = optarg; break;
case 'e': err_rate = atof(optarg); break;
case 'g': seed = atoi(optarg); break;
default: die("Unknown option: %c", c);
}
}
// Set up
seed_random(seed);
init_qual_prob();
char *outbase = NULL;
if(optind == argc) {}//print_usage(usage, "Missing <out_base>");
else if(optind + 1 == argc) outbase = argv[optind];
else if(optind + 1 < argc) print_usage(usage, "Too many args after %s", outbase);
if(depth <= 0) print_usage(usage, "Depth [-d] cannot be <= 0");
if(insert_stddev_prop < 0)
print_usage(usage, "Insert length standard deviation [-v] cannot be < 0");
if((opti > 0 || optv > 0 || optl > 0 || optd > 0) && refpath == NULL)
print_usage(usage, "Missing -r <in.fa>");
if(optr > 1 || opti > 1 || optv > 1 || optl > 1 || optd > 1)
print_usage(usage, "Duplicate args");
if(in0path == NULL && in1path != NULL)
print_usage(usage, "-2 <in> requires -1 <in>");
if(in0path != NULL && in1path == NULL) {
if(refpath == NULL) single_ended = 1;
else if(!single_ended) print_usage(usage, "Missing -2 for paired-end output");
}
if(in0path != NULL && num_profile_paths == 0)
print_usage(usage, "Need at least one -p <profile.fq.gz> to use -1 .. -2 ..");
if(num_profile_paths == 0 && refpath == NULL)
print_usage(usage, "Need one of -p or -r");
if(num_profile_paths == 0 && outbase == NULL)
print_usage(usage, "More options required");
if(num_profile_paths > 0 && err_rate >= 0)
print_usage(usage, "Cannot use both -p and -E");
// Profile reads
FileList fliststore, *flist = NULL;
if(num_profile_paths > 0) {
flist = &fliststore;
filelist_alloc(flist, profile_paths, num_profile_paths);
}
if(outbase == NULL)
{
// Summarise error profile in input
filelist_mean_err(flist);
}
else
{
size_t outlen = strlen(outbase), extlen = strlen(".1.fa.gz");
char out0path[outlen+extlen+1], out1path[outlen+extlen+1];
memcpy(out0path, outbase, outlen);
memcpy(out1path, outbase, outlen);
if(single_ended) strcpy(out0path+outlen, ".fa.gz");
else {
strcpy(out0path+outlen, ".1.fa.gz");
strcpy(out1path+outlen, ".2.fa.gz");
}
gzFile gzout0 = NULL, gzout1 = NULL;
seq_file_t *sf0 = NULL, *sf1 = NULL, *reffile = NULL;
if(in0path != NULL && (sf0 = seq_open(in0path)) == NULL) die("Cannot read: %s", in0path);
if(in1path != NULL && (sf1 = seq_open(in1path)) == NULL) die("Cannot read: %s", in1path);
if(refpath != NULL)
{
if((reffile = seq_open(refpath)) == NULL) die("Cannot read: %s", refpath);
if((gzout0 = gzopen(out0path, "w")) == NULL) die("Cannot open: %s", out0path);
if(!single_ended && (gzout1 = gzopen(out1path, "w")) == NULL)
die("Cannot open: %s", out1path);
}
if(sf0 != NULL) {
printf("Adding error to input reads...\n");
total_seq += mutate_reads(sf0, gzout0, flist, err_rate);
seq_close(sf0);
}
if(sf1 != NULL) {
total_seq += mutate_reads(sf1, single_ended ? gzout0 : gzout1, flist, err_rate);
seq_close(sf1);
}
if(refpath != NULL)
{
printf("Sampling from %s\n", refpath);
printf(" sequencing depth: %.2f\n", depth);
printf(" read length: %i\n", rlen);
printf(" read pairs: %s\n", single_ended ? "no" : "yes");
if(!single_ended) {
printf(" insert length: %i\n", insert);
printf(" insert stddev: %.2f * insert = %.2f\n",
insert_stddev_prop, insert_stddev_prop*insert);
}
if(num_profile_paths > 0) {
printf(" seq error files: %s", flist->files[0]->path);
for(i = 1; i < num_profile_paths; i++)
printf(",%s", flist->files[i]->path);
printf("\n");
} else if(err_rate >= 0) {
printf(" seq error rate: %.2f%%\n", err_rate * 100.0);
} else {
printf(" sequencing errors: no\n");
}
total_seq += sim_reads(reffile, gzout0, gzout1, flist, err_rate,
insert, insert_stddev_prop*insert, rlen, depth);
seq_close(reffile);
}
if(gzout0 != NULL && gzout1 != NULL)
printf("Wrote %zu bases to: %s and %s\n", total_seq, out0path, out1path);
else if(gzout0 != NULL)
printf("Wrote %zu bases to: %s\n", total_seq, out0path);
if(gzout0 != NULL) gzclose(gzout0);
if(gzout1 != NULL) gzclose(gzout1);
}
if(flist != NULL)
{
// Print error distribution
size_t err_total = 0;
for(i = 0; i < flist->errors_len; i++) err_total += flist->errors[i];
printf("Errors: %zu / %zu (%.2f%%)\n", err_total, total_seq,
(100.0*err_total) / total_seq);
for(i = 0; i < flist->errors_len; i++) printf(" %zu", flist->errors[i]);
printf("\n");
filelist_dealloc(flist);
}
return EXIT_SUCCESS;
}