int main(int argc, char ** argv)
{
FILE * input;
struct seq *s1=0, *s2=0;
char ori;
char c;
int fileindex;
int del_input=0;
while((c = getopt(argc, argv, "a:o:k:m:q:xd:vh")) != (char) -1) {
switch (c) {
case 'a':
align_type = optarg;
break;
case 'o':
output_format = optarg;
break;
case 'm':
min_align = atoi(optarg);
break;
case 'q':
min_qual = atof(optarg);
break;
case 'x':
del_input = 1;
break;
case 'd':
debug_flags_set(optarg);
break;
case 'v':
cctools_version_print(stdout, argv[0]);
exit(0);
break;
default:
case 'h':
show_help(argv[0]);
exit(0);
break;
}
}
cctools_version_debug(D_DEBUG, argv[0]);
fileindex = optind;
if ((argc - optind) == 1) {
input = fopen(argv[fileindex], "r");
if (!input) {
fprintf(stderr, "sand_align_kernel: couldn't open %s: %s\n",argv[fileindex],strerror(errno));
exit(1);
}
} else {
input = stdin;
}
struct cseq *c1, *c2;
if(!strcmp(output_format,"ovl") || !strcmp(output_format, "ovl_new")) {
overlap_write_begin(stdout);
}
// outer loop: read first sequence in comparison list
while((c1=cseq_read(input))) {
s1 = cseq_uncompress(c1);
cseq_free(c1);
// inner loop: read sequences until null (indicating end of list)
// then continue again with outer loop. (two nulls to halt.)
while((c2=cseq_read(input))) {
s2 = cseq_uncompress(c2);
cseq_free(c2);
int dir = 0;
int start1 = 0;
int start2 = 0;
char* tmp = strdup(s2->metadata);
int metadata_valid = 0;
char* token = strtok(tmp, " ");
start2 = atoi(token);
metadata_valid++;
while((token = strtok(NULL, " ")))
{
dir = start1;
start1 = start2;
start2 = atoi(token);
metadata_valid++;
}
if(metadata_valid>=1 && dir==-1) {
seq_reverse_complement(s2);
ori = 'I';
} else {
ori = 'N';
}
struct matrix *m = matrix_create(s1->num_bases,s2->num_bases);
if(!m) {
fprintf(stderr,"sand_align_kernel: out of memory when creating alignment matrix.\n");
exit(1);
}
struct alignment *aln;
if(!strcmp(align_type,"sw")) {
aln = align_smith_waterman(m,s1->data,s2->data);
} else if(!strcmp(align_type,"ps")) {
aln = align_prefix_suffix(m,s1->data,s2->data, min_align);
} else if(!strcmp(align_type,"banded")) {
if(metadata_valid<3) {
fprintf(stderr,"sand_align_kernel: sequence %s did not indicate start positions for the banded alignment.\n",s2->name);
exit(1);
}
/* The width of the band is proportional to the desired quality of the match. */
int k = 2 + min_qual * MIN(s1->num_bases,s2->num_bases) / 2.0;
if(k<5) k = 5;
aln = align_banded(m,s1->data, s2->data, start1, start2, k);
} else {
fprintf(stderr,"unknown alignment type: %s\n",align_type);
exit(1);
}
aln->ori = ori;
if(aln->quality <= min_qual) {
if(!strcmp(output_format,"ovl")) {
overlap_write_v5(stdout, aln, s1->name, s2->name);
} else if(!strcmp(output_format, "ovl_new")) {
overlap_write_v7(stdout, aln, s1->name, s2->name);
} else if(!strcmp(output_format,"matrix")) {
printf("*** %s alignment of sequences %s and %s (quality %lf):\n\n",align_type,s1->name,s2->name,aln->quality);
matrix_print(m,s1->data,s2->data);
} else if(!strcmp(output_format,"align")) {
printf("*** %s alignment of sequences %s and %s (quality %lf):\n\n",align_type,s1->name,s2->name,aln->quality);
alignment_print(stdout,s1->data,s2->data,aln);
} else {
printf("unknown output format '%s'\n",output_format);
exit(1);
}
}
matrix_delete(m);
seq_free(s2);
alignment_delete(aln);
}
seq_free(s1);
}
fclose(input);
if(!strcmp(output_format,"ovl") || !strcmp(output_format, "ovl_new")) {
overlap_write_end(stdout);
}
if ((argc - optind) == 1 && del_input == 1)
{
remove(argv[fileindex]);
}
return 0;
}
void load_sequences(const char *filename)
{
FILE *file;
int i, count, rect_id, rectangle_count;
struct cseq *c;
size_t size;
rectangle_count = 256;
rectangle_sizes = malloc(rectangle_count * sizeof(size_t));
file = fopen(filename, "r");
if(!file)
fatal("couldn't open %s: %s\n", filename, strerror(errno));
debug(D_DEBUG, "rectangle size: %d\n", rectangle_size);
sequences = malloc(rectangle_size * sizeof(struct cseq *));
if(!sequences)
fatal("No enough memory to hold %d sequences. (%s) \n", rectangle_size, strerror(errno));
count = 0;
rect_id = 0;
while(1) {
c = cseq_read(file);
if(!c) {
if(count != rectangle_size && count > 0) { // write the last rectangle to file
size = load_rectangle_to_file(rect_id, sequences, count);
if(!size)
fatal("Failed to write rectangle %d to file. (%s)\n", rect_id, strerror(errno));
rectangle_sizes[rect_id] = size;
rect_id++;
for(i = 0; i < count; i++)
cseq_free(sequences[i]);
debug(D_DEBUG, "Rectangle %d has been created.\n", rect_id - 1);
}
num_rectangles = rect_id;
break;
}
sequences[count] = c;
count++;
num_seqs++;
if(count == rectangle_size) {
size = load_rectangle_to_file(rect_id, sequences, count);
if(!size)
fatal("Failed to write rectangle %d to file. (%s)\n", rect_id, strerror(errno));
rectangle_sizes[rect_id] = size;
rect_id++;
if(rect_id == rectangle_count) {
rectangle_count = rectangle_count * 2;
rectangle_sizes = realloc(rectangle_sizes, rectangle_count * sizeof(size_t));
if(!rectangle_sizes)
fatal("Failed to allocate memory for holding rectangle sizes. Number of rectangles: %d. (%s)\n", rectangle_count, strerror(errno));
}
for(i = 0; i < count; i++)
cseq_free(sequences[i]);
count = 0;
debug(D_DEBUG, "Rectangle %d has been created.\n", rect_id - 1);
}
}
fclose(file);
free(sequences);
}
int main(int argc, char ** argv)
{
const char *progname = "sand_compress_reads";
FILE * infile;
FILE * outfile;
int quiet_mode = 0;
struct seq *s;
struct cseq *c;
signed char d;
int clip = 0;
int internal = 0;
char tmp_id[128];
int count = 0;
while((d=getopt(argc,argv,"cvqhi")) > -1) {
switch(d) {
case 'c':
clip = 1;
break;
case 'i':
internal = 1;
break;
case 'q':
quiet_mode = 1;
break;
case 'v':
cctools_version_print(stdout, progname);
exit(0);
break;
case 'h':
default:
show_help(progname);
exit(0);
break;
}
}
cctools_version_debug(D_DEBUG, argv[0]);
if( optind<argc ) {
infile = fopen(argv[optind], "r");
if(!infile) {
fprintf(stderr,"%s: couldn't open %s: %s\n",progname,argv[optind],strerror(errno));
return 1;
}
optind++;
} else {
infile = stdin;
}
if( optind<argc ) {
outfile = fopen(argv[optind],"w");
if(!outfile) {
fprintf(stderr,"%s: couldn't open %s: %s\n",progname,argv[optind],strerror(errno));
return 1;
}
optind++;
} else {
outfile = stdout;
}
while((s = seq_read(infile))) {
if(clip != 0 || internal != 0){
strcpy(tmp_id, s->name);
strcpy(s->name, strtok(tmp_id,","));
if(internal != 0){
strcpy(s->name, strtok(NULL,","));
}
}
c = seq_compress(s);
cseq_write(outfile,c);
cseq_free(c);
seq_free(s);
count++;
}
if(!quiet_mode) {
fprintf(stderr,"%d sequences compressed.\n",count);
}
fclose(infile);
fclose(outfile);
return 0;
}
