int main(int argc, char **argv)
{
FILE * in;
FILE * out;
boolean full_entry;
int seq_len = MAX_SEQ_LENGTH ;//To make this parametizable in the future.
//Sequence * sequence_new(int max_read_length, int max_name_length, char offset);
Sequence * seq_in = sequence_new(seq_len, 300, 0); //TODO: make this parametizable.
Sequence * seq_out = sequence_new(seq_len, 300, 0);
struct arguments arg;
arg.input_file = "-";
arg.output_file = "-";
arg.conv = BASE_TO_SOLID;
converter_parse(argc, argv, &arg);
if(strcmp(arg.input_file, "-") == 0){
in = stdin;
}else{
in = fopen(arg.input_file, "r");
if(in == NULL){
fprintf(stderr, "Unable to open file %s to read.", arg.input_file);
}
}
if(strcmp(arg.output_file, "-") == 0){
out = stdout;
}else{
out = fopen(arg.output_file, "w");
if(out == NULL){
if(in != stdin){
fclose(in);
}
fprintf(stderr, "Unable to open file %s for writing", arg.output_file);
}
}
////this routine can read long sequences (eg full chromosomes) , this is implemented by reading the sequence in chunks
//int read_sequence_from_fasta(FILE * fp, Sequence * seq, int max_chunk_length, boolean new_entry, boolean * full_entry, int offset);
while (read_sequence_from_fasta(in, seq_in, seq_len, true,&full_entry ,0) > 0){
if(arg.conv == BASE_TO_SOLID){
base_sequence_to_cs_sequence(seq_in, seq_out);
}else if(arg.conv == SOLID_TO_BASE){
fflush(stdout);
fprintf(stderr, "input seq:\n");
sequence_print_fasta(stderr, seq_in);
fprintf(stderr, "out seq:\n");
fflush(stderr);
fflush(stdout);
cs_sequence_to_base_sequence(seq_in, seq_out);
}
sequence_set_name(seq_in->name, seq_out);//TODO: use accessor
sequence_print_fasta(out, seq_out);
}
return 0;
}
tsequence *readseq_next_line(treadseq *rs){
tsequence *ts;
int pos;
ts = sequence_new();
ts->success = 0;
if (adplib_debug>1) printf("rs: success = 0\n");
if (adplib_debug>1) printf("rs: %d\n", rs->start[rs->current]);
rs->temp[0] = 0; pos = 0;
if (rs->start[rs->current] != 0) {
while ((rs->start[rs->current] != '\n') && (rs->start[rs->current] != 0))
rs->temp[pos++] = rs->start[rs->current++];
if (rs->start[rs->current]=='\n') rs->current++;
rs->temp[pos] = 0;
ts->seq = mkstr(rs->temp);
ts->original_seq = mkstr(rs->temp);
// remove additional #13 for DOS input files:
if ((pos >= 1) && (rs->temp[pos-1] == 13)) rs->temp[pos-1] = 0;
// remove additional #13 for DOS input files:
if ((pos >= 1) && (rs->temp[pos-1] == 13)) rs->temp[pos-1] = 0;
ts->length = ts->original_length = strlen(ts->seq);
ts->success = 1;
if (adplib_debug>1) printf("rs: success = 1\n");
}
return ts;
}
void *permutation_new (const setting_list_t *vars)
{
ramsey_t *rv = sequence_new (vars);
if (rv != NULL)
{
rv->type = TYPE_PERMUTATION;
rv->get_type = _permutation_get_type;
rv->recurse = _permutation_recurse;
rv->add_filter = _permutation_add_filter;
}
return rv;
}
tsequence *readseq_next_fasta(treadseq *rs){
tsequence *ts;
int pos;
char inpc,fil;
ts = sequence_new();
rs->temp[0] = 0; pos = 0;
if ((rs->start[rs->current] == '>') && (rs->start[rs->current] != 0)) {
if (!rs->first_descr_read && rs->first_input_read) {
fprintf(stderr, "error in input file: missing description for first sequence\n");
exit(1);
}
rs->first_descr_read = 1;
rs->current++;
while ((rs->start[rs->current] != '\n') && (rs->start[rs->current] != 0)) rs->temp[pos++] = rs->start[rs->current++];
if (rs->start[rs->current]) rs->current++;
}
rs->temp[pos] = 0;
ts->descr = mkstr(rs->temp);
// remove additional #13 for DOS input files:
if ((pos >= 1) && (rs->temp[pos-1] == 13)) rs->temp[pos-1] = 0;
rs->temp[0] = 0; pos = 0;
fil = 1;
while ((fil || (rs->start[rs->current] != '>')) && (rs->start[rs->current] != 0)) {
while (((inpc = rs->start[rs->current]) != '\n') && (rs->start[rs->current] != 0))
if (((inpc >= 65) && (inpc <= 90)) ||
((inpc >= 97) && (inpc <= 122))) rs->temp[pos++] = rs->start[rs->current++];
else rs->current++;
fil = 0;
if (rs->start[rs->current]) rs->current++;
rs->first_input_read = 1;
}
rs->temp[pos] = 0;
ts->seq = mkstr(rs->temp);
ts->original_seq = mkstr(rs->temp);
ts->length = ts->original_length = strlen(ts->seq);
if (ts->seq[0]) ts->success = 1;
else ts->success = 0;
return ts;
}
int main( int argc, char ** argv){
log_and_screen_printf("Demultiplexer\n\n");
log_and_screen_printf(SVN_VERSION);
log_and_screen_printf(SVN_COMMIT_DATE);
log_and_screen_printf("Compiled on %s at %s \n\n", __DATE__, __TIME__);
if (argc < 2) {
print_help();
}
log_write_timestamp(1);
if (argc == 0) {
print_help();
}
DemultiplexerCmdLine cmd = parse_args(argc, argv);
FILE * in = stdin;
if (cmd.input_reads != NULL) {
in = fopen(cmd.input_reads, "r");
if(in == NULL){
log_and_screen_printf("Unable to open file %s\n", cmd.input_reads);
exit(-1);
}
}
Sequence * seq = sequence_new(cmd.max_read_length, cmd.max_name_length, 33);
seq->header = new_sequence_header(CASAVA_1_8);
header_function * f = (header_function *) seq->header;
char * index = f->get_index(seq);
size_t prefix_length = strlen(cmd.output_folder);
char * output_file = calloc(prefix_length + MAX_FIELD_SIZE + 1, sizeof(char *));
char * index_pointer = output_file + prefix_length;
strcpy(output_file, cmd.output_folder);
printf("prefix: %s\n", output_file);
while (read_sequence_from_fastq(in, seq, cmd.max_read_length)) {
strcpy(index_pointer, index);
// printf("index: %s\n new output: %s\n", index, output_file);
append_sequence(output_file, seq, FASTQ);
}
if (in != stdin) {
fclose(in);
}
return 0;
}
piece_screen *piece_ansi_parser_read(FILE *fd, const char *filename)
{
piece_screen *display = NULL;
sauce *record = NULL;
unsigned int width = 80, height = 25;
long fsize;
piece_ansi_parser_state state = ANSI_STATE_TEXT;
unsigned char ch;
piece_list *sequences = NULL;
piece_list_node *node = NULL;
unsigned char argbuf[256];
int arg_index = 0;
int count = 0;
int x = 0;
int y = 0;
int x_saved = 0;
int y_saved = 0;
int i;
char *feature;
bool ice_colors = false;
char *extension = piece_get_extension(filename);
if (!strcmp(extension, "diz") ||
!strcmp(extension, "ion")) {
width = 45;
}
free(extension);
record = sauce_read(fd);
if (record != NULL) {
if (record->data_type == SAUCE_DATA_TYPE_CHARACTER && (
record->file_type == SAUCE_FILE_TYPE_ASCII ||
record->file_type == SAUCE_FILE_TYPE_ANSI ||
record->file_type == SAUCE_FILE_TYPE_ANSIMATION
)) {
width = (unsigned int) record->tinfo[0];
height = (unsigned int) record->tinfo[1];
}
if (piece_options->target->image->ice_colors < 2) {
piece_options->target->image->ice_colors = record->flags.flag_b;
}
} else {
record = piece_allocate(sizeof(sauce));
}
display = piece_screen_new(width, height, record, NULL);
if (display == NULL) {
fprintf(stderr, "%s: could not piece_allocate %dx%d piece_screen buffer\n",
filename, width, height);
sauce_free(display->record);
return NULL;
}
if (display->palette == NULL) {
if (piece_options->target->image->palette != NULL) {
display->palette = piece_options->target->image->palette;
} else if (piece_options->target->image->palette_name != NULL) {
display->palette = piece_palette_by_name(
piece_options->target->image->palette_name
);
} else {
display->palette = piece_palette_by_name("vga");
}
}
if (piece_options->verbose) {
printf("%s: using %s palette\n", filename, display->palette->name);
}
if (fseek(fd, 0, SEEK_END)) {
fprintf(stderr, "%s: error seeking to end of file\n", filename);
sauce_free(display->record);
return NULL;
}
fsize = ftell(fd);
rewind(fd);
sequences = piece_allocate(sizeof(piece_list));
ice_colors = (piece_options->target->image->ice_colors > 0);
piece_list_new(sequences, sequence_free);
while (state != ANSI_STATE_EXIT &&
(ch = fgetc(fd)) != 0x00 &&
!feof(fd) &&
ftell(fd) <= fsize
) {
switch (state) {
case ANSI_STATE_TEXT:
switch(ch) {
case '\x1a':
state = ANSI_STATE_EXIT;
break;
case '\x1b':
state = ANSI_STATE_CHECK_BRACE;
break;
case '\n':
x = 0;
y++;
case '\r':
break;
case '\t':
count = (x + 1) % ANSI_TABSTOP;
if (count) {
count = ANSI_TABSTOP - count;
for (i = 0; i < count; ++i) {
piece_screen_putchar(display, ' ', &x, &y, true);
}
}
break;
default:
piece_screen_putchar(display, ch, &x, &y, true);
break;
}
break;
case ANSI_STATE_CHECK_BRACE:
if (ch == '[') {
state = ANSI_STATE_WAIT_LITERAL;
} else {
piece_screen_putchar(display, '\x1b', &x, &y, true);
piece_screen_putchar(display, ch, &x, &y, true);
}
break;
case ANSI_STATE_WAIT_LITERAL:
if (isalpha(ch) || ch == ';') {
argbuf[arg_index] = '\x00';
piece_ansi_sequence *sequence = sequence_new();
memcpy(sequence->sequence, argbuf, 256);
piece_list_append(sequences, sequence);
arg_index = 0;
if (ch == ';') {
break;
}
}
if (isalpha(ch)) {
switch (ch) {
case 'm':
if (sequences != NULL) {
i = atoi(ANSI_SEQ_CC(sequences, 0));
if (piece_list_size(sequences) == 3 &&
(i == 38 || i == 48) &&
atoi(ANSI_SEQ_CC(sequences, 1)) == 5) {
piece_ansi_parser_parse_sgr256(
display,
i,
atoi(ANSI_SEQ_CC(sequences, 2))
);
} else {
node = sequences->head;
while (node != NULL) {
piece_ansi_sequence *curr = (piece_ansi_sequence *) node->data;
uint32_t sgr = atoi((const char *) curr->sequence);
piece_ansi_parser_parse_sgr(display, sgr, ice_colors);
node = node->next;
}
}
}
break;
case 'H': // CUP
case 'f':
switch (piece_list_size(sequences)) {
case 2:
y = atoi(ANSI_SEQ_CC(sequences, 0)) - 1;
x = atoi(ANSI_SEQ_CC(sequences, 1)) - 1;
break;
case 1:
y = 0;
x = atoi(ANSI_SEQ_CC(sequences, 0)) - 1;
break;
default:
y = 0;
x = 0;
break;
}
piece_list_free(sequences);
sequences = NULL;
break;
case 'A': // CUU (CUrsor Up)
i = (piece_list_size(sequences) > 0)
? atoi(ANSI_SEQ_CC(sequences, 0))
: 1;
y -= (i == 0 ? 1 : i);
if (y < 0) y = 0;
break;
case 'B': // CUD (CUrsor Down)
i = (piece_list_size(sequences) > 0)
? atoi(ANSI_SEQ_CC(sequences, 0))
: 1;
y += (i == 0 ? 1 : i);
break;
case 'C': // CUF (CUrsor Forward)
i = (piece_list_size(sequences) > 0)
? atoi(ANSI_SEQ_CC(sequences, 0))
: 1;
x += (i == 0 ? 1 : i);
break;
case 'D': // CUB (CUrsor Back)
i = (piece_list_size(sequences) > 0)
? atoi(ANSI_SEQ_CC(sequences, 0))
: 1;
x -= (i == 0 ? 1 : i);
if (x < 0) x = 0;
break;
case 'E': // CNL (Cursor Next Line)
i = (piece_list_size(sequences) > 0)
? atoi(ANSI_SEQ_CC(sequences, 0))
: 1;
x = 0;
y += i;
break;
case 'F': // CPL (Cursor Previous Line)
i = (piece_list_size(sequences) > 0)
? atoi(ANSI_SEQ_CC(sequences, 0))
: 1;
x = 0;
y -= i;
if (y < 0) y = 0;
break;
case 'G': // CHA (Cursor Horizontal Absolute)
i = (piece_list_size(sequences) > 0)
? atoi(ANSI_SEQ_CC(sequences, 0))
: 1;
x = i - 1;
if (x < 0) x = 0;
break;
case 'J': // ED (Erase Display)
i = (piece_list_size(sequences) > 0)
? atoi(ANSI_SEQ_CC(sequences, 0))
: 0;
switch (i) {
case 0: // From cursor to EOF
for (i = (display->size.width * y) + x;
i < display->tiles; ++i) {
piece_screen_tile_reset(display,
&display->tile[i]);
}
break;
case 1: // From cursor to start
for (i = (display->size.width * y) + x;
i >= 0; --i) {
piece_screen_tile_reset(display,
&display->tile[i]);
}
break;
case 2: // Entire piece_screen
default:
piece_screen_reset(display);
piece_screen_reduce(display, width, height);
y = 0;
x = 0;
}
break;
case 'K': // EL (Erase in Line)
i = (piece_list_size(sequences) > 0)
? atoi(ANSI_SEQ_CC(sequences, 0))
: 0;
int64_t start, end;
switch (i) {
case 0: // To EOL
start = (display->size.width * y) + x;
end = (display->size.width * (y + 1)) - 1;
break;
case 1: // To BOL
start = (display->size.width * (y - 1)) + 1;
end = (display->size.width * y) + x;
break;
case 2: // Entire line
default:
start = (display->size.width * (y - 1)) + 1;
end = (display->size.width * (y + 1)) - 1;
break;
}
if (start < 0) {
start = 0;
}
if (end > display->tiles) {
end = display->tiles - 1;
}
for (i = start; i < end; ++i) {
piece_screen_tile_reset(display,
&display->tile[i]);
}
break;
case 'L': // IL (Insert Line)
i = (piece_list_size(sequences) > 0)
? atoi(ANSI_SEQ_CC(sequences, 0))
: 1;
for (; i > 0; i--) {
piece_screen_insert_line(display, y);
}
break;
case 'S': // SU (Scroll Up) FIXME
i = (piece_list_size(sequences) > 0)
? atoi(ANSI_SEQ_CC(sequences, 0))
: 1;
break;
case 'T': // SD (Scroll Down) FIXME
i = (piece_list_size(sequences) > 0)
? atoi(ANSI_SEQ_CC(sequences, 0))
: 1;
break;
case 'h': // Feature on
feature = (piece_list_size(sequences) > 0)
? (char *) ANSI_SEQ_CC(sequences, 0)
: "";
if (!strcmp(feature, "?33")) { // Blink mode
display->record->flags.flag_b = 1;
}
break;
case 'i': // AUX (serial port toggle)
break; // ignored
case 'l': // Feature off
feature = (piece_list_size(sequences) > 0)
? (char *) ANSI_SEQ_CC(sequences, 0)
: "";
if (!strcmp(feature, "?33")) { // Blink mode
display->record->flags.flag_b = 0;
}
break;
case 's': // SCP (Save Cursor Position)
y_saved = y;
x_saved = x;
break;
case 't': // "24 bit ANSI", custom hack by Curtis
// Wensley (eto):
// http://picoe.ca/2014/03/07/24-bit-ansi/
if (piece_list_size(sequences) == 4) {
uint8_t i = atoi(ANSI_SEQ_CC(sequences, 0)),
r = atoi(ANSI_SEQ_CC(sequences, 1)),
g = atoi(ANSI_SEQ_CC(sequences, 2)),
b = atoi(ANSI_SEQ_CC(sequences, 3));
piece_rgba_color rgba = PIECE_RGB(r, g, b);
int c = piece_palette_add_color(
display->palette,
&rgba
);
switch (i) {
case 0:
display->current->fg = c;
break;
case 1:
display->current->bg = c;
break;
}
} else {
fprintf(stderr, "%s: invalid 24 bit color\n",
filename);
}
break;
case 'u': // RCP (Restore Cursor Position)
y = y_saved;
x = x_saved;
break;
default:
fprintf(stderr, "%s: invalid %d item sequence ",
filename, piece_list_size(sequences));
fprintf(stderr, "<ESC>[");
if (sequences != NULL) {
node = sequences->head;
while (node != NULL) {
piece_ansi_sequence *curr = (piece_ansi_sequence *) node->data;
fprintf(stderr, "%s", curr->sequence);
if (node->next != NULL) {
fprintf(stderr, ";");
}
node = node->next;
}
fprintf(stderr, "%c\n", ch);
}
}
if (sequences == NULL) {
sequences = piece_allocate(sizeof(piece_list));
piece_list_new(sequences, sequence_free);
}
else if (piece_list_size(sequences) > 0) {
piece_list_free(sequences);
sequences = piece_allocate(sizeof(piece_list));
piece_list_new(sequences, sequence_free);
}
state = ANSI_STATE_TEXT;
break;
} // if (isalpha(ch))
argbuf[arg_index] = ch;
arg_index++;
break;
case ANSI_STATE_EXIT: // We're done here
default:
break;
}
}
// We're done here
piece_list_free(sequences);
return display;
}