int size_filter(kseq_t *seq, int is_fasta, int min, int max, int length, int convert, int just_count) {
int count=0;
if (min > 0 && max > 0) { /* got a min and max */
if (seq->seq.l >= min && seq->seq.l <= max) {
count++;
if (!just_count) {
if (convert)
is_fasta ? print_fastq_seq(seq) : print_fasta_seq(seq,length);
else
is_fasta ? print_fasta_seq(seq,length) : print_fastq_seq(seq);
}
}
} else if (min > 0 || max > 0) { /* either min or max is 0 */
if (min > 0 && seq->seq.l >= min) {
count++;
if (!just_count) {
if (convert)
is_fasta ? print_fastq_seq(seq) : print_fasta_seq(seq,length);
else
is_fasta ? print_fasta_seq(seq,length) : print_fastq_seq(seq);
}
} else if (max > 0 && seq->seq.l <= max) {
count++;
if (!just_count) {
if (convert)
is_fasta ? print_fastq_seq(seq) : print_fasta_seq(seq,length);
else
is_fasta ? print_fasta_seq(seq,length) : print_fastq_seq(seq);
}
}
} else {
/* neither min nor max was > 0, so we print this sequence */
count++;
if (!just_count) {
if (convert)
is_fasta ? print_fastq_seq(seq) : print_fasta_seq(seq,length);
else
is_fasta ? print_fasta_seq(seq,length) : print_fastq_seq(seq);
}
}
return count;
}
int pull_by_name(char *input_file, FILE *names_fp, int min, int max, int length, int exclude, int convert, int just_count) {
gzFile fp;
int i,l,capacity=80;
int count=0,excluded=0;
int is_fasta = -1;
char *fasta_name;
char *line;
kseq_t *seq;
/* get some space for the line */
line = malloc(sizeof(char) * capacity); /* get memory allocated */
if (!line) {
fprintf(stderr, "%s - line malloc: %s\n",progname, strerror(errno));
exit(EXIT_FAILURE);
}
while((i = getl(&line,names_fp)) != -1) {
fasta_name = parse_name(line);
if (fasta_name) {
add_name(fasta_name); /* add fasta_name to hash */
}
}
free(line); /* free up line */
if (verbose_flag) {
fprintf(stderr,"\n");
fprintf(stderr,"done reading from input (%d entries)\n", hash_key_count());
}
/*print_hash();*/
/* open fasta file */
fp = gzopen(input_file,"r");
if (!fp) {
fprintf(stderr,"%s - Couldn't open fasta file %s\n",progname,input_file);
exit(EXIT_FAILURE);
}
seq = kseq_init(fp); /* initialize kseq */
/* determine file type */
l = kseq_read(seq); /* read the first sequence */
is_fasta = seq->qual.s == NULL ? 1 : 0;
gzrewind(fp); /* rewind to beginning for main loop */
kseq_rewind(seq);
if (verbose_flag) {
if (is_fasta)
fprintf(stderr, "Input is FASTA format\n");
else
fprintf(stderr, "Input is FASTQ format\n");
}
/* search through list and see if this header matches */
while((l = kseq_read(seq)) >= 0) {
if (exclude == 0) { /* INCLUDE names from names file */
if (find_name(seq->name.s)) { /* found name in list */
if (min > 0 && max > 0) { /* got a min and max */
if (seq->seq.l >= min && seq->seq.l <= max) {
count++;
if (!just_count) {
if (convert)
is_fasta ? print_fastq_seq(seq) : print_fasta_seq(seq,length);
else
is_fasta ? print_fasta_seq(seq,length) : print_fastq_seq(seq);
}
}
} else if (min > 0 || max > 0) { /* either min or max is 0 */
if (min > 0 && seq->seq.l >= min) {
count++;
if (!just_count) {
if (convert)
is_fasta ? print_fastq_seq(seq) : print_fasta_seq(seq,length);
else
is_fasta ? print_fasta_seq(seq,length) : print_fastq_seq(seq);
}
} else if (max > 0 && seq->seq.l <= max) {
count++;
if (!just_count) {
if (convert)
is_fasta ? print_fastq_seq(seq) : print_fasta_seq(seq,length);
else
is_fasta ? print_fasta_seq(seq,length) : print_fastq_seq(seq);
}
}
} else {
count++;
if (!just_count) {
if (convert)
is_fasta ? print_fastq_seq(seq) : print_fasta_seq(seq,length);
else
is_fasta ? print_fasta_seq(seq,length) : print_fastq_seq(seq);
}
}
}
} else { /* EXCLUDE names from names file */
if (find_name(seq->name.s)) { /* found name in list */
excluded++;
} else {
if (min > 0 && max > 0) { /* got a min and max */
if (seq->seq.l >= min && seq->seq.l <= max) {
count++;
if (!just_count) {
if (convert)
is_fasta ? print_fastq_seq(seq) : print_fasta_seq(seq,length);
else
is_fasta ? print_fasta_seq(seq,length) : print_fastq_seq(seq);
}
}
} else if (min > 0 || max > 0) { /* either min or max is 0 */
if (min > 0 && seq->seq.l >= min) {
count++;
if (!just_count) {
if (convert)
is_fasta ? print_fastq_seq(seq) : print_fasta_seq(seq,length);
else
is_fasta ? print_fasta_seq(seq,length) : print_fastq_seq(seq);
}
} else if (max > 0 && seq->seq.l <= max) {
count++;
if (!just_count) {
if (convert)
is_fasta ? print_fastq_seq(seq) : print_fasta_seq(seq,length);
else
is_fasta ? print_fasta_seq(seq,length) : print_fastq_seq(seq);
}
}
} else {
count++;
if (!just_count) {
if (convert)
is_fasta ? print_fastq_seq(seq) : print_fasta_seq(seq,length);
else
is_fasta ? print_fasta_seq(seq,length) : print_fastq_seq(seq);
}
}
}
}
}
kseq_destroy(seq);
gzclose(fp); /* done reading file */
delete_hash(); /* free the list nodes */
if (just_count) {
fprintf(stdout, "Total output: %i\n", count);
if (exclude)
fprintf(stdout, "Total excluded: %i\n", excluded);
}
if (verbose_flag) {
fprintf(stderr,"Processed %i entries\n",count);
if (exclude)
fprintf(stderr,"Excluded %i entries\n",excluded);
}
return count;
}
