void
populate_index(uint64_t *table, cmph_t *hash, BGZF *fastq_file)
{
while( 1 )
{
/* Find @ */
char c;
while( ( c = bgzf_getc( fastq_file ) ) != '@' && c >= 0 )
{
}
long pos = bgzf_tell( fastq_file );
if( pos == -1 )
{
break;
}
char *accession = NULL;
cmph_uint32 accession_length;
if( read_one_line( &accession, &accession_length, fastq_file ) != 1 )
{
break;
}
/* Next char is sequence, save pos */
unsigned int id = cmph_search( hash, accession, accession_length );
table[ id ] = (uint64_t) pos;
}
}
char *faidx_fetch_seq(const faidx_t *fai, const char *c_name, int p_beg_i, int p_end_i, int *len)
{
int l;
char c;
khiter_t iter;
faidx1_t val;
char *seq=NULL;
// Adjust position
iter = kh_get(s, fai->hash, c_name);
if(iter == kh_end(fai->hash)) return 0;
val = kh_value(fai->hash, iter);
if(p_end_i < p_beg_i) p_beg_i = p_end_i;
if(p_beg_i < 0) p_beg_i = 0;
else if(val.len <= p_beg_i) p_beg_i = val.len - 1;
if(p_end_i < 0) p_end_i = 0;
else if(val.len <= p_end_i) p_end_i = val.len - 1;
// Now retrieve the sequence
int ret = bgzf_useek(fai->bgzf, val.offset + p_beg_i / val.line_blen * val.line_len + p_beg_i % val.line_blen, SEEK_SET);
if ( ret<0 )
{
*len = -1;
fprintf(stderr, "[fai_fetch_seq] Error: fai_fetch failed. (Seeking in a compressed, .gzi unindexed, file?)\n");
return NULL;
}
l = 0;
seq = (char*)malloc(p_end_i - p_beg_i + 2);
while ( (c=bgzf_getc(fai->bgzf))>=0 && l < p_end_i - p_beg_i + 1)
if (isgraph(c)) seq[l++] = c;
seq[l] = '\0';
*len = l;
return seq;
}
int key_fastq_read(void *data, char **key, cmph_uint32 *keylen)
{
BGZF *fp = (BGZF *) data;
char c;
*keylen = 0;
/* Find header start */
while( ( c = bgzf_getc( fp ) ) != '@' && c >= 0 )
{ }
*key = NULL;
if( read_one_line( key, keylen, fp ) == 1 )
{
return (int) *keylen;
}
else
{
return -1;
}
}
char *
bgzf_fgets(char *buffer, size_t buffer_size, BGZF *fp)
{
char c = 0;
size_t i = 0;
while( i < buffer_size - 1 && ((c = bgzf_getc( fp )) > 0) )
{
buffer[ i++ ] = c;
if( c == '\n' )
{
break;
}
}
buffer[ i ] = '\0';
if( i > 0 && c != -1 )
{
return buffer;
}
else
{
return NULL;
}
}
faidx_t *fai_build_core(BGZF *bgzf)
{
char *name;
int c;
int l_name, m_name;
int line_len, line_blen, state;
int l1, l2;
faidx_t *idx;
uint64_t offset;
int64_t len;
idx = (faidx_t*)calloc(1, sizeof(faidx_t));
name = (char*)calloc(1, sizeof(char)); /* at least 1 byte, for '\0' */
idx->hash = kh_init(s);
l_name = m_name = 0;
len = line_len = line_blen = -1; state = 0; l1 = l2 = -1; offset = 0;
while ( (c=bgzf_getc(bgzf))>=0 ) {
if (c == '\n') { // an empty line
if (state == 1) {
offset = bgzf_utell(bgzf);
continue;
} else if ((state == 0 && len < 0) || state == 2) continue;
}
if (c == '>') { // fasta header
if (len >= 0)
fai_insert_index(idx, name, len, line_len, line_blen, offset);
l_name = 0;
while ( (c=bgzf_getc(bgzf))>=0 && !isspace(c)) {
if (m_name < l_name + 2) {
m_name = l_name + 2;
kroundup32(m_name);
name = (char*)realloc(name, m_name);
}
name[l_name++] = c;
}
name[l_name] = '\0';
if ( c<0 ) {
fprintf(stderr, "[fai_build_core] the last entry has no sequence\n");
free(name); fai_destroy(idx);
return 0;
}
if (c != '\n') while ( (c=bgzf_getc(bgzf))>=0 && c != '\n');
state = 1; len = 0;
offset = bgzf_utell(bgzf);
} else {
if (state == 3) {
fprintf(stderr, "[fai_build_core] inlined empty line is not allowed in sequence '%s'.\n", name);
free(name); fai_destroy(idx);
return 0;
}
if (state == 2) state = 3;
l1 = l2 = 0;
do {
++l1;
if (isgraph(c)) ++l2;
} while ( (c=bgzf_getc(bgzf))>=0 && c != '\n');
if (state == 3 && l2) {
fprintf(stderr, "[fai_build_core] different line length in sequence '%s'.\n", name);
free(name); fai_destroy(idx);
return 0;
}
++l1; len += l2;
if (state == 1) line_len = l1, line_blen = l2, state = 0;
else if (state == 0) {
if (l1 != line_len || l2 != line_blen) state = 2;
}
}
}
if ( name )
fai_insert_index(idx, name, len, line_len, line_blen, offset);
else
{
free(idx);
return NULL;
}
free(name);
return idx;
}
char *fai_fetch(const faidx_t *fai, const char *str, int *len)
{
char *s;
int c, i, l, k, name_end;
khiter_t iter;
faidx1_t val;
khash_t(s) *h;
int beg, end;
beg = end = -1;
h = fai->hash;
name_end = l = strlen(str);
s = (char*)malloc(l+1);
// remove space
for (i = k = 0; i < l; ++i)
if (!isspace(str[i])) s[k++] = str[i];
s[k] = 0; l = k;
// determine the sequence name
for (i = l - 1; i >= 0; --i) if (s[i] == ':') break; // look for colon from the end
if (i >= 0) name_end = i;
if (name_end < l) { // check if this is really the end
int n_hyphen = 0;
for (i = name_end + 1; i < l; ++i) {
if (s[i] == '-') ++n_hyphen;
else if (!isdigit(s[i]) && s[i] != ',') break;
}
if (i < l || n_hyphen > 1) name_end = l; // malformated region string; then take str as the name
s[name_end] = 0;
iter = kh_get(s, h, s);
if (iter == kh_end(h)) { // cannot find the sequence name
iter = kh_get(s, h, str); // try str as the name
if (iter == kh_end(h)) {
*len = 0;
free(s); return 0;
} else s[name_end] = ':', name_end = l;
}
} else iter = kh_get(s, h, str);
if(iter == kh_end(h)) {
fprintf(stderr, "[fai_fetch] Warning - Reference %s not found in FASTA file, returning empty sequence\n", str);
free(s);
*len = -2;
return 0;
};
val = kh_value(h, iter);
// parse the interval
if (name_end < l) {
for (i = k = name_end + 1; i < l; ++i)
if (s[i] != ',') s[k++] = s[i];
s[k] = 0;
beg = atoi(s + name_end + 1);
for (i = name_end + 1; i != k; ++i) if (s[i] == '-') break;
end = i < k? atoi(s + i + 1) : val.len;
if (beg > 0) --beg;
} else beg = 0, end = val.len;
if (beg >= val.len) beg = val.len;
if (end >= val.len) end = val.len;
if (beg > end) beg = end;
free(s);
// now retrieve the sequence
int ret = bgzf_useek(fai->bgzf, val.offset + beg / val.line_blen * val.line_len + beg % val.line_blen, SEEK_SET);
if ( ret<0 )
{
*len = -1;
fprintf(stderr, "[fai_fetch] Error: fai_fetch failed. (Seeking in a compressed, .gzi unindexed, file?)\n");
return NULL;
}
l = 0;
s = (char*)malloc(end - beg + 2);
while ( (c=bgzf_getc(fai->bgzf))>=0 && l < end - beg )
if (isgraph(c)) s[l++] = c;
s[l] = '\0';
*len = l;
return s;
}
value caml_bgzf_getc(value bgzf) {
CAMLparam1(bgzf);
CAMLreturn(Val_int(bgzf_getc(BGZF_val(bgzf))));
}
