static Fastq* fastq_processNextSequence (int freeMemory, int truncateName)
{
char *line;
static Fastq* currFQ = NULL;
int count;
Seq* currSeq = NULL;
if (ls_isEof (lsFastq)) {
if (freeMemory) {
fastq_freeFastq (currFQ);
}
return NULL;
}
count = 0;
while ( (line=ls_nextLine (lsFastq)) && (count<4) ) {
if (line[0] == '\0') {
continue;
}
if (line[0] == '@') {
if (freeMemory) {
fastq_freeFastq (currFQ);
}
count++;
AllocVar (currFQ);
AllocVar (currFQ->seq);
currSeq = currFQ->seq;
currSeq->name = hlr_strdup (line + 1);
if (truncateName) {
currSeq->name = firstWordInLine (skipLeadingSpaces (currSeq->name));
}
line = ls_nextLine (lsFastq); // reading sequence
currSeq->sequence = hlr_strdup ( line );
currSeq->size = strlen (currSeq->sequence);
count++;
line = ls_nextLine (lsFastq); // reading quality ID
if( line[0] != '+' )
die("Expected quality ID: '+' or '+%s'", currSeq->name );
count++;
line = ls_nextLine (lsFastq); // reading quality
currFQ->quality = hlr_strdup( line );
count++;
}
}
ls_back (lsFastq,1);
return currFQ;
}
/**
* Get the next BlastQuery.
* @pre The module has been initialized using blastParser_init().
*/
BlastQuery* blastParser_nextQuery (void)
{
char *line,*pos;
static char *queryName = NULL;
static char *prevBlastQueryName = NULL;
static BlastQuery *currBlastQuery = NULL;
int first;
if (!ls_isEof (ls)) {
blastParser_freeQuery (currBlastQuery);
currBlastQuery = NULL;
AllocVar (currBlastQuery);
currBlastQuery->entries = arrayCreate (5,BlastEntry);
first = 1;
while (line = ls_nextLine (ls)) {
if (line[0] == '\0') {
continue;
}
pos = strchr (line,'\t');
*pos = '\0';
strReplace (&queryName,line);
if (first == 1 || strEqual (prevBlastQueryName,queryName)) {
blastParser_processLine (pos + 1,currBlastQuery);
}
else {
ls_back (ls,1);
return currBlastQuery;
}
if (first == 1) {
currBlastQuery->qName = hlr_strdup (queryName);
first = 0;
}
strReplace(&prevBlastQueryName,queryName);
}
if (first == 1) {
return NULL;
}
else {
return currBlastQuery;
}
}
blastParser_freeQuery (currBlastQuery);
currBlastQuery = NULL;
return NULL;
}
ls_node_t* ls_pushback(ls_node_t* list, Ptr data) {
ls_node_t* result = 0;
ls_node_t* tmp = 0;
assert(list);
result = ls_create_node(data);
tmp = ls_back(list);
if(!tmp) {
tmp = list;
}
tmp->next = result;
result->prev = tmp;
list->prev = result;
return result;
}
Ptr ls_popback(ls_node_t* list) {
Ptr result = 0;
ls_node_t* tmp = 0;
assert(list);
tmp = ls_back(list);
if(tmp) {
result = tmp->data;
if(list != tmp->prev) {
list->prev = tmp->prev;
} else {
list->prev = 0;
}
tmp->prev->next = 0;
safe_free(tmp);
}
return result;
}
