// reads must ALWAYS be requested in increasing order of their ID
bool ReadStream::getRead(uint64_t r_id,
Read& read,
bool strip_slash,
uint64_t begin_id,
uint64_t end_id,
/*
GBamWriter* um_out, //unmapped reads output
char um_code, //if non-zero, write the found read to um_out with this code
int64_t* unmapped_counter, //update this counter for unmapped/skipped reads *only*
int64_t* multimapped_counter //update this counter for too multi-mapped reads
*/
GetReadProc* rProc,
bool is_unmapped )
{
if (!fstream.file)
err_die("Error: calling ReadStream::getRead() with no file handle!");
if (r_id<last_id)
err_die("Error: ReadStream::getRead() called with out-of-order id#!");
last_id=r_id;
bool found=false;
read.clear();
while (!found) {
QReadData rdata;
if (!next_read(rdata))
break;
/*
if (strip_slash) {
string::size_type slash = rdata.read.name.rfind("/");
if (slash != string::npos)
rdata.read.name.resize(slash);
}
uint64_t id = (uint64_t)atol(read.name.c_str());
*/
if (rdata->id >= end_id)
return false;
if (rdata->id < begin_id)
continue; //silently skip until begin_id found
//does not trigger rProc->process() until begin_id
if (rdata->id == r_id)
{
read=rdata->read; //it will be returned
found=true;
}
else if (rdata->id > r_id)
{ //can't find it, went too far
//only happens when reads [mates] were removed for some reason
//read_pq.push(make_pair(id, read));
read_pq.push(rdata);
break;
}
if (rProc) { //skipped read processing (unmapped reads)
if (!rProc->process(rdata, found)) //, is_unmapped))
// rProc->process() should normally return TRUE
return false; //abort search for r_id, return "not found"
}
} //while target read id not found
return found;
}
void bam2Read(bam1_t *b, Read& rd, bool alt_name=false) {
GBamRecord bamrec(b);
rd.clear();
rd.seq=bamrec.seqData(&rd.qual);
rd.name=bam1_qname(b);
if (alt_name)
rd.alt_name=bamrec.tag_str("ZN");
}
bool next_fastx_read(FLineReader& fr, Read& read, ReadFormat rd_format,
FLineReader* frq) {
/*
if (fr.pushed_read)
{
read = fr.last_read;
fr.pushed_read = false;
return true;
}
*/
read.clear();
char* buf=NULL;
while ((buf=fr.nextLine())!=NULL) {
if (buf[0]==0) continue; //skip empty lines
if ((rd_format == FASTA && buf[0] == '>') ||
(rd_format == FASTQ && (buf[0] == '+' || buf[0] == '@'))) { //next record
if (read.seq.length()>0) { //current record ending
fr.pushBack();
break;
}
read.name=buf+1;
string::size_type space_pos = read.name.find_first_of(" \t");
if (space_pos != string::npos) {
read.name.resize(space_pos);
}
continue;
} //defline
// sequence line
read.seq.append(buf);
} //line reading loop
replace(read.seq.begin(), read.seq.end(), '.', color ? '4' : 'N'); //shouldn't really be needed for FASTA files
if (rd_format != FASTQ && frq==NULL)
return (!read.seq.empty());
if (frq==NULL) frq=&fr; //FASTQ
//FASTQ or quals in a separate file -- now read quality values
buf=frq->nextLine();
if (buf==NULL) return false;
while (buf[0]==0) { //skip empty lines
buf=frq->nextLine();
if (buf==NULL) return false;
}
//must be on '+' line here
if (buf==NULL || (rd_format == FASTQ && buf[0] != '+') ||
(rd_format == FASTA && buf[0] != '>')) {
err_exit("Error: beginning of quality values record not found! (%s)\n",buf);
return false;
}
read.alt_name=buf+1;
string::size_type space_pos = read.alt_name.find_first_of(" \t");
if (space_pos != string::npos) read.alt_name.resize(space_pos);
//read qv line(s) now:
while ((buf=frq->nextLine())!=NULL) {
if (integer_quals)
{
vector<string> integer_qual_values;
tokenize(string(buf), " ", integer_qual_values);
string temp_qual;
for (size_t i = 0; i < integer_qual_values.size(); ++i)
{
int qual_value = atoi(integer_qual_values[i].c_str());
if (qual_value < 0) qual_value = 0;
temp_qual.push_back((char)(qual_value + 33));
}
read.qual.append(temp_qual);
}
else {
read.qual.append(buf);
}
if (read.qual.length()>=read.seq.length()-1)
break;
} //while qv lines
// final check
if (color) {
if (read.seq.length()==read.qual.length()) {
//discard first qv
read.qual=read.qual.substr(1);
}
if (read.seq.length()!=read.qual.length()+1) {
err_exit("Error: length of quality string does not match sequence length (%d) for color read %s!\n",
read.seq.length(), read.alt_name.c_str());
}
}
else {
if (read.seq.length()!=read.qual.length()) {
err_exit("Error: qual length (%d) differs from seq length (%d) for fastq record %s!\n",
read.qual.length(), read.seq.length(), read.alt_name.c_str());
return false;
}
}
//fr.last_read = read;
return !(read.seq.empty());
}
