/**
* Print insertions in BED format.
* Note, as per the BED-standard (http://genome.ucsc.edu/FAQ/FAQformat)
* -The coordinates should be 0-based
* -The chromEnd field should not include the actual feature
* -The name will be the inserted sequence
* -The score will be the number of supporing counts, which is capped at 1,000
* By (my) convention, the chromStart will be the last genome postion
* before hte insertio.
*
* <chrom>\t<left>\t<left>\t<inserted sequence>\t<read count>\n
* @param insertions_out The output file
* @param insertions Maps from insertions to number of supporting reads
* @param ref_sequences The table of reference sequences
*/
void print_insertions(FILE* insertions_out, const InsertionSet& insertions, RefSequenceTable& ref_sequences){
fprintf(insertions_out, "track name=insertions description=\"TopHat insertions\"\n");
for(InsertionSet::const_iterator i = insertions.begin(); i != insertions.end(); ++i){
int counts = i->second;
if(counts > 1000){
counts = 1000;
}
fprintf(insertions_out, "%s\t%d\t%d\t%s\t%d\n",
ref_sequences.get_name(i->first.refid),
i->first.left,
i->first.left,
(i->first.sequence).c_str(),
counts);
}
}
/**
* Add insertions from an alignment to an InsertionSet.
* This will look for insertion in the alignment specified by bh. If the
* insertion is already in insertions, it will updated the count. Otherwise,
* it will add the insertion to the set and initialize the count to 1.
* @param bh The bowtie hit to be used to specify alignment infromation.
* @param insertions The InsertionSet that will be updated with the insertion information from teh alignment.
*/
void insertions_from_alignment(const BowtieHit& bh, InsertionSet& insertions){
vector<Insertion> new_insertions;
insertions_from_spliced_hit(bh, new_insertions);
for(size_t i = 0; i < new_insertions.size(); ++i){
Insertion insertion = new_insertions[i];
InsertionSet::iterator itr = insertions.find(insertion);
if (itr != insertions.end()){
itr->second += 1;
}
else{
assert(insertion.refid != VMAXINT32);
insertions[insertion] = 1;
}
}
return;
}