void indexJunctionsFromStack(istream& stack_stream, JunctionIndex& index)
{
Feature j;
while (StackReader::getNextFeature(stack_stream, j))
{
index.add(j);
}
}
void indexJunctionsFromGFF(istream& gff_stream, JunctionIndex& index)
{
vector<Feature> all;
vector<Feature> genes;
vector<Feature> transcripts;
getGenesAndTranscriptsFromGFF(gff_stream, all, genes, transcripts);
vector<string> exon_types;
exon_types.push_back("exon");
exon_types.push_back("pseudogenic_exon");
vector<Feature> juncs;
for (vector<Feature>::iterator transcript = transcripts.begin();
transcript != transcripts.end(); ++transcript)
{
transcript->spliceJunctions(juncs, exon_types);
}
// TODO optimize to add directly to index
index.add(juncs.begin(), juncs.end());
}
TEST(JunctionIndexTest, unique)
{
// JunctionIndex::unique() allows getting all unique junctions in this index
Feature f;
JunctionIndex index;
f.seqid = "Chr1";
f.source = "A";
f.start = 10;
f.end = 20;
index.add(f);
// add a duplicate
f.source = "B";
index.add(f);
f.source = "C";
f.start = 15;
index.add(f);
f.source = "D";
f.seqid = "Chr2";
index.add(f);
std::vector<std::string> sources;
std::vector<Feature> ret;
index.unique(ret);
for (std::vector<Feature>::iterator it = ret.begin(); it != ret.end(); ++it)
{
sources.push_back((*it).source);
}
EXPECT_THAT(sources, WhenSorted(ElementsAre("A", "C", "D")));
// test count()
EXPECT_EQ(3, index.uniqueCount());
}
TEST(JunctionIndexTest, overlappingFeature)
{
JunctionIndex index;
// a and b are valid junctions and will be returned from the query
Feature a;
a.seqid = "one";
a.source = "A";
a.start = 20;
a.end = 40;
index.add(a);
Feature b;
b.start = 60;
b.end = 80;
b.seqid = "one";
b.source = "B";
index.add(b);
// The query range will fall in the middle of this junction,
// so it won't be returned.
// i.e. valid junctions must fall entirely within the query range
Feature c;
c.seqid = "one";
c.source = "C";
c.start = 100;
c.end = 150;
index.add(c);
// duplicate of Feature a.
// JunctionIndex only returns unique junctions,
// so this won't be returned as a duplicate
Feature d;
d.seqid = "one";
d.start = 20;
d.end = 40;
index.add(d);
// will fall in a valid range, but has a different seqid than the query
// so won't be returned as overlapping query feature
Feature e;
e.seqid = "two";
e.start = 20;
e.end = 40;
index.add(e);
Feature query;
query.seqid = "one";
query.start = 10;
query.end = 110;
std::vector<Feature> ret;
index.overlappingFeature(query, ret);
std::vector<std::string> sources;
for (std::vector<Feature>::iterator it = ret.begin(); it != ret.end(); ++it)
{
sources.push_back((*it).source);
}
EXPECT_THAT(sources, WhenSorted(ElementsAre("A", "B")));
}
