TEST_F(RegionUtilTestFixture, GetHighQulitySubreadsIntervals) {
vector<ReadInterval> intervals;
intervals.push_back(ReadInterval(0, 712));
intervals.push_back(ReadInterval(760, 2040));
intervals.push_back(ReadInterval(2098, 3452));
vector<int> directions;
directions.push_back(0);
directions.push_back(1);
directions.push_back(0);
int indx = GetHighQualitySubreadsIntervals(intervals, directions, hqStart, hqEnd);
EXPECT_EQ(intervals.size(), 3);
EXPECT_EQ(indx, 2);
int starts [3] = {0, 760, 2098};
int ends [3] = {712, 2040, 3424};
int ds [3] = {0, 1, 0};
for(int i=0; i < 3; i++) {
EXPECT_EQ(intervals[i].start, starts[i]);
EXPECT_EQ(intervals[i].end , ends[i] );
EXPECT_EQ(directions[i] , ds[i] );
}
indx = GetHighQualitySubreadsIntervals(intervals, directions, hqStart, hqEnd, 800);
EXPECT_EQ(intervals.size(), 2);
// The first interval and its direction has been removed as the length is less
// than 800.
for(int i=0; i < 2; i++) {
EXPECT_EQ(intervals[i].start, starts[i+1]);
EXPECT_EQ(intervals[i].end , ends[i+1] );
}
}
void handleVector(std::vector < libmaus2::dazzler::align::Overlap > & VOVL, libmaus2::dazzler::align::AlignmentWriter & AW)
{
uint64_t maxaepos = 0;
for ( uint64_t i = 0; i < VOVL.size(); ++i )
maxaepos = std::max(maxaepos,static_cast<uint64_t>(VOVL[i].path.aepos));
libmaus2::util::SimpleQueue< libmaus2::geometry::RangeSet<ReadInterval>::search_q_element > SQ;
libmaus2::geometry::RangeSet<ReadInterval> RS(maxaepos);
for ( uint64_t i = 0; i < VOVL.size(); ++i )
{
uint64_t const abpos = VOVL[i].path.abpos;
uint64_t const aepos = VOVL[i].path.aepos;
uint64_t const nf = RS.search(ReadInterval(abpos,aepos,i),SQ);
bool const primary = (! nf);
if ( primary )
{
VOVL[i].setPrimary();
//std::cerr << "primary " << VOVL[i] << std::endl;
RS.insert(ReadInterval(abpos,aepos,i));
}
else
{
//std::cerr << "secondary " << VOVL[i] << std::endl;
}
}
for ( uint64_t i = 0; i < VOVL.size(); ++i )
AW.put(VOVL[i]);
VOVL.resize(0);
}
std::vector<ReadInterval>
RegionAnnotations::SubreadIntervals(const DNALength wholeLength,
const bool byAdapter,
const bool byHQRegion) const {
std::vector<RegionAnnotation> inserts;
if (not byAdapter) {
inserts = Inserts();
} else {
if (Adapters().size() != 0) {
// Must have at least one adapter in order find inserts by adapter.
std::vector<DNALength> starts, ends;
starts.push_back(0);
for(auto adapter: Adapters()) {
assert(wholeLength >= static_cast<DNALength>(adapter.GetStart()) and
wholeLength >= static_cast<DNALength>(adapter.GetEnd())); // bug if fail assert
starts.push_back(adapter.GetEnd());
ends.push_back(adapter.GetStart());
}
ends.push_back(wholeLength);
for (size_t i = 0; i < starts.size(); i++) {
// Use adapter to infer subreads, read score considered unknown.
if (ends[i] > starts[i]) {
inserts.push_back(RegionAnnotation(holeNumber_, Insert, starts[i], ends[i], 0));
}
}
} // else no inserts can be found
}
std::vector<ReadInterval> ret;
for (auto insert: inserts) {
if (byHQRegion) {
if (HasHQRegion()) {
DNALength s = std::max(static_cast<UInt>(insert.GetStart()), HQStart());
DNALength e = std::min(static_cast<UInt>(insert.GetEnd()), HQEnd());
if (s < e) {
// subreads' read score = HQRegion score.
ret.push_back(ReadInterval(s, e, HQScore()));
}
} // else ret = {}
} else {
ret.push_back(ReadInterval(insert));
}
}
return ret;
}
std::vector<ReadInterval>
RegionAnnotations::AdapterIntervals() const {
std::vector<ReadInterval> ret;
for (auto adapter: Adapters()) {
ret.push_back(ReadInterval(adapter));
}
return ret;
}
void MakeSubreadIntervals(vector<SMRTSequence> & subreads,
vector<ReadInterval> & subreadIntervals)
{
subreadIntervals.clear();
for (auto subread: subreads) {
subreadIntervals.push_back(ReadInterval(subread.SubreadStart(),
subread.SubreadEnd(), subread.highQualityRegionScore));
}
}
void CSoundParametersInternal::SoundLevelFromString( const char *sz )
{
if ( !Q_strncasecmp( sz, "SNDLVL_", strlen( "SNDLVL_" ) ) )
{
soundlevel.start = TextToSoundLevel( sz );
soundlevel.range = 0;
}
else
{
soundlevel.FromInterval( ReadInterval( sz ) );
}
}
void CSoundParametersInternal::VolumeFromString( const char *sz )
{
if ( !Q_strcasecmp( sz, "VOL_NORM" ) )
{
volume.start = VOL_NORM;
volume.range = 0.0f;
}
else
{
volume.FromInterval( ReadInterval( sz ) );
}
}
void CSoundEmitterSystemBase::CSoundParametersInternal::SoundLevelFromString( const char *sz )
{
if ( !Q_strncasecmp( sz, "SNDLVL_", strlen( "SNDLVL_" ) ) )
{
soundlevel.start = TextToSoundLevel( sz );
soundlevel.range = 0.0f;
}
else
{
soundlevel = ReadInterval( sz );
}
Q_strncpy( m_szSoundLevel, sz, sizeof( m_szSoundLevel ) );
}
void CSoundEmitterSystemBase::CSoundParametersInternal::VolumeFromString( const char *sz )
{
if ( !Q_strcasecmp( sz, "VOL_NORM" ) )
{
volume.start = VOL_NORM;
volume.range = 0.0f;
}
else
{
volume = ReadInterval( sz );
}
Q_strncpy( m_szVolume, sz, sizeof( m_szVolume ) );
}
void CSoundParametersInternal::PitchFromString( const char *sz )
{
if ( !Q_strcasecmp( sz, "PITCH_NORM" ) )
{
pitch.start = PITCH_NORM;
pitch.range = 0;
}
else if ( !Q_strcasecmp( sz, "PITCH_LOW" ) )
{
pitch.start = PITCH_LOW;
pitch.range = 0;
}
else if ( !Q_strcasecmp( sz, "PITCH_HIGH" ) )
{
pitch.start = PITCH_HIGH;
pitch.range = 0;
}
else
{
pitch.FromInterval( ReadInterval( sz ) );
}
}
void CSoundEmitterSystemBase::CSoundParametersInternal::PitchFromString( const char *sz )
{
if ( !Q_strcasecmp( sz, "PITCH_NORM" ) )
{
pitch.start = PITCH_NORM;
pitch.range = 0.0f;
}
else if ( !Q_strcasecmp( sz, "PITCH_LOW" ) )
{
pitch.start = PITCH_LOW;
pitch.range = 0.0f;
}
else if ( !Q_strcasecmp( sz, "PITCH_HIGH" ) )
{
pitch.start = PITCH_HIGH;
pitch.range = 0.0f;
}
else
{
pitch= ReadInterval( sz ) ;
}
Q_strncpy( m_szPitch, sz, sizeof( m_szPitch ) );
}
void SetUp() {
/* The region table for hole number 14798 is as follows.
* type start end score
* 1 0 712 -1
* 1 760 2040 -1
* 1 2098 3452 -1
* 0 712 760 937
* 0 2040 2098 741
* 2 0 3424 819
* where type 1 = insertion, 0 = adapter, 2 = HQRegion
* */
hqStart = 0;
hqEnd = 3424;
hqScore = 819;
holeNumber = 14798;
int srs[29][2] = {{95, 353},
{404, 955},
{998, 1243},
{1289, 1529},
{1576, 1824},
{1869, 2132},
{2178, 2444},
{2486, 2727},
{2767, 3004},
{3047, 3286},
{3329, 3537},
{3583, 3818},
{3862, 4096},
{4139, 4404},
{4447, 4673},
{4717, 4956},
{5004, 5228},
{5275, 5508},
{5552, 5790},
{5835, 6072},
{6113, 6338},
{6389, 6604},
{6647, 7145},
{7189, 7421},
{7468, 7693},
{7733, 7951},
{7989, 8197},
{8243, 8482},
{8522, 9244}
};
int rgn[59][5] = {{9, 1, 95, 353, -1},
{9, 1, 404, 955, -1},
{9, 1, 998, 1243, -1},
{9, 1, 1289, 1529, -1},
{9, 1, 1576, 1824, -1},
{9, 1, 1869, 2132, -1},
{9, 1, 2178, 2444, -1},
{9, 1, 2486, 2727, -1},
{9, 1, 2767, 3004, -1},
{9, 1, 3047, 3286, -1},
{9, 1, 3329, 3537, -1},
{9, 1, 3583, 3818, -1},
{9, 1, 3862, 4096, -1},
{9, 1, 4139, 4404, -1},
{9, 1, 4447, 4673, -1},
{9, 1, 4717, 4956, -1},
{9, 1, 5004, 5228, -1},
{9, 1, 5275, 5508, -1},
{9, 1, 5552, 5790, -1},
{9, 1, 5835, 6072, -1},
{9, 1, 6113, 6338, -1},
{9, 1, 6389, 6604, -1},
{9, 1, 6647, 7145, -1},
{9, 1, 7189, 7421, -1},
{9, 1, 7468, 7693, -1},
{9, 1, 7733, 7951, -1},
{9, 1, 7989, 8197, -1},
{9, 1, 8243, 8482, -1},
{9, 1, 8522, 9244, -1},
{9, 0, 41, 95, 722},
{9, 0, 353, 404, 784},
{9, 0, 955, 998, 697},
{9, 0, 1243, 1289, 804},
{9, 0, 1529, 1576, 744},
{9, 0, 1824, 1869, 844},
{9, 0, 2132, 2178, 847},
{9, 0, 2444, 2486, 666},
{9, 0, 2727, 2767, 824},
{9, 0, 3004, 3047, 883},
{9, 0, 3286, 3329, 860},
{9, 0, 3537, 3583, 891},
{9, 0, 3818, 3862, 795},
{9, 0, 4096, 4139, 906},
{9, 0, 4404, 4447, 906},
{9, 0, 4673, 4717, 886},
{9, 0, 4956, 5004, 708},
{9, 0, 5228, 5275, 957},
{9, 0, 5508, 5552, 886},
{9, 0, 5790, 5835, 733},
{9, 0, 6072, 6113, 804},
{9, 0, 6338, 6389, 666},
{9, 0, 6604, 6647, 813},
{9, 0, 7145, 7189, 795},
{9, 0, 7421, 7468, 829},
{9, 0, 7693, 7733, 774},
{9, 0, 7951, 7989, 657},
{9, 0, 8197, 8243, 760},
{9, 0, 8482, 8522, 675},
{9, 2, 0, 9244, 834}
};
for (int i = 0; i < 29; i++) {
subreadIntervals.push_back(ReadInterval(srs[i][0], srs[i][1]));
}
for (int i = 0; i < 59; i++) {
adapterIntervals.push_back(ReadInterval(rgn[i][2], rgn[i][3], rgn[i][4]));
}
}
//-----------------------------------------------------------------------------
// Purpose:
// Input : *soundname -
// params -
// Output : Returns true on success, false on failure.
//-----------------------------------------------------------------------------
bool CSoundEmitterSystemBase::InitSoundInternalParameters( const char *soundname, KeyValues *kv, CSoundParametersInternal& params )
{
KeyValues *pKey = kv->GetFirstSubKey();
while ( pKey )
{
if ( !Q_strcasecmp( pKey->GetName(), "channel" ) )
{
params.ChannelFromString( pKey->GetString() );
}
else if ( !Q_strcasecmp( pKey->GetName(), "volume" ) )
{
params.VolumeFromString( pKey->GetString() );
}
else if ( !Q_strcasecmp( pKey->GetName(), "pitch" ) )
{
params.PitchFromString( pKey->GetString() );
}
else if ( !Q_strcasecmp( pKey->GetName(), "wave" ) )
{
CUtlSymbol sym = m_Waves.AddString( pKey->GetString() );
params.soundnames.AddToTail( sym );
}
else if ( !Q_strcasecmp( pKey->GetName(), "rndwave" ) )
{
KeyValues *pWaves = pKey->GetFirstSubKey();
while ( pWaves )
{
CUtlSymbol sym = m_Waves.AddString( pWaves->GetString() );
params.soundnames.AddToTail( sym );
pWaves = pWaves->GetNextKey();
}
}
else if ( !Q_strcasecmp( pKey->GetName(), "attenuation" ) )
{
if ( !Q_strncasecmp( pKey->GetString(), "SNDLVL_", strlen( "SNDLVL_" ) ) )
{
DevMsg( "CSoundEmitterSystemBase::GetParametersForSound: sound %s has \"attenuation\" with %s value!\n",
soundname, pKey->GetString() );
}
if ( !Q_strncasecmp( pKey->GetString(), "ATTN_", strlen( "ATTN_" ) ) )
{
params.soundlevel.start = ATTN_TO_SNDLVL( TranslateAttenuation( pKey->GetString() ) );
params.soundlevel.range = 0.0f;
}
else
{
interval_t interval;
interval = ReadInterval( pKey->GetString() );
// Translate from attenuation to soundlevel
float start = interval.start;
float end = interval.start + interval.range;
params.soundlevel.start = ATTN_TO_SNDLVL( start );
params.soundlevel.range = ATTN_TO_SNDLVL( end ) - ATTN_TO_SNDLVL( start );
}
}
else if ( !Q_strcasecmp( pKey->GetName(), "soundlevel" ) )
{
if ( !Q_strncasecmp( pKey->GetString(), "ATTN_", strlen( "ATTN_" ) ) )
{
DevMsg( "CSoundEmitterSystemBase::GetParametersForSound: sound %s has \"soundlevel\" with %s value!\n",
soundname, pKey->GetString() );
}
params.SoundLevelFromString( pKey->GetString() );
}
else if ( !Q_strcasecmp( pKey->GetName(), "play_to_owner_only" ) )
{
params.play_to_owner_only = pKey->GetInt() ? true : false;
}
else if ( !Q_strcasecmp( pKey->GetName(), "precache" ) )
{
params.precache = pKey->GetInt() ? true : false;
}
pKey = pKey->GetNextKey();
}
return true;
}
