TEST(RangeTest, SetRanges) {
Ranges rs;
rs.setRanges("199");
EXPECT_TRUE(rs.contains(199));
EXPECT_EQ(rs.size(), 1);
}
int
main(int /*argc*/, char** /*argv*/)
{
typedef gnash::geometry::SnappingRanges2d<int> Ranges;
typedef gnash::geometry::Range2d<int> Bounds;
string filename = string(TGTDIR) + string("/") + string(INPUT_FILENAME);
MovieTester tester(filename);
gnash::LogFile& dbglogfile = gnash::LogFile::getDefaultInstance();
dbglogfile.setVerbosity(1);
// Colors we'll use during the test
rgba red(255,0,0,255);
rgba white(255,255,255,255);
rgba black(0,0,0,255);
// Ranges we'll use during the test
Range2d<int> redRange(300,300,360,360);
Range2d<int> blackRange(330,270,450,390);
// Coordinates we'll use during testing
int x_left = 270; // on the left of any DisplayObject
int x_red = 310; // on the red square
int x_int = 340; // on the intersection between the red and black squares
int x_black = 370; // on black square
int x_right = 460; // on the right of any DisplayObject
int y = 330;
Ranges invalidated;
MovieClip* root = tester.getRootMovie();
assert(root);
// FRAME 1 (start)
check_equals(root->get_frame_count(), 4);
check_equals(root->getPlayState(), MovieClip::PLAYSTATE_PLAY);
check_equals(root->get_current_frame(), 0);
check_equals(root->getDisplayList().size(), 1); // dejagnu clip
invalidated = tester.getInvalidatedRanges();
check( invalidated.contains(76, 4) ); // the "-xtrace enabled-" label...
tester.advance(); // FRAME 2, place DisplayObjects (black on top)
invalidated = tester.getInvalidatedRanges();
check_equals(root->getPlayState(), MovieClip::PLAYSTATE_PLAY);
check_equals(root->get_current_frame(), 1);
check_equals(root->getDisplayList().size(), 3); // dejagnu + red square + black square
// check invalidated bounds contain both the red and black square
check( invalidated.contains(redRange) );
check( invalidated.contains(blackRange) );
// Check that the black square is over the red square
check_pixel(x_left, y, 2, white, 2);
check_pixel(x_red, y, 2, red, 2);
check_pixel(x_int, y, 2, black, 2); // black is *over* red square
check_pixel(x_black, y, 2, black, 2);
check_pixel(x_right, y, 2, white, 2);
tester.advance(); // FRAME 3, depth-swap the two DisplayObjects
invalidated = tester.getInvalidatedRanges();
check_equals(root->getPlayState(), MovieClip::PLAYSTATE_PLAY);
check_equals(root->get_current_frame(), 2);
check_equals(root->getDisplayList().size(), 3); // dejagnu + red square + black square
// check invalidated bounds to contain the intersection
// between the two DisplayObjects.
//
check( invalidated.contains(Intersection(redRange,blackRange)) );
// Check that the black square is now behind the red square
check_pixel(x_left, y, 2, white, 2);
check_pixel(x_red, y, 2, red, 2);
check_pixel(x_int, y, 2, red, 2); // black is *behind* red square
check_pixel(x_black, y, 2, black, 2);
check_pixel(x_right, y, 2, white, 2);
tester.advance(); // FRAME 4, jump to frame 2 and stop
invalidated = tester.getInvalidatedRanges();
check_equals(root->getPlayState(), MovieClip::PLAYSTATE_STOP);
check_equals(root->get_current_frame(), 1);
check_equals(root->getDisplayList().size(), 3); // dejagnu + red square + black square
// Invalidated bounds can't be Null because something is printed
// in the XTRACE window... Anyway, the squares should be far enoguh
// to assume the invalidated bounds won't contain their intersection
//
// Gnash has an huge invalidated bounds for the whole movie lifetime, btw....
//
xcheck( ! invalidated.intersects(Intersection(redRange,blackRange)) );
// Check that the black square is still behind the red square
check_pixel(x_left, y, 2, white, 2);
check_pixel(x_red, y, 2, red, 2);
check_pixel(x_int, y, 2, red, 2); // black is *behind* red square
check_pixel(x_black, y, 2, black, 2);
check_pixel(x_right, y, 2, white, 2);
}
int
main(int /*argc*/, char** /*argv*/)
{
typedef gnash::geometry::SnappingRanges2d<int> Ranges;
typedef gnash::geometry::Range2d<int> Bounds;
string filename = string(TGTDIR) + string("/") + string(INPUT_FILENAME);
MovieTester tester(filename);
gnash::LogFile& dbglogfile = gnash::LogFile::getDefaultInstance();
dbglogfile.setVerbosity(1);
// Colors we'll use during the test
rgba red(255,0,0,255);
rgba green(0,255,0,255);
rgba white(255,255,255,255);
// Ranges we'll use during the test
Range2d<int> redRange(100,300,160,360);
Range2d<int> greenRange(130,330,190,390);
Ranges invalidated;
MovieClip* root = tester.getRootMovie();
assert(root);
// FRAME 1 (start)
check_equals(root->get_frame_count(), 4);
check_equals(root->getPlayState(), MovieClip::PLAYSTATE_PLAY);
check_equals(root->get_current_frame(), 0);
check_equals(root->getDisplayList().size(), 1); // dejagnu clip
invalidated = tester.getInvalidatedRanges();
check( invalidated.contains(76, 4) ); // the "-xtrace enabled-" label...
tester.advance(); // FRAME 2, place DisplayObject
invalidated = tester.getInvalidatedRanges();
check_equals(root->getPlayState(), MovieClip::PLAYSTATE_PLAY);
check_equals(root->get_current_frame(), 1);
check_equals(root->getDisplayList().size(), 2); // dejagnu + red char
// check invalidated bounds contain the red instance (100,300 - 160,360)
check( invalidated.contains(redRange) );
// check that we have a red square at (100,300 - 160,360)
check_pixel(104, 304, 2, red, 2); // UL
check_pixel(156, 304, 2, red, 2); // UR
check_pixel(156, 356, 2, red, 2); // LL
check_pixel(104, 356, 2, red, 2); // LR
// and nothing around it...
check_pixel( 96, 330, 2, white, 2); // Left
check_pixel(164, 330, 2, white, 2); // Right
check_pixel(130, 296, 2, white, 2); // Top
check_pixel(130, 364, 2, white, 2); // Bottom
tester.advance(); // FRAME 3, replace DisplayObject
invalidated = tester.getInvalidatedRanges();
check_equals(root->getPlayState(), MovieClip::PLAYSTATE_PLAY);
check_equals(root->get_current_frame(), 2);
check_equals(root->getDisplayList().size(), 2); // dejagnu + green char
// check invalidated bounds to contain:
// - the green square (added)
// - the red square (removed)
//
check( invalidated.contains(redRange) );
check( invalidated.contains(greenRange) );
// check that we have a green square at (130,330 - 190,390)
check_pixel(134, 334, 2, green, 2); // UL
check_pixel(186, 334, 2, green, 2); // UR
check_pixel(186, 386, 2, green, 2); // LL
check_pixel(134, 386, 2, green, 2); // LR
// and nothing around it...
check_pixel(126, 360, 2, white, 2); // Left
check_pixel(194, 360, 2, white, 2); // Right
check_pixel(160, 326, 2, white, 2); // Top
check_pixel(160, 394, 2, white, 2); // Bottom
tester.advance(); // FRAME 4, jump to frame 2 and stop
invalidated = tester.getInvalidatedRanges();
check_equals(root->getPlayState(), MovieClip::PLAYSTATE_STOP);
check_equals(root->get_current_frame(), 1);
check_equals(root->getDisplayList().size(), 2); // dejagnu + red char
// check invalidated bounds to contain:
// - the green square (removed)
// - the red square (added)
//
check( invalidated.contains(redRange) );
check( invalidated.contains(greenRange) );
// check that we have a red square at (100,300 - 160,360)
check_pixel(104, 304, 2, red, 2); // UL
check_pixel(156, 304, 2, red, 2); // UR
check_pixel(156, 356, 2, red, 2); // LL
check_pixel(104, 356, 2, red, 2); // LR
// and nothing around it...
check_pixel( 96, 330, 2, white, 2); // Left
check_pixel(164, 330, 2, white, 2); // Right
check_pixel(130, 296, 2, white, 2); // Top
check_pixel(130, 364, 2, white, 2); // Bottom
}
int main(int argc, char* argv[]) {
#ifdef USE_GOOGLE_PROFILER
char *profileFileName = getenv("CPUPROFILE");
if (profileFileName != NULL) {
ProfilerStart(profileFileName);
}
else {
ProfilerStart("google_profile.txt");
}
#endif
// Register inputs and outputs.
string samFileName, refFileName, outFileName;
CommandLineParser clp;
clp.RegisterStringOption("file.sam", &samFileName,
"Input SAM file.");
clp.RegisterStringOption("reference.fasta", &refFileName,
"Reference used to generate reads.");
clp.RegisterStringOption("out.sam", &outFileName,
"Output SAM file.");
clp.RegisterPreviousFlagsAsHidden();
// Register filter criteria options.
int minAlnLength = 50;
float minPctSimilarity = 70, minPctAccuracy = 70;
string hitPolicyStr = "randombest";
bool useScoreCutoff = false;
int scoreCutoff = INF_INT;
int scoreSignInt = -1;
RegisterFilterOptions(clp, minAlnLength, minPctSimilarity,
minPctAccuracy, hitPolicyStr, useScoreCutoff,
scoreSignInt, scoreCutoff);
int seed = 1;
clp.RegisterIntOption("seed", &seed,
"(1) Seed for random number generator.\n"
"If seed is 0, then use current time as seed.",
CommandLineParser::Integer);
string holeNumberStr;
Ranges holeNumberRanges;
clp.RegisterStringOption("holeNumbers", &holeNumberStr,
"A string of comma-delimited hole number ranges to output hits, "
"such as '1,2,10-12'. "
"This requires hit titles to be in SMRT read title format.");
bool parseSmrtTitle = false;
clp.RegisterFlagOption("smrtTitle", &parseSmrtTitle,
"Use this option when filtering alignments generated by "
"programs other than blasr, e.g. bwa-sw or gmap. "
" Parse read coordinates from the SMRT read title. "
"The title is in the format /name/hole/coordinates, where"
" coordinates are in the format \\d+_\\d+, and represent "
"the interval of the read that was aligned.");
/* This experimental option can be useful for metagenomics, in which case
* there are hundreds of sequences in the target, of which many titles are
* long and may contain white spaces (e.g., ' ', '\t').
* In order to save disc space and avoid the (possibly) none unique mapping
* between full and short reference names, one may call blasr with
* -titleTable option to represent all target sequences in the output
* by their indices in the title table.*/
string titleTableName = "";
clp.RegisterStringOption("titleTable", &titleTableName,
"Use this experimental option when filtering alignments generated by "
"blasr with -titleTable titleTableName, in which case "
"reference titles in SAM are represented by their "
"indices (e.g., 0, 1, 2, ...) in the title table.");
string adapterGffFileName = "";
clp.RegisterStringOption("filterAdapterOnly", &adapterGffFileName,
"Use this option to remove reads which can only map to adapters "
"specified in the GFF file.");
bool verbose = false;
clp.RegisterFlagOption("v", &verbose, "Be verbose.");
clp.SetExamples(
"Because SAM has optional tags that have different meanings"
" in different programs, careful usage is required in order "
"to have proper output. The \"xs\" tag in bwa-sw is used to "
"show the suboptimal score, but in PacBio SAM (blasr) it is "
"defined as the start in the query sequence of the alignment.\n"
"When \"-smrtTitle\" is specified, the xs tag is ignored, but "
"when it is not specified, the coordinates given by the xs and "
"xe tags are used to define the interval of a read that is "
"aligned. The CIGAR string is relative to this interval.");
clp.ParseCommandLine(argc, argv);
// Set random number seed.
if (seed == 0) {
srand(time(NULL));
} else {
srand(seed);
}
scoreSign = (scoreSignInt == -1)?ScoreSign::NEGATIVE:ScoreSign::POSITIVE;
Score s(static_cast<float>(scoreCutoff), scoreSign);
FilterCriteria filterCriteria(minAlnLength, minPctSimilarity,
minPctAccuracy, true, s);
filterCriteria.Verbose(verbose);
HitPolicy hitPolicy(hitPolicyStr, scoreSign);
string errMsg;
if (not filterCriteria.MakeSane(errMsg)) {
cout << errMsg << endl;
exit(1);
}
// Parse hole number ranges.
if (holeNumberStr.size() != 0) {
if (not holeNumberRanges.setRanges(holeNumberStr)) {
cout << "Could not parse hole number ranges: "
<< holeNumberStr << "." << endl;
exit(1);
}
}
// Open output file.
ostream * outFilePtr = &cout;
ofstream outFileStrm;
if (outFileName != "") {
CrucialOpen(outFileName, outFileStrm, std::ios::out);
outFilePtr = &outFileStrm;
}
GFFFile adapterGffFile;
if (adapterGffFileName != "")
adapterGffFile.ReadAll(adapterGffFileName);
SAMReader<SAMFullReferenceSequence, SAMReadGroup, SAMAlignment> samReader;
FASTAReader fastaReader;
//
// Initialize samReader and fastaReader.
//
samReader.Initialize(samFileName);
fastaReader.Initialize(refFileName);
//
// Configure the file log.
//
string command;
CommandLineParser::CommandLineToString(argc, argv, command);
string log = "Filter sam hits.";
string program = "samFilter";
string versionString = VERSION;
AppendPerforceChangelist(PERFORCE_VERSION_STRING, versionString);
//
// Read necessary input.
//
vector<FASTASequence> references;
fastaReader.ReadAllSequences(references);
// If the SAM file is generated by blasr with -titleTable,
// then references in the SAM are represented by
// their corresponding indices in the title table.
// In that case, we need to convert reference titles in fasta file
// to their corresponding indices in the title table, such that
// references in both SAM and fasta files are represented
// by title table indices and therefore can match.
if (titleTableName != "") {
ConvertTitlesToTitleTableIndices(references, titleTableName);
}
AlignmentSet<SAMFullReferenceSequence, SAMReadGroup, SAMAlignment> alignmentSet;
vector<string> allHeaders = samReader.ReadHeader(alignmentSet);
// Process SAM Header.
string commandLineString;
clp.CommandLineToString(argc, argv, commandLineString);
allHeaders.push_back("@PG\tID:SAMFILTER\tVN:" + versionString + \
"\tCL:" + program + " " + commandLineString);
for (int i = 0; i < allHeaders.size(); i++) {
outFileStrm << allHeaders[i] << endl;
}
//
// The order of references in vector<FASTASequence> references and
// AlignmentSet<, , >alignmentSet.references can be different.
// Rearrange alignmentSet.references such that they are ordered in
// exactly the same way as vector<FASTASequence> references.
//
alignmentSet.RearrangeReferences(references);
// Map reference name obtained from SAM file to indices
map<string, int> refNameToIndex;
for (int i = 0; i < references.size(); i++) {
string refName = alignmentSet.references[i].GetSequenceName();
refNameToIndex[refName] = i;
}
//
// Store the alignments.
//
SAMAlignment samAlignment;
int alignIndex = 0;
//
// For 150K, each chip produces about 300M sequences
// (not including quality values and etc.).
// Let's assume that the sam file and reference data can
// fit in the memory.
// Need to scale for larger sequal data in the future.
//
vector<SAMAlignment> allSAMAlignments;
while (samReader.GetNextAlignment(samAlignment)) {
if (samAlignment.rName == "*") {
continue;
}
if (parseSmrtTitle and holeNumberStr.size() != 0) {
string movieName;
int thisHoleNumber;
if (not ParsePBIReadName(samAlignment.qName,
movieName,
thisHoleNumber)) {
cout << "ERROR, could not parse SMRT title: "
<< samAlignment.qName << "." << endl;
exit(1);
}
if (not holeNumberRanges.contains(UInt(thisHoleNumber))) {
if (verbose)
cout << thisHoleNumber << " is not in range." << endl;
continue;
}
}
if (samAlignment.cigar.find('P') != string::npos) {
cout << "WARNING. Could not process SAM record with 'P' in "
<< "its cigar string." << endl;
continue;
}
vector<AlignmentCandidate<> > convertedAlignments;
SAMAlignmentsToCandidates(samAlignment,
references, refNameToIndex,
convertedAlignments, parseSmrtTitle, false);
if (convertedAlignments.size() > 1) {
cout << "WARNING. Ignore multiple segments." << endl;
continue;
}
for (int i = 0; i < 1; i++) {
AlignmentCandidate<> & alignment = convertedAlignments[i];
//score func does not matter
DistanceMatrixScoreFunction<DNASequence, DNASequence> distFunc;
ComputeAlignmentStats(alignment, alignment.qAlignedSeq.seq,
alignment.tAlignedSeq.seq, distFunc);
// Check whether this alignment can only map to adapters in
// the adapter GFF file.
if (adapterGffFileName != "" and
CheckAdapterOnly(adapterGffFile, alignment, refNameToIndex)) {
if (verbose)
cout << alignment.qName << " filter adapter only."
<< endl;
continue;
}
// Assign score to samAlignment.
samAlignment.score = samAlignment.as;
if (not filterCriteria.Satisfy(static_cast<AlignmentCandidate<> *>(&alignment))) {
continue;
}
allSAMAlignments.push_back( samAlignment );
alignment.FreeSubsequences();
}
++alignIndex;
}
// Sort all SAM alignments by qName, score and target position.
sort(allSAMAlignments.begin(), allSAMAlignments.end(),
byQNameScoreTStart);
unsigned int groupBegin = 0;
unsigned int groupEnd = -1;
vector<SAMAlignment> filteredSAMAlignments;
while(groupBegin < allSAMAlignments.size()) {
// Get the next group of SAM alignments which have the same qName
// from allSAMAlignments[groupBegin ... groupEnd)
GetNextSAMAlignmentGroup(allSAMAlignments, groupBegin, groupEnd);
vector<unsigned int> hitIndices = ApplyHitPolicy(
hitPolicy, allSAMAlignments, groupBegin, groupEnd);
for(unsigned int i = 0; i < hitIndices.size(); i++) {
filteredSAMAlignments.push_back(allSAMAlignments[hitIndices[i]]);
}
groupBegin = groupEnd;
}
// Sort all SAM alignments by reference name and query name
sort(filteredSAMAlignments.begin(), filteredSAMAlignments.end(),
byRNameQName);
for(unsigned int i = 0; i < filteredSAMAlignments.size(); i++) {
filteredSAMAlignments[i].PrintSAMAlignment(outFileStrm);
}
if (outFileName != "") {
outFileStrm.close();
}
#ifdef USE_GOOGLE_PROFILER
ProfilerStop();
#endif
return 0;
}