Classes | |
class | Alignment |
class | BottomSegment |
class | BottomSegmentIterator |
class | CLParser |
class | ColumnIterator |
class | DNAIterator |
class | GappedBottomSegmentIterator |
class | GappedSegmentIterator |
class | GappedTopSegmentIterator |
class | Genome |
class | MappedSegment |
class | MetaData |
class | PositionCache |
class | Rearrangement |
class | Segment |
class | SegmentedSequence |
class | SegmentIterator |
class | Sequence |
class | SequenceIterator |
class | SlicedSegment |
class | TopSegment |
class | TopSegmentIterator |
Functions | |
AlignmentPtr | hdf5AlignmentInstance () |
AlignmentConstPtr | hdf5AlignmentInstanceReadOnly () |
AlignmentPtr | hdf5AlignmentInstance (const H5::FileCreatPropList &fileCreateProps, const H5::FileAccPropList &fileAccessProps, const H5::DSetCreatPropList &datasetCreateProps, bool inMemory=false) |
AlignmentConstPtr | hdf5AlignmentInstanceReadOnly (const H5::FileCreatPropList &fileCreateProps, const H5::FileAccPropList &fileAccessProps, const H5::DSetCreatPropList &datasetCreateProps, bool inMemory=false) |
AlignmentPtr | openHalAlignment (const std::string &path, CLParserConstPtr options) |
AlignmentConstPtr | openHalAlignmentReadOnly (const std::string &path, CLParserConstPtr options) |
bool | operator== (BottomSegmentIteratorConstPtr p1, BottomSegmentIteratorConstPtr p2) |
bool | operator!= (BottomSegmentIteratorConstPtr p1, BottomSegmentIteratorConstPtr p2) |
template<> | |
std::string | CLParser::convertFromString< std::string > (const std::string &token) const |
CLParserPtr | hdf5CLParserInstance (bool createOptions=false) |
std::ostream & | operator<< (std::ostream &os, const ColumnIterator &cit) |
bool | compatibleWithVersion (const std::string &version) |
std::vector< std::string > | chopString (const std::string &inString, const std::string &separator) |
char | reverseComplement (char c) |
void | reverseComplement (std::string &s) |
bool | isNucleotide (char c) |
bool | isTransition (char c1, char c2) |
bool | isSubstitution (char c1, char c2) |
bool | isTransversion (char c1, char c2) |
bool | isMissingData (char c) |
bool | isMasked (char c) |
bool | isFourfoldDegenerate (char c1, char c2) |
hal_size_t | hammingDistance (const std::string &s1, const std::string &s2) |
const Genome * | getLowestCommonAncestor (const std::set< const Genome * > &inputSet) |
void | getGenomesInSpanningTree (const std::set< const Genome * > &inputSet, std::set< const Genome * > &outputSet) |
void | getGenomesInSubTree (const Genome *root, std::set< const Genome * > &outputSet) |
std::ostream & | operator<< (std::ostream &os, const DNAIterator *dna) |
bool | operator== (GappedBottomSegmentIteratorConstPtr p1, GappedBottomSegmentIteratorConstPtr p2) |
bool | operator!= (GappedBottomSegmentIteratorConstPtr p1, GappedBottomSegmentIteratorConstPtr p2) |
bool | operator== (GappedTopSegmentIteratorConstPtr p1, GappedTopSegmentIteratorConstPtr p2) |
bool | operator!= (GappedTopSegmentIteratorConstPtr p1, GappedTopSegmentIteratorConstPtr p2) |
std::ostream & | operator<< (std::ostream &os, const Segment &s) |
bool | operator< (SegmentIteratorConstPtr segmentIt, hal_index_t genomePos) |
bool | operator> (SegmentIteratorConstPtr segmentIt, hal_index_t genomePos) |
bool | operator== (SequenceIteratorConstPtr p1, SequenceIteratorConstPtr p2) |
bool | operator!= (SequenceIteratorConstPtr p1, SequenceIteratorConstPtr p2) |
bool | operator< (SlicedSegmentConstPtr segmentIt, hal_index_t genomePos) |
bool | operator> (SlicedSegmentConstPtr segmentIt, hal_index_t genomePos) |
bool | operator== (TopSegmentIteratorConstPtr p1, TopSegmentIteratorConstPtr p2) |
bool | operator!= (TopSegmentIteratorConstPtr p1, TopSegmentIteratorConstPtr p2) |
void | validateBottomSegment (const BottomSegment *bottomSegment) |
void | validateTopSegment (const TopSegment *topSegment) |
void | validateSequence (const Sequence *sequence) |
void | validateGenome (const Genome *genome) |
void | validateDuplications (const Genome *genome) |
void | validateAlignment (AlignmentConstPtr alignment) |
Variables | |
const hal_index_t | NULL_INDEX |
HAL API namespace
std::vector<std::string> hal::chopString | ( | const std::string & | inString, |
const std::string & | separator | ||
) |
C++ style strtok-type function. Can't remember why I wrote it
|
inline |
Count the mutations between two DNA strings
AlignmentPtr hal::hdf5AlignmentInstance | ( | ) |
Get an instance of an HDF5-implemented Alignment with default parameters for everything
AlignmentPtr hal::hdf5AlignmentInstance | ( | const H5::FileCreatPropList & | fileCreateProps, |
const H5::FileAccPropList & | fileAccessProps, | ||
const H5::DSetCreatPropList & | datasetCreateProps, | ||
bool | inMemory = false |
||
) |
Get an instance of an HDF5-implemented Alignment while specifying
fileCreateProps | File creation properties. fairly low-level and should generally be set to H5::FileCreatPropList::DEFAULT |
fileAccessProps | File access properties. Contains cache-related stuff |
datasetCreateProps | Compression and chunking parameters among others |
inMemory | Store all data in memory (overrides and disables hdf5 cache) |
AlignmentConstPtr hal::hdf5AlignmentInstanceReadOnly | ( | ) |
Get read-only instance of an HDF5-implemented Alignment with default parameters for everything
AlignmentConstPtr hal::hdf5AlignmentInstanceReadOnly | ( | const H5::FileCreatPropList & | fileCreateProps, |
const H5::FileAccPropList & | fileAccessProps, | ||
const H5::DSetCreatPropList & | datasetCreateProps, | ||
bool | inMemory = false |
||
) |
Get a read-only instance of an HDF5-implemented Alignment while specifying
fileCreateProps | File creation properties. fairly low-level and should generally be set to H5::FileCreatPropList::DEFAULT |
fileAccessProps | File access properties. Contains cache-related stuff |
datasetCreateProps | Compression and chunking parameters among others |
inMemory | Store all data in memory (overrides and disables hdf5 cache) |
CLParserPtr hal::hdf5CLParserInstance | ( | bool | createOptions = false | ) |
Get an instance of an HDF5-implemented CLParser
createOptions | set to true if tool will need to create a new hal file (as opposed to just reading an existing one) |
|
inline |
test if 3rd codon position is 4-fold degenerate given first 2 positions
|
inline |
Check if a DNA character is a valid base (or n-chracter)
AlignmentPtr hal::openHalAlignment | ( | const std::string & | path, |
CLParserConstPtr | options | ||
) |
Get an alignment instance from a file by automatically detecting which implementation to use. (will currently (and probably forever more) just return an HDF5 instance since that's all that exists)
path | Path of file to open |
options | Command line options information |
AlignmentConstPtr hal::openHalAlignmentReadOnly | ( | const std::string & | path, |
CLParserConstPtr | options | ||
) |
Get a read-only alignment instance from a file by automatically detecting which implementation to use. (will currently (and probably forever more) just return an HDF5 instance since that's all that exists)
path | Path of file to open |
options | Command line options information |
|
inline |
Get the DNA reverse complement of a character. If the input is not a nucleotide, then just return it as is (ie no error checking)
void hal::reverseComplement | ( | std::string & | s | ) |
Get the reversed complement of a string (in place
void hal::validateAlignment | ( | AlignmentConstPtr | alignment | ) |
Go through an alignment, and throw an excpetion if anything appears out of whack.
void hal::validateBottomSegment | ( | const BottomSegment * | bottomSegment | ) |
Go through a bottom segment, and throw an exception if anything appears out of whack.
void hal::validateDuplications | ( | const Genome * | genome | ) |
Go through a genome, and throw an exception if any duplications appears out of whack.
void hal::validateGenome | ( | const Genome * | genome | ) |
Go through a genome, and throw an exception if anything appears out of whack.
void hal::validateSequence | ( | const Sequence * | sequence | ) |
Go through a sequence, and throw an exception if anything appears out of whack.
void hal::validateTopSegment | ( | const TopSegment * | topSegment | ) |
Go through a top segment, and throw an exception if anything appears out of whack.