// ***************************************************************************
// BamMultiReader.cpp (c) 2010 Erik Garrison, Derek Barnett
// Marth Lab, Department of Biology, Boston College
-// All rights reserved.
// ---------------------------------------------------------------------------
-// Last modified: 23 December 2010 (DB)
+// Last modified: 14 January 2013 (DB)
// ---------------------------------------------------------------------------
-// Uses BGZF routines were adapted from the bgzf.c code developed at the Broad
-// Institute.
-// ---------------------------------------------------------------------------
-// Functionality for simultaneously reading multiple BAM files.
+// Convenience class for reading multiple BAM files.
//
// This functionality allows applications to work on very large sets of files
// without requiring intermediate merge, sort, and index steps for each file
-// subset. It also improves the performance of our merge system as it
+// subset. It also improves the performance of our merge system as it
// precludes the need to sort merged files.
// ***************************************************************************
-#include <api/BamMultiReader.h>
-#include <api/BGZF.h>
-#include <api/internal/BamMultiReader_p.h>
+#include "api/BamMultiReader.h"
+#include "api/internal/bam/BamMultiReader_p.h"
using namespace BamTools;
#include <string>
#include <vector>
using namespace std;
-// -----------------------------------------------------
-// BamMultiReader implementation
-// -----------------------------------------------------
+/*! \class BamTools::BamMultiReader
+ \brief Convenience class for reading multiple BAM files.
+*/
+
+/*! \enum BamMultiReader::MergeOrder
+ \brief A description of the enum type.
+*/
+/*! \var BamMultiReader::MergeOrder BamMultiReader::MergeByCoordinate
+ \brief The description of the first enum value.
+*/
+/*! \var BamMultiReader::MergeOrder BamMultiReader::MergeByName
+ \brief BAM files are
+*/
+
+
+/*! \fn BamMultiReader::BamMultiReader(void)
+ \brief constructor
+*/
BamMultiReader::BamMultiReader(void)
: d(new Internal::BamMultiReaderPrivate)
{ }
+/*! \fn BamMultiReader::~BamMultiReader(void)
+ \brief destructor
+*/
BamMultiReader::~BamMultiReader(void) {
delete d;
d = 0;
}
-void BamMultiReader::Close(void) {
- d->Close();
+/*! \fn void BamMultiReader::Close(void)
+ \brief Closes all open BAM files.
+
+ Also clears out all header and reference data.
+
+ \sa CloseFile(), IsOpen(), Open(), BamReader::Close()
+*/
+bool BamMultiReader::Close(void) {
+ return d->Close();
+}
+
+/*! \fn void BamMultiReader::CloseFile(const std::string& filename)
+ \brief Closes requested BAM file.
+
+ Leaves any other file(s) open, along with header and reference data.
+
+ \param[in] filename name of specific BAM file to close
+
+ \sa Close(), IsOpen(), Open(), BamReader::Close()
+*/
+bool BamMultiReader::CloseFile(const std::string& filename) {
+ return d->CloseFile(filename);
+}
+
+/*! \fn bool BamMultiReader::CreateIndexes(const BamIndex::IndexType& type)
+ \brief Creates index files for the current BAM files.
+
+ \param[in] type file format to create, see BamIndex::IndexType for available formats
+ \return \c true if index files created OK
+ \sa LocateIndexes(), OpenIndexes(), BamReader::CreateIndex()
+*/
+bool BamMultiReader::CreateIndexes(const BamIndex::IndexType& type) {
+ return d->CreateIndexes(type);
}
-bool BamMultiReader::CreateIndexes(bool useStandardIndex) {
- return d->CreateIndexes(useStandardIndex);
+/*! \fn const std::vector<std::string> BamMultiReader::Filenames(void) const
+ \brief Returns list of filenames for all open BAM files.
+
+ Retrieved filenames will contain whatever was passed via Open().
+ If you need full directory paths here, be sure to include them
+ when you open the BAM files.
+
+ \returns names of open BAM files. If no files are open, returns an empty vector.
+ \sa IsOpen(), BamReader::GetFilename()
+*/
+const std::vector<std::string> BamMultiReader::Filenames(void) const {
+ return d->Filenames();
}
-void BamMultiReader::SetIndexCacheMode(const BamIndex::BamIndexCacheMode mode) {
- d->SetIndexCacheMode(mode);
+/*! \fn std::string BamMultiReader::GetErrorString(void) const
+ \brief Returns a human-readable description of the last error that occurred
+
+ This method allows elimination of STDERR pollution. Developers of client code
+ may choose how the messages are displayed to the user, if at all.
+
+ \return error description
+*/
+std::string BamMultiReader::GetErrorString(void) const {
+ return d->GetErrorString();
+}
+
+/*! \fn SamHeader BamMultiReader::GetHeader(void) const
+ \brief Returns unified SAM-format header for all files
+
+ \note Modifying the retrieved text does NOT affect the current
+ BAM files. These files have been opened in a read-only mode. However,
+ your modified header text can be used in conjunction with BamWriter
+ to generate a new BAM file with the appropriate header information.
+
+ \returns header data wrapped in SamHeader object
+ \sa GetHeaderText(), BamReader::GetHeader()
+*/
+SamHeader BamMultiReader::GetHeader(void) const {
+ return d->GetHeader();
}
-const string BamMultiReader::GetHeaderText(void) const {
+/*! \fn std::string BamMultiReader::GetHeaderText(void) const
+ \brief Returns unified SAM-format header text for all files
+
+ \note Modifying the retrieved text does NOT affect the current
+ BAM files. These files have been opened in a read-only mode. However,
+ your modified header text can be used in conjunction with BamWriter
+ to generate a new BAM file with the appropriate header information.
+
+ \returns SAM-formatted header text
+ \sa GetHeader(), BamReader::GetHeaderText()
+*/
+std::string BamMultiReader::GetHeaderText(void) const {
return d->GetHeaderText();
}
+/*! \fn BamMultiReader::MergeOrder BamMultiReader::GetMergeOrder(void) const
+ \brief Returns curent merge order strategy.
+
+ \returns current merge order enum value
+ \sa BamMultiReader::MergeOrder, SetExplicitMergeOrder()
+*/
+BamMultiReader::MergeOrder BamMultiReader::GetMergeOrder(void) const {
+ return d->GetMergeOrder();
+}
+
+/*! \fn bool BamMultiReader::GetNextAlignment(BamAlignment& alignment)
+ \brief Retrieves next available alignment.
+
+ Equivalent to BamReader::GetNextAlignment() with respect to what is a valid
+ overlapping alignment and what data gets populated.
+
+ This method takes care of determining which alignment actually is 'next'
+ across multiple files, depending on their sort order.
+
+ \param[out] alignment destination for alignment record data
+ \returns \c true if a valid alignment was found
+ \sa GetNextAlignmentCore(), SetExplicitMergeOrder(), SetRegion(), BamReader::GetNextAlignment()
+*/
bool BamMultiReader::GetNextAlignment(BamAlignment& nextAlignment) {
return d->GetNextAlignment(nextAlignment);
}
+/*! \fn bool BamMultiReader::GetNextAlignmentCore(BamAlignment& alignment)
+ \brief Retrieves next available alignment.
+
+ Equivalent to BamReader::GetNextAlignmentCore() with respect to what is a valid
+ overlapping alignment and what data gets populated.
+
+ This method takes care of determining which alignment actually is 'next'
+ across multiple files, depending on their sort order.
+
+ \param[out] alignment destination for alignment record data
+ \returns \c true if a valid alignment was found
+ \sa GetNextAlignment(), SetExplicitMergeOrder(), SetRegion(), BamReader::GetNextAlignmentCore()
+*/
bool BamMultiReader::GetNextAlignmentCore(BamAlignment& nextAlignment) {
return d->GetNextAlignmentCore(nextAlignment);
}
-const int BamMultiReader::GetReferenceCount(void) const {
+/*! \fn int BamMultiReader::GetReferenceCount(void) const
+ \brief Returns number of reference sequences.
+ \sa BamReader::GetReferenceCount()
+*/
+int BamMultiReader::GetReferenceCount(void) const {
return d->GetReferenceCount();
}
+/*! \fn const RefVector& BamMultiReader::GetReferenceData(void) const
+ \brief Returns all reference sequence entries.
+ \sa RefData, BamReader::GetReferenceData()
+*/
const BamTools::RefVector BamMultiReader::GetReferenceData(void) const {
return d->GetReferenceData();
}
-const int BamMultiReader::GetReferenceID(const string& refName) const {
+/*! \fn int BamMultiReader::GetReferenceID(const std::string& refName) const
+ \brief Returns the ID of the reference with this name.
+
+ If \a refName is not found, returns -1.
+
+ \param[in] refName name of reference to look up
+ \sa BamReader::GetReferenceID()
+*/
+int BamMultiReader::GetReferenceID(const std::string& refName) const {
return d->GetReferenceID(refName);
}
-bool BamMultiReader::HasOpenReaders() {
- return d->HasOpenReaders();
+/*! \fn bool BamMultiReader::HasIndexes(void) const
+ \brief Returns \c true if all BAM files have index data available.
+ \sa BamReader::HasIndex()
+*/
+bool BamMultiReader::HasIndexes(void) const {
+ return d->HasIndexes();
}
-bool BamMultiReader::IsIndexLoaded(void) const {
- return d->IsIndexLoaded();
+/*! \fn bool BamMultiReader::HasOpenReaders(void) const
+ \brief Returns \c true if there are any open BAM files.
+*/
+bool BamMultiReader::HasOpenReaders(void) const {
+ return d->HasOpenReaders();
}
+/*! \fn bool BamMultiReader::Jump(int refID, int position)
+ \brief Performs a random-access jump within current BAM files.
+
+ This is a convenience method, equivalent to calling SetRegion()
+ with only a left boundary specified.
+
+ \param[in] refID ID of reference to jump to
+ \param[in] position (0-based) left boundary
+
+ \returns \c true if jump was successful
+ \sa HasIndex(), BamReader::Jump()
+*/
+
bool BamMultiReader::Jump(int refID, int position) {
return d->Jump(refID, position);
}
-bool BamMultiReader::Open(const vector<string>& filenames,
- bool openIndexes,
- bool coreMode,
- bool preferStandardIndex)
-{
- return d->Open(filenames, openIndexes, coreMode, preferStandardIndex);
+/*! \fn bool BamMultiReader::LocateIndexes(const BamIndex::IndexType& preferredType)
+ \brief Looks for index files that match current BAM files.
+
+ Use this function when you need index files, and perhaps have a
+ preferred index format, but do not depend heavily on which indexes
+ actually get loaded at runtime.
+
+ For each BAM file, this function will defer to your \a preferredType
+ whenever possible. However, if an index file of \a preferredType can
+ not be found, then it will look for any other index file that matches
+ that BAM file.
+
+ An example case would look this:
+ \code
+ BamMultiReader reader;
+
+ // do setup...
+
+ // ensure that all files have an index
+ if ( !reader.LocateIndexes() ) // opens any existing index files that match our BAM files
+ reader.CreateIndexes(); // creates index files for any BAM files that still lack one
+
+ // do interesting stuff using random-access...
+
+ \endcode
+
+ If you want precise control over which index files are loaded, use OpenIndexes()
+ with the desired index filenames. If that function returns false, you can use
+ CreateIndexes() to then build index files of the exact requested format.
+
+ \param[in] preferredType desired index file format, see BamIndex::IndexType for available formats
+ \returns \c true if index files could be found for \b ALL open BAM files
+ \sa BamReader::LocateIndex()
+*/
+bool BamMultiReader::LocateIndexes(const BamIndex::IndexType& preferredType) {
+ return d->LocateIndexes(preferredType);
+}
+
+/*! \fn bool BamMultiReader::Open(const std::vector<std::string>& filenames)
+ \brief Opens BAM files.
+
+ \note Opening BAM files will invalidate any current region set on the multireader.
+ All file pointers will be returned to the beginning of the alignment data. Follow
+ this with Jump() or SetRegion() to establish a region of interest.
+
+ \param[in] filenames list of BAM filenames to open
+ \returns \c true if BAM files were opened successfully
+ \sa Close(), HasOpenReaders(), OpenFile(), OpenIndexes(), BamReader::Open()
+*/
+bool BamMultiReader::Open(const std::vector<std::string>& filenames) {
+ return d->Open(filenames);
}
-void BamMultiReader::PrintFilenames(void) const {
- d->PrintFilenames();
+/*! \fn bool BamMultiReader::OpenFile(const std::string& filename)
+ \brief Opens a single BAM file.
+
+ Adds another BAM file to multireader "on-the-fly".
+
+ \note Opening a BAM file will invalidate any current region set on the multireader.
+ All file pointers will be returned to the beginning of the alignment data. Follow
+ this with Jump() or SetRegion() to establish a region of interest.
+
+ \param[in] filename BAM filename to open
+ \returns \c true if BAM file was opened successfully
+ \sa Close(), HasOpenReaders(), Open(), OpenIndexes(), BamReader::Open()
+*/
+bool BamMultiReader::OpenFile(const std::string& filename) {
+ return d->OpenFile(filename);
}
+/*! \fn bool BamMultiReader::OpenIndexes(const std::vector<std::string>& indexFilenames)
+ \brief Opens index files for current BAM files.
+
+ \note Currently assumes that index filenames match the order (and number) of
+ BAM files passed to Open().
+
+ \param[in] indexFilenames list of BAM index file names
+ \returns \c true if BAM index file was opened & data loaded successfully
+ \sa LocateIndex(), Open(), SetIndex(), BamReader::OpenIndex()
+*/
+bool BamMultiReader::OpenIndexes(const std::vector<std::string>& indexFilenames) {
+ return d->OpenIndexes(indexFilenames);
+}
+
+/*! \fn bool BamMultiReader::Rewind(void)
+ \brief Returns the internal file pointers to the beginning of alignment records.
+
+ Useful for performing multiple sequential passes through BAM files.
+ Calling this function clears any prior region that may have been set.
+
+ \returns \c true if rewind operation was successful
+ \sa Jump(), SetRegion(), BamReader::Rewind()
+*/
bool BamMultiReader::Rewind(void) {
return d->Rewind();
}
-bool BamMultiReader::SetRegion(const int& leftRefID,
- const int& leftPosition,
- const int& rightRefID,
- const int& rightPosition)
-{
- BamRegion region(leftRefID, leftPosition, rightRefID, rightPosition);
- return d->SetRegion(region);
+/*! \fn void BamMultiReader::SetExplicitMergeOrder(BamMultiReader::MergeOrder order)
+ \brief Sets an explicit merge order, regardless of the BAM files' SO header tag.
+
+ The default behavior of the BamMultiReader is to check the SO tag in the BAM files'
+ SAM header text to determine the merge strategy". The merge strategy is used to
+ determine from which BAM file the next alignment should come when either
+ GetNextAlignment() or GetNextAlignmentCore() are called. If files share a
+ 'coordinate' or 'queryname' value for this tag, then the merge strategy is
+ selected accordingly. If any of them do not match, or if any fileis marked as
+ 'unsorted', then the merge strategy is simply a round-robin.
+
+ This method allows client code to explicitly override the lookup behavior. This
+ method can be useful when you know, for example, that your BAM files are sorted
+ by coordinate but upstream processes did not set the header tag properly.
+
+ \note This method should \bold not be called while reading alignments via
+ GetNextAlignment() or GetNextAlignmentCore(). For proper results, you should
+ call this method before (or immediately after) opening files, rewinding,
+ jumping, etc. but \bold not once alignment fetching has started. There is
+ nothing in the API to prevent you from doing so, but the results may be
+ unexpected.
+
+ \sa BamMultiReader::MergeOrder, GetMergeOrder(), GetNextAlignment(), GetNextAlignmentCore()
+*/
+void BamMultiReader::SetExplicitMergeOrder(BamMultiReader::MergeOrder order) {
+ d->SetExplicitMergeOrder(order);
}
+/*! \fn bool BamMultiReader::SetRegion(const BamRegion& region)
+ \brief Sets a target region of interest
+
+ Equivalent to calling BamReader::SetRegion() on all open BAM files.
+
+ \warning BamRegion now represents a zero-based, HALF-OPEN interval.
+ In previous versions of BamTools (0.x & 1.x) all intervals were treated
+ as zero-based, CLOSED.
+
+ \param[in] region desired region-of-interest to activate
+ \returns \c true if ALL readers set the region successfully
+ \sa HasIndexes(), Jump(), BamReader::SetRegion()
+*/
bool BamMultiReader::SetRegion(const BamRegion& region) {
return d->SetRegion(region);
}
-void BamMultiReader::SetSortOrder(const SortOrder& order) {
- d->SetSortOrder(order);
+/*! \fn bool BamMultiReader::SetRegion(const int& leftRefID,
+ const int& leftPosition,
+ const int& rightRefID,
+ const int& rightPosition)
+ \brief Sets a target region of interest
+
+ This is an overloaded function. Equivalent to calling BamReader::SetRegion() on all open BAM files.
+
+ \warning This function now expects a zero-based, HALF-OPEN interval.
+ In previous versions of BamTools (0.x & 1.x) all intervals were treated
+ as zero-based, CLOSED.
+
+ \param[in] leftRefID referenceID of region's left boundary
+ \param[in] leftPosition position of region's left boundary
+ \param[in] rightRefID reference ID of region's right boundary
+ \param[in] rightPosition position of region's right boundary
+
+ \returns \c true if ALL readers set the region successfully
+ \sa HasIndexes(), Jump(), BamReader::SetRegion()
+*/
+bool BamMultiReader::SetRegion(const int& leftRefID,
+ const int& leftPosition,
+ const int& rightRefID,
+ const int& rightPosition)
+{
+ return d->SetRegion( BamRegion(leftRefID, leftPosition, rightRefID, rightPosition) );
}
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