// BamMultiReader.cpp (c) 2010 Erik Garrison, Derek Barnett
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
-// Last modified: 8 October 2011 (DB)
+// Last modified: 14 January 2013 (DB)
// ---------------------------------------------------------------------------
// Convenience class for reading multiple BAM files.
//
// precludes the need to sort merged files.
// ***************************************************************************
-#include <api/BamMultiReader.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;
-/*! \class BamTools::BamReader
+/*! \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
*/
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) {
/*! \fn bool BamMultiReader::CreateIndexes(const BamIndex::IndexType& type)
\brief Creates index files for the current BAM files.
- \param type file format to create, see BamIndex::IndexType for available formats
+ \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()
*/
return d->Filenames();
}
-// returns a description of the last error that occurred
+/*! \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
- N.B. - Modifying the retrieved text does NOT affect the current
- BAM files. Thesse file have been opened in a read-only mode. However,
+ \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.
/*! \fn std::string BamMultiReader::GetHeaderText(void) const
\brief Returns unified SAM-format header text for all files
- N.B. - Modifying the retrieved text does NOT affect the current
- BAM files. Thesse file have been opened in a read-only mode. However,
+ \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.
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.
overlapping alignment and what data gets populated.
This method takes care of determining which alignment actually is 'next'
- across multiple files, depending on current SortOrder.
+ across multiple files, depending on their sort order.
- \param alignment destination for alignment record data
+ \param[out] alignment destination for alignment record data
\returns \c true if a valid alignment was found
- \sa GetNextAlignmentCore(), SetRegion(), SetSortOrder(), BamReader::GetNextAlignment()
+ \sa GetNextAlignmentCore(), SetExplicitMergeOrder(), SetRegion(), BamReader::GetNextAlignment()
*/
bool BamMultiReader::GetNextAlignment(BamAlignment& nextAlignment) {
return d->GetNextAlignment(nextAlignment);
overlapping alignment and what data gets populated.
This method takes care of determining which alignment actually is 'next'
- across multiple files, depending on current SortOrder.
+ across multiple files, depending on their sort order.
- \param alignment destination for alignment record data
+ \param[out] alignment destination for alignment record data
\returns \c true if a valid alignment was found
- \sa GetNextAlignment(), SetRegion(), SetSortOrder(), BamReader::GetNextAlignmentCore()
+ \sa GetNextAlignment(), SetExplicitMergeOrder(), SetRegion(), BamReader::GetNextAlignmentCore()
*/
bool BamMultiReader::GetNextAlignmentCore(BamAlignment& nextAlignment) {
return d->GetNextAlignmentCore(nextAlignment);
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 {
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()
*/
An example case would look this:
\code
-
BamMultiReader reader;
- // do setup
+
+ // 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 BAM files that still lack one
+ reader.CreateIndexes(); // creates index files for any BAM files that still lack one
- // do interesting stuff
- // ...
+ // do interesting stuff using random-access...
\endcode
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 preferredType desired index file format, see BamIndex::IndexType for available formats
+ \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()
*/
/*! \fn bool BamMultiReader::Open(const std::vector<std::string>& filenames)
\brief Opens BAM files.
- N.B. - 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.
+ \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 filenames list of BAM filenames to open
+ \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()
*/
Adds another BAM file to multireader "on-the-fly".
- N.B. - Opening a BAM file invalidates 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.
+ \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 filename BAM filename to open
+ \param[in] filename BAM filename to open
\returns \c true if BAM file was opened successfully
\sa Close(), HasOpenReaders(), Open(), OpenIndexes(), BamReader::Open()
*/
/*! \fn bool BamMultiReader::OpenIndexes(const std::vector<std::string>& indexFilenames)
\brief Opens index files for current BAM files.
- N.B. - Currently assumes that index filenames match the order (and number) of
+ \note Currently assumes that index filenames match the order (and number) of
BAM files passed to Open().
- \param indexFilenames list of BAM index file names
+ \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()
*/
return d->Rewind();
}
-/*! \fn void BamMultiReader::SetIndexCacheMode(const BamIndex::IndexCacheMode& mode)
- \brief Changes the caching behavior of the index data.
-
- Default mode is BamIndex::LimitedIndexCaching.
-
- \param mode desired cache mode for index, see BamIndex::IndexCacheMode for
- description of the available cache modes
- \sa HasIndex(), BamReader::SetIndexCacheMode()
+/*! \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::SetIndexCacheMode(const BamIndex::IndexCacheMode& mode) {
- d->SetIndexCacheMode(mode);
+void BamMultiReader::SetExplicitMergeOrder(BamMultiReader::MergeOrder order) {
+ d->SetExplicitMergeOrder(order);
}
/*! \fn bool BamMultiReader::SetRegion(const BamRegion& region)
Equivalent to calling BamReader::SetRegion() on all open BAM files.
- \param region desired region-of-interest to activate
+ \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()
*/
const int& rightPosition)
\brief Sets a target region of interest
- This is an overloaded function.
+ This is an overloaded function. Equivalent to calling BamReader::SetRegion() on all open BAM files.
- 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 leftRefID referenceID of region's left boundary
- \param leftPosition position of region's left boundary
- \param rightRefID reference ID of region's right boundary
- \param rightPosition position of region's right boundary
+ \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()
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