// Marth Lab, Department of Biology, Boston College\r
// All rights reserved.\r
// ---------------------------------------------------------------------------\r
-// Last modified: 14 April 2010 (DB)\r
+// Last modified: 8 June 2010 (DB)\r
// ---------------------------------------------------------------------------\r
// Uses BGZF routines were adapted from the bgzf.c code developed at the Broad\r
// Institute.\r
using namespace BamTools;\r
using namespace std;\r
\r
-namespace BamTools {\r
- struct BamAlignmentSupportData {\r
- string AllCharData;\r
- uint32_t BlockLength;\r
- uint32_t NumCigarOperations;\r
- uint32_t QueryNameLength;\r
- uint32_t QuerySequenceLength;\r
- };\r
-} // namespace BamTools\r
-\r
struct BamReader::BamReaderPrivate {\r
\r
// -------------------------------\r
int64_t AlignmentsBeginOffset;\r
string Filename;\r
string IndexFilename;\r
-
+ \r
// system data\r
bool IsBigEndian;\r
\r
\r
// access alignment data\r
bool GetNextAlignment(BamAlignment& bAlignment);\r
+ bool GetNextAlignmentCore(BamAlignment& bAlignment, BamAlignmentSupportData& supportData);\r
\r
// access auxiliary data\r
int GetReferenceID(const string& refName) const;\r
\r
// access alignment data\r
bool BamReader::GetNextAlignment(BamAlignment& bAlignment) { return d->GetNextAlignment(bAlignment); }\r
+bool BamReader::GetNextAlignmentCore(BamAlignment& bAlignment, BamAlignmentSupportData& supportData) { return d->GetNextAlignmentCore(bAlignment, supportData); }\r
\r
// access auxiliary data\r
const string BamReader::GetHeaderText(void) const { return d->HeaderText; }\r
int BamReader::GetReferenceCount(void) const { return d->References.size(); }\r
const RefVector BamReader::GetReferenceData(void) const { return d->References; }\r
int BamReader::GetReferenceID(const string& refName) const { return d->GetReferenceID(refName); }\r
-const std::string BamReader::GetFilename(void) const { return d->Filename; }
+const std::string BamReader::GetFilename(void) const { return d->Filename; }\r
\r
// index operations\r
bool BamReader::CreateIndex(void) { return d->CreateIndex(); }\r
// load next alignment until region overlap is found\r
while ( !IsOverlap(bAlignment) ) {\r
// if no valid alignment available (likely EOF) return failure\r
- if ( !LoadNextAlignment(bAlignment, supportData) ) { return false; }\r
+ if ( !LoadNextAlignment(bAlignment, supportData) ) return false;\r
}\r
\r
// return success (alignment found that overlaps region)\r
}\r
\r
// no valid alignment\r
- else { return false; }\r
+ else \r
+ return false;\r
+}\r
+\r
+// retrieves next available alignment core data (returns success/fail)\r
+// ** DOES NOT parse any character data (bases, qualities, tag data)\r
+// these can be accessed, if necessary, from the supportData \r
+// useful for operations requiring ONLY positional or other alignment-related information\r
+bool BamReader::BamReaderPrivate::GetNextAlignmentCore(BamAlignment& bAlignment, BamAlignmentSupportData& supportData) {\r
+\r
+ // if valid alignment available\r
+ if ( LoadNextAlignment(bAlignment, supportData) ) {\r
+\r
+ // if region not specified, return success\r
+ if ( !IsRegionSpecified ) return true;\r
+\r
+ // load next alignment until region overlap is found\r
+ while ( !IsOverlap(bAlignment) ) {\r
+ // if no valid alignment available (likely EOF) return failure\r
+ if ( !LoadNextAlignment(bAlignment, supportData) ) return false;\r
+ }\r
+\r
+ // return success (alignment found that overlaps region)\r
+ return true;\r
+ }\r
+\r
+ // no valid alignment\r
+ else\r
+ return false;\r
}\r
\r
// calculate closest indexed file offset for region specified\r
const uint64_t& lastOffset)\r
{\r
// get converted offsets\r
- int beginOffset = bAlignment.Position >> BAM_LIDX_SHIFT;
+ int beginOffset = bAlignment.Position >> BAM_LIDX_SHIFT;\r
int endOffset = (bAlignment.GetEndPosition() - 1) >> BAM_LIDX_SHIFT;\r
\r
// resize vector if necessary\r
// read starts after left boundary\r
if ( bAlignment.Position >= CurrentLeft) { return true; }\r
\r
- // return whether alignment end overlaps left boundary
+ // return whether alignment end overlaps left boundary\r
return ( bAlignment.GetEndPosition() >= CurrentLeft );\r
}\r
\r