// ***************************************************************************
// BamHeader_p.cpp (c) 2010 Derek Barnett
// Marth Lab, Department of Biology, Boston College
-// All rights reserved.
// ---------------------------------------------------------------------------
-// Last modified: 25 December 2010 (DB)
+// Last modified: 10 October 2011 (DB)
// ---------------------------------------------------------------------------
// Provides the basic functionality for handling BAM headers.
// ***************************************************************************
-#include <api/BamAux.h>
-#include <api/BamConstants.h>
-#include <api/BGZF.h>
-#include <api/internal/BamHeader_p.h>
+#include "api/BamAux.h"
+#include "api/BamConstants.h"
+#include "api/internal/BamException_p.h"
+#include "api/internal/BamHeader_p.h"
+#include "api/internal/BgzfStream_p.h"
using namespace BamTools;
using namespace BamTools::Internal;
-#include <cstdio>
#include <cstdlib>
#include <cstring>
-#include <iostream>
using namespace std;
-// ---------------------------------
-// BamHeaderPrivate implementation
+// ------------------------
+// static utility methods
+// ------------------------
-struct BamHeader::BamHeaderPrivate {
-
- // data members
- SamHeader* m_samHeader;
-
- // ctor
- BamHeaderPrivate(void)
- : m_samHeader(0)
- { }
-
- // 'public' interface
- bool Load(BgzfData* stream);
+static inline
+bool isValidMagicNumber(const char* buffer) {
+ return ( strncmp(buffer, Constants::BAM_HEADER_MAGIC,
+ Constants::BAM_HEADER_MAGIC_LENGTH) == 0 );
+}
- // internal methods
- bool CheckMagicNumber(BgzfData* stream);
- bool ReadHeaderLength(BgzfData* stream, uint32_t& length);
- bool ReadHeaderText(BgzfData* stream, const uint32_t& length);
-};
+// --------------------------
+// BamHeader implementation
+// --------------------------
-bool BamHeader::BamHeaderPrivate::Load(BgzfData* stream) {
+// ctor
+BamHeader::BamHeader(void) { }
- // cannot load if invalid stream
- if ( stream == 0 )
- return false;
+// dtor
+BamHeader::~BamHeader(void) { }
- // cannot load if magic number is invalid
- if ( !CheckMagicNumber(stream) )
- return false;
+// reads magic number from BGZF stream, returns true if valid
+void BamHeader::CheckMagicNumber(BgzfStream* stream) {
- // cannot load header if cannot read header length
- uint32_t length(0);
- if ( !ReadHeaderLength(stream, length) )
- return false;
+ // try to read magic number
+ char buffer[Constants::BAM_HEADER_MAGIC_LENGTH];
+ const size_t numBytesRead = stream->Read(buffer, Constants::BAM_HEADER_MAGIC_LENGTH);
+ if ( numBytesRead != (int)Constants::BAM_HEADER_MAGIC_LENGTH )
+ throw BamException("BamHeader::CheckMagicNumber", "could not read magic number");
- // cannot load header if cannot read header text
- if ( !ReadHeaderText(stream, length) )
- return false;
+ // validate magic number
+ if ( !isValidMagicNumber(buffer) )
+ throw BamException("BamHeader::CheckMagicNumber", "invalid magic number");
+}
- // otherwise, everything OK
- return true;
+// clear SamHeader data
+void BamHeader::Clear(void) {
+ m_header.Clear();
}
-bool BamHeader::BamHeaderPrivate::CheckMagicNumber(BgzfData* stream) {
+// return true if SamHeader data is valid
+bool BamHeader::IsValid(void) const {
+ return m_header.IsValid();
+}
- // try to read magic number
- char buffer[Constants::BAM_HEADER_MAGIC_SIZE];
- if ( stream->Read(buffer, Constants::BAM_HEADER_MAGIC_SIZE) != (int)Constants::BAM_HEADER_MAGIC_SIZE ) {
- fprintf(stderr, "BAM header error - could not read magic number\n");
- return false;
- }
+// load BAM header ('magic number' and SAM header text) from BGZF stream
+void BamHeader::Load(BgzfStream* stream) {
- // validate magic number
- if ( strncmp(buffer, Constants::BAM_HEADER_MAGIC, Constants::BAM_HEADER_MAGIC_SIZE) != 0 ) {
- fprintf(stderr, "BAM header error - invalid magic number\n");
- return false;
- }
+ // read & check magic number
+ CheckMagicNumber(stream);
- // all checks out
- return true;
+ // read header (length, then actual text)
+ uint32_t length(0);
+ ReadHeaderLength(stream, length);
+ ReadHeaderText(stream, length);
}
-bool BamHeader::BamHeaderPrivate::ReadHeaderLength(BgzfData* stream, uint32_t& length) {
+// reads SAM header text length from BGZF stream, stores it in @length
+void BamHeader::ReadHeaderLength(BgzfStream* stream, uint32_t& length) {
- // attempt to read BAM header text length
+ // read BAM header text length
char buffer[sizeof(uint32_t)];
- if ( stream->Read(buffer, sizeof(uint32_t)) != sizeof(uint32_t) ) {
- fprintf(stderr, "BAM header error - could not read header length\n");
- return false;
- }
+ const size_t numBytesRead = stream->Read(buffer, sizeof(uint32_t));
+ if ( numBytesRead != sizeof(uint32_t) )
+ throw BamException("BamHeader::ReadHeaderLength", "could not read header length");
- // convert char buffer to length, return success
- length = BgzfData::UnpackUnsignedInt(buffer);
+ // convert char buffer to length
+ length = BamTools::UnpackUnsignedInt(buffer);
if ( BamTools::SystemIsBigEndian() )
- SwapEndian_32(length);
- return true;
+ BamTools::SwapEndian_32(length);
}
-bool BamHeader::BamHeaderPrivate::ReadHeaderText(BgzfData* stream, const uint32_t& length) {
+// reads SAM header text from BGZF stream, stores in SamHeader object
+void BamHeader::ReadHeaderText(BgzfStream* stream, const uint32_t& length) {
- // set up destination buffer
+ // read header text
char* headerText = (char*)calloc(length + 1, 1);
+ const size_t bytesRead = stream->Read(headerText, length);
- // attempt to read header text
- const unsigned bytesRead = stream->Read(headerText, length);
- const bool readOk = ( bytesRead == length );
- if ( readOk )
- m_samHeader = new SamHeader( (string)((const char*)headerText) );
- else
- fprintf(stderr, "BAM header error - could not read header text\n");
+ // if error reading, clean up buffer & throw
+ if ( bytesRead != length ) {
+ free(headerText);
+ throw BamException("BamHeader::ReadHeaderText", "could not read header text");
+ }
- // clean up calloc-ed temp variable (on success or fail)
+ // otherwise, text was read OK
+ // store & cleanup
+ m_header.SetHeaderText( (string)((const char*)headerText) );
free(headerText);
-
- // return read success
- return readOk;
-}
-
-// --------------------------
-// BamHeader implementation
-
-BamHeader::BamHeader(void)
- : d(new BamHeaderPrivate)
-{ }
-
-BamHeader::~BamHeader(void) {
- delete d;
- d = 0;
-}
-
-void BamHeader::Clear(void) {
- delete d->m_samHeader;
- d->m_samHeader = new SamHeader("");
-}
-
-bool BamHeader::IsValid(void) const {
- return d->m_samHeader->IsValid();
-}
-
-bool BamHeader::Load(BgzfData* stream) {
- return d->Load(stream);
}
+// returns *copy* of SamHeader data object
SamHeader BamHeader::ToSamHeader(void) const {
- return *(d->m_samHeader);
+ return m_header;
}
+// returns SAM-formatted string of header data
string BamHeader::ToString(void) const {
- return d->m_samHeader->ToString();
+ return m_header.ToString();
}
projects / bamtools.git / blobdiff