From ab96a16b4af2581ce5971da4dd426a7ea555ffdd Mon Sep 17 00:00:00 2001
From: Aaron <aaronquinlan@gmail.com>
Date: Mon, 11 Jan 2010 15:50:21 -0500
Subject: [PATCH] Added Derek's changes to BamTools that were causing compile
errors.
---
src/utils/BamTools/BGZF.cpp | 54 ++++++++++-----------
src/utils/BamTools/BGZF.h | 32 +++++++------
src/utils/BamTools/BamAux.h | 80 ++++++++++++++++++--------------
src/utils/BamTools/BamReader.cpp | 22 +++++----
src/utils/BamTools/BamWriter.cpp | 1 -
5 files changed, 101 insertions(+), 88 deletions(-)
diff --git a/src/utils/BamTools/BGZF.cpp b/src/utils/BamTools/BGZF.cpp
index d0242d6c..225ddf08 100644
--- a/src/utils/BamTools/BGZF.cpp
+++ b/src/utils/BamTools/BGZF.cpp
@@ -3,7 +3,7 @@
// Marth Lab, Department of Biology, Boston College
// All rights reserved.
// ---------------------------------------------------------------------------
-// Last modified: 8 December 2009 (DB)
+// Last modified: 11 January 2010 (DB)
// ---------------------------------------------------------------------------
// BGZF routines were adapted from the bgzf.c code developed at the Broad
// Institute.
@@ -40,19 +40,24 @@ BgzfData::BgzfData(void)
// destructor
BgzfData::~BgzfData(void) {
- if(CompressedBlock) delete [] CompressedBlock;
- if(UncompressedBlock) delete [] UncompressedBlock;
+ if(CompressedBlock) { delete[] CompressedBlock; }
+ if(UncompressedBlock) { delete[] UncompressedBlock; }
}
// closes BGZF file
void BgzfData::Close(void) {
+ // skip if file not open, otherwise set flag
if (!IsOpen) { return; }
IsOpen = false;
- // flush the BGZF block
- if ( IsWriteOnly ) { FlushBlock(); }
+ // flush the current BGZF block
+ if (IsWriteOnly) { FlushBlock(); }
+ // write an empty block (as EOF marker)
+ int blockLength = DeflateBlock();
+ fwrite(CompressedBlock, 1, blockLength, Stream);
+
// flush and close
fflush(Stream);
fclose(Stream);
@@ -63,8 +68,6 @@ int BgzfData::DeflateBlock(void) {
// initialize the gzip header
char* buffer = CompressedBlock;
- unsigned int bufferSize = CompressedBlockSize;
-
memset(buffer, 0, 18);
buffer[0] = GZIP_ID1;
buffer[1] = (char)GZIP_ID2;
@@ -79,9 +82,11 @@ int BgzfData::DeflateBlock(void) {
// loop to retry for blocks that do not compress enough
int inputLength = BlockOffset;
int compressedLength = 0;
+ unsigned int bufferSize = CompressedBlockSize;
while(true) {
-
+
+ // initialize zstream values
z_stream zs;
zs.zalloc = NULL;
zs.zfree = NULL;
@@ -89,7 +94,7 @@ int BgzfData::DeflateBlock(void) {
zs.avail_in = inputLength;
zs.next_out = (Bytef*)&buffer[BLOCK_HEADER_LENGTH];
zs.avail_out = bufferSize - BLOCK_HEADER_LENGTH - BLOCK_FOOTER_LENGTH;
-
+
// initialize the zlib compression algorithm
if(deflateInit2(&zs, Z_DEFAULT_COMPRESSION, Z_DEFLATED, GZIP_WINDOW_BITS, Z_DEFAULT_MEM_LEVEL, Z_DEFAULT_STRATEGY) != Z_OK) {
printf("ERROR: zlib deflate initialization failed.\n");
@@ -171,8 +176,8 @@ void BgzfData::FlushBlock(void) {
if(numBytesWritten != blockLength) {
printf("ERROR: Expected to write %u bytes during flushing, but wrote %u bytes.\n", blockLength, numBytesWritten);
exit(1);
- }
-
+ }
+
BlockAddress += blockLength;
}
}
@@ -213,6 +218,7 @@ int BgzfData::InflateBlock(const int& blockLength) {
void BgzfData::Open(const string& filename, const char* mode) {
+ // determine open mode
if ( strcmp(mode, "rb") == 0 ) {
IsWriteOnly = false;
} else if ( strcmp(mode, "wb") == 0) {
@@ -222,25 +228,21 @@ void BgzfData::Open(const string& filename, const char* mode) {
exit(1);
}
- /***********************************************************
- ARQ, 2010-Jan-03: set Stream to a file, stdin, or stdout.
- ************************************************************/
- if ( (filename != "stdin") && (filename != "stdout") ) { // BAM to/from file
- // open the file using the requested mode
+ // open Stream to read to/write from file, stdin, or stdout
+ // stdin/stdout option contributed by Aaron Quinlan (2010-Jan-03)
+ if ( (filename != "stdin") && (filename != "stdout") ) {
+ // read/wrtie BGZF data to/from a file
Stream = fopen(filename.c_str(), mode);
}
- else if ( (filename == "stdin") && (strcmp(mode, "rb") == 0 ) ) { // BAM from stdin
- // need freopen() as stdin is already open
- Stream = freopen(NULL, mode, stdin);
- }
- else if ( (filename == "stdout") && (strcmp(mode, "wb") == 0) ) { // BAM to stdout
- // need freopen() as stdout is already open
+ else if ( (filename == "stdin") && (strcmp(mode, "rb") == 0 ) ) {
+ // read BGZF data from stdin
+ Stream = freopen(NULL, mode, stdin);
+ }
+ else if ( (filename == "stdout") && (strcmp(mode, "wb") == 0) ) {
+ // write BGZF data to stdout
Stream = freopen(NULL, mode, stdout);
}
- /***********************************************************
- End ARQ, 2010-Jan-03
- ************************************************************/
-
+
if(!Stream) {
printf("ERROR: Unable to open the BAM file %s\n", filename.c_str() );
exit(1);
diff --git a/src/utils/BamTools/BGZF.h b/src/utils/BamTools/BGZF.h
index 28965427..894e460e 100644
--- a/src/utils/BamTools/BGZF.h
+++ b/src/utils/BamTools/BGZF.h
@@ -3,7 +3,7 @@
// Marth Lab, Department of Biology, Boston College
// All rights reserved.
// ---------------------------------------------------------------------------
-// Last modified: 8 December 2009 (DB)
+// Last modified: 11 January 2010 (DB)
// ---------------------------------------------------------------------------
// BGZF routines were adapted from the bgzf.c code developed at the Broad
// Institute.
@@ -26,18 +26,21 @@
#include "zlib.h"
// Platform-specific type definitions
-#ifdef _MSC_VER
- typedef char int8_t;
- typedef unsigned char uint8_t;
- typedef short int16_t;
- typedef unsigned short uint16_t;
- typedef int int32_t;
- typedef unsigned int uint32_t;
- typedef long long int64_t;
- typedef unsigned long long uint64_t;
-#else
- #include <stdint.h>
-#endif
+#ifndef BAMTOOLS_TYPES
+#define BAMTOOLS_TYPES
+ #ifdef _MSC_VER
+ typedef char int8_t;
+ typedef unsigned char uint8_t;
+ typedef short int16_t;
+ typedef unsigned short uint16_t;
+ typedef int int32_t;
+ typedef unsigned int uint32_t;
+ typedef long long int64_t;
+ typedef unsigned long long uint64_t;
+ #else
+ #include <stdint.h>
+ #endif
+#endif // BAMTOOLS_TYPES
namespace BamTools {
@@ -117,7 +120,6 @@ struct BgzfData {
inline
bool BgzfData::CheckBlockHeader(char* header) {
-
return (header[0] == GZIP_ID1 &&
header[1] == (char)GZIP_ID2 &&
header[2] == Z_DEFLATED &&
@@ -171,7 +173,7 @@ unsigned int BgzfData::UnpackUnsignedInt(char* buffer) {
// unpacks a buffer into an unsigned short
inline
unsigned short BgzfData::UnpackUnsignedShort(char* buffer) {
- union { unsigned short value; unsigned char valueBuffer[sizeof(unsigned short)];} un;
+ union { unsigned short value; unsigned char valueBuffer[sizeof(unsigned short)]; } un;
un.value = 0;
un.valueBuffer[0] = buffer[0];
un.valueBuffer[1] = buffer[1];
diff --git a/src/utils/BamTools/BamAux.h b/src/utils/BamTools/BamAux.h
index 5f5eee38..fb046421 100644
--- a/src/utils/BamTools/BamAux.h
+++ b/src/utils/BamTools/BamAux.h
@@ -3,7 +3,7 @@
// Marth Lab, Department of Biology, Boston College
// All rights reserved.
// ---------------------------------------------------------------------------
-// Last modified: 8 December 2009 (DB)
+// Last modified: 11 Janaury 2010 (DB)
// ---------------------------------------------------------------------------
// Provides the basic constants, data structures, etc. for using BAM files
// ***************************************************************************
@@ -12,6 +12,7 @@
#define BAMAUX_H
// C inclues
+#include <cstdio>
#include <cstdlib>
#include <cstring>
@@ -22,6 +23,23 @@
#include <utility>
#include <vector>
+// Platform-specific type definitions
+#ifndef BAMTOOLS_TYPES
+#define BAMTOOLS_TYPES
+ #ifdef _MSC_VER
+ typedef char int8_t;
+ typedef unsigned char uint8_t;
+ typedef short int16_t;
+ typedef unsigned short uint16_t;
+ typedef int int32_t;
+ typedef unsigned int uint32_t;
+ typedef long long int64_t;
+ typedef unsigned long long uint64_t;
+ #else
+ #include <stdint.h>
+ #endif
+#endif // BAMTOOLS_TYPES
+
namespace BamTools {
// BAM constants
@@ -73,41 +91,31 @@ struct BamAlignment {
// Returns true if alignment is second mate on read
bool IsSecondMate(void) const { return ( (AlignmentFlag & READ_2) != 0 ); }
-
- /*
- Aaron's Additions
- */
-
-
- // Sets "PCR duplicate" bit to TRUE
- void SetAsDuplicate(void) { AlignmentFlag |= DUPLICATE; }
- // Sets "failed quality control" bit to TRUE
- void SetAsFailedQC(void) { AlignmentFlag |= QC_FAILED; }
- // Sets "alignment is first mate" bit to TRUE
- void SetAsFirstMate(void) { AlignmentFlag |= READ_1; }
- // Sets "alignment is mapped" bit to TRUE
- void SetAsUnMapped(void) { AlignmentFlag |= UNMAPPED; }
- // Sets "alignment's mate is mapped" bit to TRUE
- void SetAsMateUnMapped(void) { AlignmentFlag |= MATE_UNMAPPED; }
- // Sets "alignment's mate mapped to reverse strand" bit to TRUE
- void SetAsMateReverseStrand(void) { AlignmentFlag |= MATE_REVERSE; }
- // Sets "alignment part of paired-end read" bit to TRUE
- void SetAsPaired(void) { AlignmentFlag |= PAIRED; }
- // Sets "position is primary alignment (determined by external app)" to true.
- void SetAsSecondaryAlignment(void) { AlignmentFlag |= SECONDARY; }
- // Sets "alignment is part of read that satisfied paired-end resolution" bit to TRUE
- void SetAsProperPair(void) { AlignmentFlag |= PROPER_PAIR; }
- // Sets "alignment mapped to reverse strand" bit to TRUE
- void SetAsReverseStrand(void) { AlignmentFlag |= REVERSE; }
- // Sets "alignment is second mate on read" bit to TRUE
- void SetAsSecondMate(void) { AlignmentFlag |= READ_2; }
-
+ // Manipulate alignment flag
+ public:
+ // Sets "PCR duplicate" bit
+ void SetIsDuplicate(bool ok) { if (ok) AlignmentFlag |= DUPLICATE; else AlignmentFlag &= ~DUPLICATE; }
+ // Sets "failed quality control" bit
+ void SetIsFailedQC(bool ok) { if (ok) AlignmentFlag |= QC_FAILED; else AlignmentFlag &= ~QC_FAILED; }
+ // Sets "alignment is first mate" bit
+ void SetIsFirstMate(bool ok) { if (ok) AlignmentFlag |= READ_1; else AlignmentFlag &= ~READ_1; }
+ // Sets "alignment's mate is mapped" bit
+ void SetIsMateUnmapped(bool ok) { if (ok) AlignmentFlag |= MATE_UNMAPPED; else AlignmentFlag &= ~MATE_UNMAPPED; }
+ // Sets "alignment's mate mapped to reverse strand" bit
+ void SetIsMateReverseStrand(bool ok) { if (ok) AlignmentFlag |= MATE_REVERSE; else AlignmentFlag &= ~MATE_REVERSE; }
+ // Sets "alignment part of paired-end read" bit
+ void SetIsPaired(bool ok) { if (ok) AlignmentFlag |= PAIRED; else AlignmentFlag &= ~PAIRED; }
+ // Sets "alignment is part of read that satisfied paired-end resolution" bit
+ void SetIsProperPair(bool ok) { if (ok) AlignmentFlag |= PROPER_PAIR; else AlignmentFlag &= ~PROPER_PAIR; }
+ // Sets "alignment mapped to reverse strand" bit
+ void SetIsReverseStrand(bool ok) { if (ok) AlignmentFlag |= REVERSE; else AlignmentFlag &= ~REVERSE; }
+ // Sets "position is primary alignment (determined by external app)"
+ void SetIsSecondaryAlignment(bool ok) { if (ok) AlignmentFlag |= SECONDARY; else AlignmentFlag &= ~SECONDARY; }
+ // Sets "alignment is second mate on read" bit
+ void SetIsSecondMate(bool ok) { if (ok) AlignmentFlag |= READ_2; else AlignmentFlag &= ~READ_2; }
+ // Sets "alignment is mapped" bit
+ void SetIsUnmapped(bool ok) { if (ok) AlignmentFlag |= UNMAPPED; else AlignmentFlag &= ~UNMAPPED; }
- void SetInsertSize(int32_t size) { InsertSize = size; }
- /*
- END: Aaron's Additions
- */
-
public:
// get "RG" tag data
@@ -233,7 +241,7 @@ struct BamAlignment {
int32_t Position; // Position (0-based) where alignment starts
uint16_t Bin; // Bin in BAM file where this alignment resides
uint16_t MapQuality; // Mapping quality score
- uint32_t AlignmentFlag; // Alignment bit-flag - see Is<something>() methods for available queries
+ uint32_t AlignmentFlag; // Alignment bit-flag - see Is<something>() methods to query this value, SetIs<something>() methods to manipulate
std::vector<CigarOp> CigarData; // CIGAR operations for this alignment
int32_t MateRefID; // ID number for reference sequence where alignment's mate was aligned
int32_t MatePosition; // Position (0-based) where alignment's mate starts
diff --git a/src/utils/BamTools/BamReader.cpp b/src/utils/BamTools/BamReader.cpp
index 560b5679..5dd65f22 100644
--- a/src/utils/BamTools/BamReader.cpp
+++ b/src/utils/BamTools/BamReader.cpp
@@ -3,7 +3,7 @@
// Marth Lab, Department of Biology, Boston College
// All rights reserved.
// ---------------------------------------------------------------------------
-// Last modified: 8 December 2009 (DB)
+// Last modified: 11 January 2010(DB)
// ---------------------------------------------------------------------------
// Uses BGZF routines were adapted from the bgzf.c code developed at the Broad
// Institute.
@@ -586,9 +586,11 @@ bool BamReader::BamReaderPrivate::LoadIndex(void) {
return false;
}
+ size_t elementsRead = 0;
+
// see if index is valid BAM index
char magic[4];
- fread(magic, 1, 4, indexStream);
+ elementsRead = fread(magic, 1, 4, indexStream);
if (strncmp(magic, "BAI\1", 4)) {
printf("Problem with index file - invalid format.\n");
fclose(indexStream);
@@ -597,7 +599,7 @@ bool BamReader::BamReaderPrivate::LoadIndex(void) {
// get number of reference sequences
uint32_t numRefSeqs;
- fread(&numRefSeqs, 4, 1, indexStream);
+ elementsRead = fread(&numRefSeqs, 4, 1, indexStream);
// intialize space for BamIndex data structure
Index.reserve(numRefSeqs);
@@ -607,7 +609,7 @@ bool BamReader::BamReaderPrivate::LoadIndex(void) {
// get number of bins for this reference sequence
int32_t numBins;
- fread(&numBins, 4, 1, indexStream);
+ elementsRead = fread(&numBins, 4, 1, indexStream);
if (numBins > 0) {
RefData& refEntry = References[i];
@@ -622,11 +624,11 @@ bool BamReader::BamReaderPrivate::LoadIndex(void) {
// get binID
uint32_t binID;
- fread(&binID, 4, 1, indexStream);
+ elementsRead = fread(&binID, 4, 1, indexStream);
// get number of regionChunks in this bin
uint32_t numChunks;
- fread(&numChunks, 4, 1, indexStream);
+ elementsRead = fread(&numChunks, 4, 1, indexStream);
// intialize ChunkVector
ChunkVector regionChunks;
@@ -638,8 +640,8 @@ bool BamReader::BamReaderPrivate::LoadIndex(void) {
// get chunk boundaries (left, right)
uint64_t left;
uint64_t right;
- fread(&left, 8, 1, indexStream);
- fread(&right, 8, 1, indexStream);
+ elementsRead = fread(&left, 8, 1, indexStream);
+ elementsRead = fread(&right, 8, 1, indexStream);
// save ChunkPair
regionChunks.push_back( Chunk(left, right) );
@@ -656,7 +658,7 @@ bool BamReader::BamReaderPrivate::LoadIndex(void) {
// get number of linear offsets
int32_t numLinearOffsets;
- fread(&numLinearOffsets, 4, 1, indexStream);
+ elementsRead = fread(&numLinearOffsets, 4, 1, indexStream);
// intialize LinearOffsetVector
LinearOffsetVector offsets;
@@ -666,7 +668,7 @@ bool BamReader::BamReaderPrivate::LoadIndex(void) {
uint64_t linearOffset;
for (int j = 0; j < numLinearOffsets; ++j) {
// read a linear offset & store
- fread(&linearOffset, 8, 1, indexStream);
+ elementsRead = fread(&linearOffset, 8, 1, indexStream);
offsets.push_back(linearOffset);
}
diff --git a/src/utils/BamTools/BamWriter.cpp b/src/utils/BamTools/BamWriter.cpp
index 1e30a567..c834d45a 100644
--- a/src/utils/BamTools/BamWriter.cpp
+++ b/src/utils/BamTools/BamWriter.cpp
@@ -276,7 +276,6 @@ void BamWriter::BamWriterPrivate::SaveAlignment(const BamAlignment& al) {
// write the base qualities
string baseQualities = al.Qualities;
char* pBaseQualities = (char*)al.Qualities.data();
-
for(unsigned int i = 0; i < queryLen; i++) { pBaseQualities[i] -= 33; }
mBGZF.Write(pBaseQualities, queryLen);
--
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