From 1ee9b6b3d98a4bfd5a60c583bc7847c545a60e32 Mon Sep 17 00:00:00 2001
From: Erik Garrison <erik.garrison@bc.edu>
Date: Fri, 20 Aug 2010 12:22:34 -0400
Subject: [PATCH] change printf's to fprint(stderr,
This pushes errors to the expected output, stderr, instead of mixing
them into the standard output stream.
---
src/api/BGZF.cpp | 36 ++++++++++++++++++------------------
src/api/BamAux.h | 10 +++++-----
src/api/BamIndex.cpp | 18 +++++++++---------
src/api/BamReader.cpp | 12 ++++++------
src/api/BamWriter.cpp | 6 +++---
5 files changed, 41 insertions(+), 41 deletions(-)
diff --git a/src/api/BGZF.cpp b/src/api/BGZF.cpp
index 92afb96..2b74343 100644
--- a/src/api/BGZF.cpp
+++ b/src/api/BGZF.cpp
@@ -34,7 +34,7 @@ BgzfData::BgzfData(void)
CompressedBlock = new char[CompressedBlockSize];
UncompressedBlock = new char[UncompressedBlockSize];
} catch( std::bad_alloc& ba ) {
- printf("BGZF ERROR: unable to allocate memory for our BGZF object.\n");
+ fprintf(stderr, "BGZF ERROR: unable to allocate memory for our BGZF object.\n");
exit(1);
}
}
@@ -103,7 +103,7 @@ int BgzfData::DeflateBlock(void) {
// initialize the zlib compression algorithm
if ( deflateInit2(&zs, compressionLevel, Z_DEFLATED, GZIP_WINDOW_BITS, Z_DEFAULT_MEM_LEVEL, Z_DEFAULT_STRATEGY) != Z_OK ) {
- printf("BGZF ERROR: zlib deflate initialization failed.\n");
+ fprintf(stderr, "BGZF ERROR: zlib deflate initialization failed.\n");
exit(1);
}
@@ -117,26 +117,26 @@ int BgzfData::DeflateBlock(void) {
if ( status == Z_OK ) {
inputLength -= 1024;
if( inputLength < 0 ) {
- printf("BGZF ERROR: input reduction failed.\n");
+ fprintf(stderr, "BGZF ERROR: input reduction failed.\n");
exit(1);
}
continue;
}
- printf("BGZF ERROR: zlib::deflateEnd() failed.\n");
+ fprintf(stderr, "BGZF ERROR: zlib::deflateEnd() failed.\n");
exit(1);
}
// finalize the compression routine
if ( deflateEnd(&zs) != Z_OK ) {
- printf("BGZF ERROR: zlib::deflateEnd() failed.\n");
+ fprintf(stderr, "BGZF ERROR: zlib::deflateEnd() failed.\n");
exit(1);
}
compressedLength = zs.total_out;
compressedLength += BLOCK_HEADER_LENGTH + BLOCK_FOOTER_LENGTH;
if ( compressedLength > MAX_BLOCK_SIZE ) {
- printf("BGZF ERROR: deflate overflow.\n");
+ fprintf(stderr, "BGZF ERROR: deflate overflow.\n");
exit(1);
}
@@ -156,7 +156,7 @@ int BgzfData::DeflateBlock(void) {
int remaining = BlockOffset - inputLength;
if ( remaining > 0 ) {
if ( remaining > inputLength ) {
- printf("BGZF ERROR: after deflate, remainder too large.\n");
+ fprintf(stderr, "BGZF ERROR: after deflate, remainder too large.\n");
exit(1);
}
memcpy(UncompressedBlock, UncompressedBlock + inputLength, remaining);
@@ -179,7 +179,7 @@ void BgzfData::FlushBlock(void) {
int numBytesWritten = fwrite(CompressedBlock, 1, blockLength, Stream);
if ( numBytesWritten != blockLength ) {
- printf("BGZF ERROR: expected to write %u bytes during flushing, but wrote %u bytes.\n", blockLength, numBytesWritten);
+ fprintf(stderr, "BGZF ERROR: expected to write %u bytes during flushing, but wrote %u bytes.\n", blockLength, numBytesWritten);
exit(1);
}
@@ -201,20 +201,20 @@ int BgzfData::InflateBlock(const int& blockLength) {
int status = inflateInit2(&zs, GZIP_WINDOW_BITS);
if ( status != Z_OK ) {
- printf("BGZF ERROR: could not decompress block - zlib::inflateInit() failed\n");
+ fprintf(stderr, "BGZF ERROR: could not decompress block - zlib::inflateInit() failed\n");
return -1;
}
status = inflate(&zs, Z_FINISH);
if ( status != Z_STREAM_END ) {
inflateEnd(&zs);
- printf("BGZF ERROR: could not decompress block - zlib::inflate() failed\n");
+ fprintf(stderr, "BGZF ERROR: could not decompress block - zlib::inflate() failed\n");
return -1;
}
status = inflateEnd(&zs);
if ( status != Z_OK ) {
- printf("BGZF ERROR: could not decompress block - zlib::inflateEnd() failed\n");
+ fprintf(stderr, "BGZF ERROR: could not decompress block - zlib::inflateEnd() failed\n");
return -1;
}
@@ -230,7 +230,7 @@ bool BgzfData::Open(const string& filename, const char* mode, bool isWriteUncomp
else if ( strcmp(mode, "wb") == 0)
IsWriteOnly = true;
else {
- printf("BGZF ERROR: unknown file mode: %s\n", mode);
+ fprintf(stderr, "BGZF ERROR: unknown file mode: %s\n", mode);
return false;
}
@@ -251,7 +251,7 @@ bool BgzfData::Open(const string& filename, const char* mode, bool isWriteUncomp
Stream = freopen(NULL, mode, stdout);
if ( !Stream ) {
- printf("BGZF ERROR: unable to open file %s\n", filename.c_str() );
+ fprintf(stderr, "BGZF ERROR: unable to open file %s\n", filename.c_str() );
return false;
}
@@ -308,12 +308,12 @@ bool BgzfData::ReadBlock(void) {
}
if ( count != sizeof(header) ) {
- printf("BGZF ERROR: read block failed - could not read block header\n");
+ fprintf(stderr, "BGZF ERROR: read block failed - could not read block header\n");
return false;
}
if ( !BgzfData::CheckBlockHeader(header) ) {
- printf("BGZF ERROR: read block failed - invalid block header\n");
+ fprintf(stderr, "BGZF ERROR: read block failed - invalid block header\n");
return false;
}
@@ -324,13 +324,13 @@ bool BgzfData::ReadBlock(void) {
count = fread(&compressedBlock[BLOCK_HEADER_LENGTH], 1, remaining, Stream);
if ( count != remaining ) {
- printf("BGZF ERROR: read block failed - could not read data from block\n");
+ fprintf(stderr, "BGZF ERROR: read block failed - could not read data from block\n");
return false;
}
count = InflateBlock(blockLength);
if ( count < 0 ) {
- printf("BGZF ERROR: read block failed - could not decompress block data\n");
+ fprintf(stderr, "BGZF ERROR: read block failed - could not decompress block data\n");
return false;
}
@@ -351,7 +351,7 @@ bool BgzfData::Seek(int64_t position) {
int64_t blockAddress = (position >> 16) & 0xFFFFFFFFFFFFLL;
if ( fseek64(Stream, blockAddress, SEEK_SET) != 0 ) {
- printf("BGZF ERROR: unable to seek in file\n");
+ fprintf(stderr, "BGZF ERROR: unable to seek in file\n");
return false;
}
diff --git a/src/api/BamAux.h b/src/api/BamAux.h
index 73e8838..a39abb0 100644
--- a/src/api/BamAux.h
+++ b/src/api/BamAux.h
@@ -783,12 +783,12 @@ bool BamAlignment::GetTag(const std::string& tag, uint32_t& destination) const {
case 'f':
case 'Z':
case 'H':
- printf("ERROR: Cannot store tag of type %c in integer destination\n", type);
+ fprintf(stderr, "ERROR: Cannot store tag of type %c in integer destination\n", type);
return false;
// unknown tag type
default:
- printf("ERROR: Unknown tag storage class encountered: [%c]\n", type);
+ fprintf(stderr, "ERROR: Unknown tag storage class encountered: [%c]\n", type);
return false;
}
@@ -851,12 +851,12 @@ bool BamAlignment::GetTag(const std::string& tag, float& destination) const {
// unsupported type (var-length strings)
case 'Z':
case 'H':
- printf("ERROR: Cannot store tag of type %c in integer destination\n", type);
+ fprintf(stderr, "ERROR: Cannot store tag of type %c in integer destination\n", type);
return false;
// unknown tag type
default:
- printf("ERROR: Unknown tag storage class encountered: [%c]\n", type);
+ fprintf(stderr, "ERROR: Unknown tag storage class encountered: [%c]\n", type);
return false;
}
@@ -978,7 +978,7 @@ bool BamAlignment::SkipToNextTag(const char storageType, char* &pTagData, unsign
default:
// error case
- printf("ERROR: Unknown tag storage class encountered: [%c]\n", storageType);
+ fprintf(stderr, "ERROR: Unknown tag storage class encountered: [%c]\n", storageType);
return false;
}
diff --git a/src/api/BamIndex.cpp b/src/api/BamIndex.cpp
index d74e751..5f636d1 100644
--- a/src/api/BamIndex.cpp
+++ b/src/api/BamIndex.cpp
@@ -213,8 +213,8 @@ bool BamDefaultIndex::Build(void) {
// if lastCoordinate greater than BAM position - file not sorted properly
else if ( lastCoordinate > bAlignment.Position ) {
- printf("BAM file not properly sorted:\n");
- printf("Alignment %s : %d > %d on reference (id = %d)", bAlignment.Name.c_str(), lastCoordinate, bAlignment.Position, bAlignment.RefID);
+ fprintf(stderr, "BAM file not properly sorted:\n");
+ fprintf(stderr, "Alignment %s : %d > %d on reference (id = %d)", bAlignment.Name.c_str(), lastCoordinate, bAlignment.Position, bAlignment.RefID);
exit(1);
}
@@ -255,7 +255,7 @@ bool BamDefaultIndex::Build(void) {
// make sure that current file pointer is beyond lastOffset
if ( m_BGZF->Tell() <= (int64_t)lastOffset ) {
- printf("Error in BGZF offsets.\n");
+ fprintf(stderr, "Error in BGZF offsets.\n");
exit(1);
}
@@ -397,7 +397,7 @@ bool BamDefaultIndex::Load(const string& filename) {
// open index file, abort on error
FILE* indexStream = fopen(filename.c_str(), "rb");
if( !indexStream ) {
- printf("ERROR: Unable to open the BAM index file %s for reading.\n", filename.c_str());
+ fprintf(stderr, "ERROR: Unable to open the BAM index file %s for reading.\n", filename.c_str());
return false;
}
@@ -408,7 +408,7 @@ bool BamDefaultIndex::Load(const string& filename) {
char magic[4];
elementsRead = fread(magic, 1, 4, indexStream);
if ( strncmp(magic, "BAI\1", 4) ) {
- printf("Problem with index file - invalid format.\n");
+ fprintf(stderr, "Problem with index file - invalid format.\n");
fclose(indexStream);
return false;
}
@@ -578,7 +578,7 @@ bool BamDefaultIndex::Write(const std::string& bamFilename) {
string indexFilename = bamFilename + ".bai";
FILE* indexStream = fopen(indexFilename.c_str(), "wb");
if ( indexStream == 0 ) {
- printf("ERROR: Could not open file to save index.\n");
+ fprintf(stderr, "ERROR: Could not open file to save index.\n");
return false;
}
@@ -810,7 +810,7 @@ bool BamToolsIndex::Load(const string& filename) {
// open index file, abort on error
FILE* indexStream = fopen(filename.c_str(), "rb");
if( !indexStream ) {
- printf("ERROR: Unable to open the BAM index file %s for reading.\n", filename.c_str());
+ fprintf(stderr, "ERROR: Unable to open the BAM index file %s for reading.\n", filename.c_str());
return false;
}
@@ -821,7 +821,7 @@ bool BamToolsIndex::Load(const string& filename) {
char magic[4];
elementsRead = fread(magic, 1, 4, indexStream);
if ( strncmp(magic, "BTI\1", 4) ) {
- printf("Problem with index file - invalid format.\n");
+ fprintf(stderr, "Problem with index file - invalid format.\n");
fclose(indexStream);
return false;
}
@@ -876,7 +876,7 @@ bool BamToolsIndex::Write(const std::string& bamFilename) {
string indexFilename = bamFilename + ".bti";
FILE* indexStream = fopen(indexFilename.c_str(), "wb");
if ( indexStream == 0 ) {
- printf("ERROR: Could not open file to save index.\n");
+ fprintf(stderr, "ERROR: Could not open file to save index.\n");
return false;
}
diff --git a/src/api/BamReader.cpp b/src/api/BamReader.cpp
index b1b1b5d..bb70f1f 100644
--- a/src/api/BamReader.cpp
+++ b/src/api/BamReader.cpp
@@ -291,7 +291,7 @@ bool BamReader::BamReaderPrivate::BuildCharData(BamAlignment& bAlignment) {
break; // for 'H' - hard clip, do nothing to AlignedBases, move to next op
default:
- printf("ERROR: Invalid Cigar op type\n"); // shouldn't get here
+ fprintf(stderr, "ERROR: Invalid Cigar op type\n"); // shouldn't get here
exit(1);
}
}
@@ -339,7 +339,7 @@ bool BamReader::BamReaderPrivate::BuildCharData(BamAlignment& bAlignment) {
break;
default :
- printf("ERROR: Invalid tag value type\n"); // shouldn't get here
+ fprintf(stderr, "ERROR: Invalid tag value type\n"); // shouldn't get here
exit(1);
}
}
@@ -525,7 +525,7 @@ bool BamReader::BamReaderPrivate::Jump(int refID, int position) {
// determine possible offsets
vector<int64_t> offsets;
if ( !NewIndex->GetOffsets(Region, IsRightBoundSpecified, offsets) ) {
- printf("ERROR: Could not jump: unable to calculate offset for specified region.\n");
+ fprintf(stderr, "ERROR: Could not jump: unable to calculate offset for specified region.\n");
return false;
}
@@ -555,12 +555,12 @@ void BamReader::BamReaderPrivate::LoadHeaderData(void) {
// check to see if proper BAM header
char buffer[4];
if (mBGZF.Read(buffer, 4) != 4) {
- printf("Could not read header type\n");
+ fprintf(stderr, "Could not read header type\n");
exit(1);
}
if (strncmp(buffer, "BAM\001", 4)) {
- printf("wrong header type!\n");
+ fprintf(stderr, "wrong header type!\n");
exit(1);
}
@@ -602,7 +602,7 @@ bool BamReader::BamReaderPrivate::LoadIndex(void) {
// else unknown
else {
- printf("ERROR: Unknown index file extension.\n");
+ fprintf(stderr, "ERROR: Unknown index file extension.\n");
return false;
}
diff --git a/src/api/BamWriter.cpp b/src/api/BamWriter.cpp
index f83ff1c..2be38bb 100644
--- a/src/api/BamWriter.cpp
+++ b/src/api/BamWriter.cpp
@@ -131,7 +131,7 @@ void BamWriter::BamWriterPrivate::CreatePackedCigar(const vector<CigarOp>& cigar
cigarOp = BAM_CPAD;
break;
default:
- printf("ERROR: Unknown cigar operation found: %c\n", coIter->Type);
+ fprintf(stderr, "ERROR: Unknown cigar operation found: %c\n", coIter->Type);
exit(1);
}
@@ -182,7 +182,7 @@ void BamWriter::BamWriterPrivate::EncodeQuerySequence(const string& query, strin
break;
default:
- printf("ERROR: Only the following bases are supported in the BAM format: {=, A, C, G, T, N}. Found [%c]\n", *pQuery);
+ fprintf(stderr, "ERROR: Only the following bases are supported in the BAM format: {=, A, C, G, T, N}. Found [%c]\n", *pQuery);
exit(1);
}
@@ -417,7 +417,7 @@ void BamWriter::BamWriterPrivate::SaveAlignment(const BamAlignment& al) {
break;
default :
- printf("ERROR: Invalid tag value type\n"); // shouldn't get here
+ fprintf(stderr, "ERROR: Invalid tag value type\n"); // shouldn't get here
free(tagData);
exit(1);
}
--
2.39.5