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check read errors in fastqreader #533

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check read errors in fastqreader #533

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12 changes: 12 additions & 0 deletions src/fastqreader.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -84,6 +84,7 @@ void FastqReader::readToBufIgzip(){
if (mGzipState.avail_in == 0) {
mGzipState.next_in = mGzipInputBuffer;
mGzipState.avail_in = fread(mGzipState.next_in, 1, mGzipInputBufferSize, mFile);
check_error();
mGzipInputUsedBytes += mGzipState.avail_in;
}
mGzipState.next_out = mGzipOutputBuffer;
Expand All @@ -105,6 +106,7 @@ void FastqReader::readToBufIgzip(){
isal_inflate_reset(&mGzipState);
mGzipState.next_in = mGzipInputBuffer;
mGzipState.avail_in = fread(mGzipState.next_in, 1, mGzipInputBufferSize, mFile);
check_error();
mGzipInputUsedBytes += mGzipState.avail_in;
} else if (mGzipState.avail_in >= GZIP_HEADER_BYTES_REQ){
unsigned char* old_next_in = mGzipState.next_in;
Expand All @@ -118,6 +120,7 @@ void FastqReader::readToBufIgzip(){
size_t added = 0;
if(!eof()) {
added = fread(mGzipInputBuffer + mGzipState.avail_in, 1, mGzipInputBufferSize - mGzipState.avail_in, mFile);
check_error();
mGzipInputUsedBytes += added;
}
isal_inflate_reset(&mGzipState);
Expand Down Expand Up @@ -146,6 +149,7 @@ void FastqReader::readToBuf() {
} else {
if(!eof())
mBufDataLen = fread(mFastqBuf, 1, FQ_BUF_SIZE, mFile);
check_error();
}
mBufUsedLen = 0;

Expand All @@ -166,6 +170,7 @@ void FastqReader::init(){
mGzipState.crc_flag = ISAL_GZIP_NO_HDR_VER;
mGzipState.next_in = mGzipInputBuffer;
mGzipState.avail_in = fread(mGzipState.next_in, 1, mGzipInputBufferSize, mFile);
check_error();
mGzipInputUsedBytes += mGzipState.avail_in;
int ret = isal_read_gzip_header(&mGzipState, &mGzipHeader);
if (ret != ISAL_DECOMP_OK) {
Expand Down Expand Up @@ -216,6 +221,13 @@ bool FastqReader::eof() {
return feof(mFile);//mFile.eof();
}

void FastqReader::check_error() {
if(ferror(mFile)) {
std::perror("reading fastq failed");
error_exit("Failed reading: " + mFilename);
}
}

void FastqReader::getLine(string* line){
int copied = 0;

Expand Down
1 change: 1 addition & 0 deletions src/fastqreader.h
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Original file line number Diff line number Diff line change
Expand Up @@ -46,6 +46,7 @@ class FastqReader{
//do not call read() of a same FastqReader object from different threads concurrently
Read* read();
bool eof();
void check_error();
bool hasNoLineBreakAtEnd();
void setReadPool(ReadPool* rp);

Expand Down