Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Fix for 2 bugs in the fastq reader: #497

Open
wants to merge 1 commit into
base: master
Choose a base branch
from
Open

Fix for 2 bugs in the fastq reader: #497

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
49 changes: 35 additions & 14 deletions src/fastqreader.cpp
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -33,6 +33,7 @@ SOFTWARE.

FastqReader::FastqReader(string filename, bool hasQuality, bool phred64){
mFilename = filename;
mSkipNewline = false;
mZipped = false;
mFile = NULL;
mStdinMode = false;
Expand Down Expand Up @@ -223,6 +224,15 @@ void FastqReader::getLine(string* line){
int end = start;

while(end < mBufDataLen) {
// May still need to skip \n from a \r\n pair
if (mSkipNewline) {
mSkipNewline = false;
if (mFastqBuf[end] == '\n') {
start++;
end++;
continue;
}
}
if(mFastqBuf[end] != '\r' && mFastqBuf[end] != '\n')
end++;
else
Expand All @@ -236,9 +246,9 @@ void FastqReader::getLine(string* line){

// skip \n or \r
end++;
// handle \r\n
if(end < mBufDataLen-1 && mFastqBuf[end-1]=='\r' && mFastqBuf[end] == '\n')
end++;
// handle \r\n - not now because we may be at end of buffer
if(mFastqBuf[end-1]=='\r')
mSkipNewline = true;

mBufUsedLen = end;

Expand All @@ -252,7 +262,18 @@ void FastqReader::getLine(string* line){
readToBuf();
start = 0;
end = 0;


while(end < mBufDataLen) {
// May still need to skip \n from a \r\n pair
if (mSkipNewline) {
mSkipNewline = false;
if (mFastqBuf[end] == '\n') {
start++;
end++;
continue;
}
}
if(mFastqBuf[end] != '\r' && mFastqBuf[end] != '\n')
end++;
else
Expand All @@ -265,9 +286,9 @@ void FastqReader::getLine(string* line){

// skip \n or \r
end++;
// handle \r\n
if(end < mBufDataLen-1 && mFastqBuf[end] == '\n')
end++;
// handle \r\n - not now because we may be at end of buffer
if(mFastqBuf[end-1] == '\r')
mSkipNewline = true;

mBufUsedLen = end;
return;
Expand All @@ -280,10 +301,6 @@ void FastqReader::getLine(string* line){
}

Read* FastqReader::read(){
if(mBufUsedLen >= mBufDataLen && bufferFinished()) {
return NULL;
}

string* name;
string* sequence;
string* strand;
Expand All @@ -306,12 +323,16 @@ Read* FastqReader::read(){
}

getLine(name);
if(name->empty() && mBufUsedLen >= mBufDataLen && bufferFinished()) {
// EOF is triggered only after reading past end of file; that
// can happen at the start of a new read.
return NULL;
}
// name should start with @
while((name->empty() && !(mBufUsedLen >= mBufDataLen && bufferFinished())) || (!name->empty() && (*name)[0]!='@')){
getLine(name);
if (name->empty() || (*name)[0]!='@') {
cerr << *name << endl;
error_exit("Read name line should start with '@'");
}
if(name->empty())
return NULL;

getLine(sequence);
getLine(strand);
Expand Down
1 change: 1 addition & 0 deletions src/fastqreader.h
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -65,6 +65,7 @@ class FastqReader{

private:
string mFilename;
bool mSkipNewline;
struct isal_gzip_header mGzipHeader;
struct inflate_state mGzipState;
unsigned char *mGzipInputBuffer;
Expand Down