void
GLScreenBuffer::DeprecatedReadback(SharedSurface_GL* src, gfxImageSurface* dest)
{
MOZ_ASSERT(src && dest);
MOZ_ASSERT(ToIntSize(dest->GetSize()) == src->Size());
MOZ_ASSERT(dest->Format() == (src->HasAlpha() ? gfxImageFormat::ARGB32
: gfxImageFormat::RGB24));
mGL->MakeCurrent();
bool needsSwap = src != SharedSurf();
if (needsSwap) {
SharedSurf()->UnlockProd();
src->LockProd();
}
ReadBuffer* buffer = CreateRead(src);
MOZ_ASSERT(buffer);
ScopedBindFramebuffer autoFB(mGL, buffer->FB());
ReadPixelsIntoImageSurface(mGL, dest);
delete buffer;
if (needsSwap) {
src->UnlockProd();
SharedSurf()->LockProd();
}
}
int main(int argc, char *argv[]){
Read *Read = CreateRead(65536+GUARD, 65535+GUARD);
int32_t seqSize = 0, x, n;
uint64_t cutted = 0, totalReads = 0;
if(argc < 2 || ArgBin(0, argv, argc, "-h") || ArgBin(0, argv, argc, "?")){
PrintArgs(argv[0]);
return EXIT_SUCCESS;
}
int k = ArgNum(5, argv, argc, "-k", 0, 9999999);
int min_QS_window = ArgNum(25, argv, argc, "-w", 0, 9999999);
int min_QS = ArgNum(33, argv, argc, "-m", 0, 9999999);
fprintf(stderr, "Minimum QS: %d\n", min_QS);
uint32_t position = 0;
while(GetRead(stdin, Read)){
seqSize = strlen((char *) Read->bases) - 1;
for(x = seqSize ; x >= 0 ; x--){
if(x >= k){
int tmp_QS = 0;
for(n = 0 ; n < k ; ++n){
tmp_QS += ((int) Read->scores[x - 1 - n]) - min_QS;
}
if(((double) tmp_QS / k) < (double) min_QS_window){
++cutted;
position = x;
break;
}
}
}
++totalReads;
if(x > seqSize - k) continue;
// PRINT READ
fprintf(stdout, "@");
for(n = 0 ; n < strlen((char *) Read->header1) ; ++n)
fprintf(stdout, "%c", Read->header1[n]);
for(n = position ; n < seqSize ; ++n)
fprintf(stdout, "%c", Read->bases[n]);
fprintf(stdout, "\n+\n");
for(n = position ; n < seqSize ; ++n)
fprintf(stdout, "%c", Read->scores[n]);
fprintf(stdout, "\n");
}
fprintf(stderr, "Total reads : %"PRIu64"\n", totalReads);
fprintf(stderr, "Trimmed reads : %"PRIu64"\n", cutted);
FreeRead(Read);
return EXIT_SUCCESS;
}
int main(int argc, char *argv[]){
Read *Read = CreateRead(65536+GUARD, 65535+GUARD);
int32_t seqSize = 0, x;
uint64_t *QS = (uint64_t *) Calloc(65536, sizeof(uint64_t));
if(ArgBin(0, argv, argc, "-h") || ArgBin(0, argv, argc, "?")){
PrintArgs(argv[0]);
return EXIT_SUCCESS;
}
while(GetRead(stdin, Read)){
seqSize = strlen((char *) Read->bases) - 1;
for(x = 0 ; x < seqSize ; ++x){
int tmp_QS = (int) Read->scores[x];
if(QS[x] < tmp_QS)
QS[x] = tmp_QS;
if(x == 65535){
fprintf(stderr, "Error: read to long. Increase buffer!\n");
exit(1);
}
}
}
int maxs = atoi(argv[argc-1]);
for(x = 0 ; x < maxs ; ++x)
fprintf(stdout, "%2d ", x+1);
fprintf(stdout, "\n");
for(x = 0 ; x < maxs ; ++x)
fprintf(stdout, "--+");
fprintf(stdout, "\n");
for(x = 0 ; x < maxs ; ++x)
fprintf(stdout, "%2d ", (int) QS[x]);
fprintf(stdout, "\n");
Free(QS, 0);
FreeRead(Read);
return EXIT_SUCCESS;
}
void
GLScreenBuffer::Attach(SharedSurface* surface, const gfx::IntSize& size)
{
ScopedBindFramebuffer autoFB(mGL);
SharedSurface_GL* surf = SharedSurface_GL::Cast(surface);
if (mRead && SharedSurf())
SharedSurf()->UnlockProd();
surf->LockProd();
if (mRead &&
surf->AttachType() == SharedSurf()->AttachType() &&
size == Size())
{
// Same size, same type, ready for reuse!
mRead->Attach(surf);
} else {
// Else something changed, so resize:
DrawBuffer* draw = CreateDraw(size); // Can be null.
ReadBuffer* read = CreateRead(surf);
MOZ_ASSERT(read); // Should never fail if SwapProd succeeded.
delete mDraw;
delete mRead;
mDraw = draw;
mRead = read;
}
// Check that we're all set up.
MOZ_ASSERT(SharedSurf() == surf);
if (!PreserveBuffer()) {
// DiscardFramebuffer here could help perf on some mobile platforms.
}
}
int main(int argc, char *argv[]){
Read *Read = CreateRead(65536+GUARD, 65535+GUARD);
uint32_t seqSize = 0, totalQS = 0, N = 0, x, n;
uint64_t okReads = 0, totalReads = 0;
if(ArgBin(0, argv, argc, "-h") || ArgBin(0, argv, argc, "?")){
PrintArgs(argv[0]);
return EXIT_SUCCESS;
}
int max_n = ArgNum(0, argv, argc, "-n", 0, 9999999);
int k = ArgNum(5, argv, argc, "-k", 0, 9999999);
int min_QS_window = ArgNum(25, argv, argc, "-w", 0, 9999999);
int min_avg_qs = ArgNum(25, argv, argc, "-a", 0, 9999999);
int min_read_size = ArgNum(35, argv, argc, "-m", 0, 9999999);
// LOAD PARAMETERS
while(GetRead(stdin, Read)){
seqSize = strlen((char *) Read->bases) - 1;
totalQS = 0;
N = 0;
for(x = 0 ; x < seqSize ; ++x){
if(Read->bases[x] == 'N'){
++N;
}
totalQS += ((int) Read->scores[x]) - 33; // PHRED +33
if(x < seqSize - k){
int tmp_QS = 0;
for(n = 0 ; n < k ; ++n)
tmp_QS += ((int) Read->scores[x + n]) - 33;
if(tmp_QS / k < min_QS_window)
break;
}
}
++totalReads;
// EVALUATE TO DISCARD:
if(N > max_n) continue;
if((totalQS / seqSize) < min_avg_qs) continue;
if(x < min_read_size) continue;
// PRINT READ
for(n = 0 ; n < strlen((char *) Read->header1) ; ++n)
fprintf(stdout, "%c", Read->header1[n]);
for(n = 0 ; n < x ; ++n)
fprintf(stdout, "%c", Read->bases[n]);
fprintf(stdout, "\n+\n");
for(n = 0 ; n < x ; ++n)
fprintf(stdout, "%c", Read->scores[n]);
fprintf(stdout, "\n");
++okReads;
}
fprintf(stderr, "Total reads : %"PRIu64"\n", totalReads);
fprintf(stderr, "Filtered reads : %"PRIu64"\n", totalReads-okReads);
FreeRead(Read);
return EXIT_SUCCESS;
}
/*
* This application filters the FASTQ reads with the length higher than the value defined
*/
int main(int argc, char *argv[])
{
Read *Read = CreateRead(65536+GUARD, 65535+GUARD);
uint32_t sequenceSize = 0, index;
uint64_t okReads = 0, totalReads = 0;
int min_read_size = 0;
char *programName = argv[0];
struct argparse_option options[] = {
OPT_HELP(),
OPT_GROUP("Basic options"),
OPT_INTEGER('s', "size", &min_read_size, "The maximum read length"),
OPT_BUFF('<', "input.fastq", "Input FASTQ file format (stdin)"),
OPT_BUFF('>', "output", "Output read information (stdout)"),
OPT_END(),
};
struct argparse argparse;
char usage[250] = "\nExample: ";
strcat(usage, programName);
strcat(usage, " < input.fastq > output\n"
"\nOutput example :\n"
"<FASTQ non-filtered reads>\n"
"Total reads : value\n"
"Filtered reads : value\n");
argparse_init(&argparse, options, NULL, programName, 0);
argparse_describe(&argparse, "\nIt filters the FASTQ reads with the length higher than the value defined. "
"If present, it will erase the second header (after +).", usage);
argc = argparse_parse(&argparse, argc, argv);
if(argc != 0)
argparse_help_cb(&argparse, options);
if(min_read_size <= 0 || min_read_size > UINT_MAX)
{
fprintf(stderr, "\nERROR: The size value most be a positive unsigned int!\n");
argparse_help_cb(&argparse, options);
exit(1);
}
while(GetRead(stdin, Read))
{
sequenceSize = strlen((char *) Read->bases) - 1;
++totalReads;
// Evaluate to discard
if(sequenceSize > min_read_size) continue;
// Print the read
fprintf(stdout, "@");
for(index = 0 ; index < strlen((char *) Read->header1) ; ++index)
fprintf(stdout, "%c", Read->header1[index]);
for(index = 0 ; index < sequenceSize ; ++index)
fprintf(stdout, "%c", Read->bases[index]);
fprintf(stdout, "\n+\n");
for(index = 0 ; index < sequenceSize ; ++index)
fprintf(stdout, "%c", Read->scores[index]);
fprintf(stdout, "\n");
++okReads;
}
fprintf(stderr, "Total reads : %"PRIu64"\n", totalReads);
fprintf(stderr, "Filtered reads : %"PRIu64"\n", totalReads-okReads);
FreeRead(Read);
return EXIT_SUCCESS;
}
/*
* This application discards the FASTQ reads with the minimum number of \"N\" symbols.
* If present, it will erase the second header (after +).
*/
int main(int argc, char *argv[])
{
Read *Read = CreateRead(65536+GUARD, 65535+GUARD);
uint32_t sequenceSize = 0, N_counter = 0, globalIndex, index;
uint64_t okReads = 0, totalReads = 0;
int max_n_read = 0;
char *programName = argv[0];
struct argparse_option options[] = {
OPT_HELP(),
OPT_GROUP("Basic options"),
OPT_INTEGER('m', "max", &max_n_read, "The maximum of of \"N\" symbols in the read"),
OPT_BUFF('<', "input.fastq", "Input FASTQ file format (stdin)"),
OPT_BUFF('>', "output", "Output read information (stdout)"),
OPT_END(),
};
struct argparse argparse;
char usage[250] = "\nExample: ";
strcat(usage, programName);
strcat(usage, " < input.fastq > output\n"
"\nOutput example :\n"
"<FASTQ non-filtered reads>\n"
"Total reads : value\n"
"Filtered reads : value\n");
argparse_init(&argparse, options, NULL, programName, 0);
argparse_describe(&argparse, "\nIt discards the FASTQ reads with the minimum number of \"N\" symbols."
"If present, it will erase the second header (after +).", usage);
argc = argparse_parse(&argparse, argc, argv);
if(argc != 0)
argparse_help_cb(&argparse, options);
if(max_n_read <= 0 || max_n_read > UINT_MAX)
{
fprintf(stderr, "\nERROR: The number of \"N\" symbols most be a positive unsigned int!\n");
argparse_help_cb(&argparse, options);
exit(1);
}
// LOAD PARAMETERS
while(GetRead(stdin, Read))
{
sequenceSize = strlen((char *) Read->bases) - 1;
N_counter = 0;
for(globalIndex = 0 ; globalIndex < sequenceSize ; ++globalIndex)
if(Read->bases[globalIndex] == 'N')
++N_counter;
++totalReads;
// Evaluate to discard
if(N_counter > max_n_read) continue;
// Print read
fprintf(stdout, "@");
for(index = 0 ; index < strlen((char *) Read->header1) ; ++index)
fprintf(stdout, "%c", Read->header1[index]);
for(index = 0 ; index < globalIndex ; ++index)
fprintf(stdout, "%c", Read->bases[index]);
fprintf(stdout, "\n+\n");
for(index = 0 ; index < globalIndex ; ++index)
fprintf(stdout, "%c", Read->scores[index]);
fprintf(stdout, "\n");
++okReads;
}
fprintf(stderr, "Total reads : %"PRIu64"\n", totalReads);
fprintf(stderr, "Filtered reads : %"PRIu64"\n", totalReads-okReads);
FreeRead(Read);
return EXIT_SUCCESS;
}
