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- #include <nvbio/fastq/fastq.h>
- using namespace nvbio;
- namespace {
- struct Writer
- {
- Writer() : n(0) {}
- void push_back(const uint32 read_len, const char* name, const uint8* bp, const uint8* q)
- {
- #if 0
- if ((n & 0x00FF) == 0)
- {
- char read[16*1024];
- for (uint32 i = 0; i < read_len; ++i)
- read[i] = bp[i];
- read[read_len] = '\0';
- fprintf( stderr, " len: %u, read: %s\n", read_len, read );
- }
- #endif
- n++;
- }
- uint32 n;
- };
- }
- int fastq_test(const char* filename)
- {
- fprintf(stderr, "FASTQ test... started\n");
- FASTQ_file fastq_file( filename );
- if (fastq_file.valid() == false)
- {
- fprintf(stderr, "*** error *** : file \"%s\" not found\n", filename);
- return 1;
- }
- FASTQ_reader<FASTQ_file> fastq( fastq_file );
- Writer writer;
- int n;
- while ((n = fastq.read( 100u, writer )))
- {
- if (n < 0)
- {
- fprintf(stderr, "*** parsing error ***\n");
- char error[1024];
- fastq.error_string( error );
- fprintf(stderr, " %s\n", error);
- return 1;
- }
- }
- fprintf(stderr, "FASTQ test... done: %u reads\n", writer.n);
- return 0;
- }
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