/**
* @param read Read to generate k-mers from.
* @param bad_quality_threshold This class virtually cuts
* nucleotides with quality lower the threshold from the ends of the
* read.
*/
explicit ValidKMerGenerator(const Read &read,
uint8_t bad_quality_threshold = 2) {
Reset(read.getSequenceString().data(),
read.getQualityString().data(),
read.getSequenceString().size(),
bad_quality_threshold);
}
void TestIReadStreamFull() {
ireadstream ifs("./test/data/s_6_1.fastq.gz");
ASSERT(ifs.is_open());
Read r;
while (!ifs.eof()) {
ifs >> r;
}
ifs.close();
ASSERT_EQUAL("TEST/1", r.getName());
ASSERT_EQUAL("CATACGGGTTTCCGCCAGTNTTTCCATGCCGCGATGGACGTAGAACAGACGGTAGTCGGCGTCGATAATGTTTTCGCCATCGACGCACAGACGGAAGTGG", r.getSequenceString());
//ASSERT_EQUAL("HHHGHHGIHIHHEHHHHHGHHHHHHHHGHEHHHHDHAHHHA?HFHEFHEHHHGHGGHGG@B2BEBEF=HHGEEA:C?CCD?B@EF/4=2<4188.?BA5=", r.getQuality());
}
void TestIReadStreamSingleRead() {
ireadstream ifs("./test/data/s_6_1.fastq.gz");
ASSERT(ifs.is_open());
Read r;
ifs >> r;
ASSERT_EQUAL("EAS20_8_6_1_2_768/1", r.getName());
ASSERT_EQUAL("CAGCACAGAGGATATCGCTGTTACANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN", r.getSequenceString());
//ASSERT_EQUAL("HGHIHHHGHECHHHHHHHGGHHHHH###########################################################################", r.getQuality());
ifs >> r;
ASSERT_EQUAL("EAS20_8_6_1_2_1700/1", r.getName());
ASSERT_EQUAL("CTTGGTGCGGAACTGAAAAGTGGTANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN", r.getSequenceString());
//ASSERT_EQUAL("GGGGCGGGGEGGGGGBGAGF:CCCC###########################################################################", r.getQuality());
}
