/** * @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()); }