db_file <- file.path("..", "data-tests", "test_seq.tsv")
fastq_file <- file.path("..", "data-tests", "test_seq.fastq")

# db_file <- file.path("tests", "data-tests", "test_seq.tsv")
# fastq_file <- file.path("tests", "data-tests", "test_seq.fastq")


test_that("readFastq: reads fastq and loads quality scores.", {
    
    expect_warning(
        db <- readChangeoDb(db_file),
        regexp="airr::read_rearrangement")

    db <- readFastqDb(db, fastq_file, quality_offset = -33, style="both", quality_sequence=T)
    
    expected_sequence_quality <- "90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,60,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90"
    expect_equal(db$quality_num, expected_sequence_quality)
    
    expected_sequence_phred <- "{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{]{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{"
    expect_equal(db$quality, expected_sequence_phred)
    
    expected_sequence_alignment_quality <- "90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,NA,NA,NA,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,90,90,90,90,90,90,90,90,90,90,60,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,NA,NA,NA,NA,NA,NA,NA,NA,NA,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,NA,NA,NA,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90,90"
    expect_equal(db[['quality_alignment_num']], expected_sequence_alignment_quality)
    
    expected_sequence_alignment_phred <- "{{{{{{{{{{{{{{{{{{{{{{{{{{{   {{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{            {{{{{{{{{{]{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{         {{{{{{{{{{{{{{{{{{{{{{{{{{{{{{   {{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{{"
    expect_equal(db[['quality_alignment']], expected_sequence_alignment_phred)
    
    quality <- sequenceAlignmentQuality(db, raw=TRUE)
    # Expect FALSE. Position 93 is an I, a gap in sequence_alignment, so it doesn't
    # exist in input sequence and will not exist in the positions data.frame
    expect_false(any(quality$sequence_alignment_position == 93))
    
    # Expect aligned position 194 be matched to sequence input position 272
    row <- which(quality$sequence_alignment_position == 194)
    expect_equal(quality$sequence_position[row], 272)
    
    # Input positions 263 to 271 have been removed in sequence_alignment.
    # As they are not part of the alignment, they should not exist in
    # the positions data.frame
    expect_true(all(c(263:271) %in% quality$sequence_position == FALSE))
    
})