5e2e73c8f504d2d794bb674aff116bcc64ec2f07,skbio/io/fastq.py,,_parse_quality_scores,#Any#Any#Any#Any#,480

Before Change

def _parse_quality_scores(fh, seq_len, variant, phred_offset):
    phred_scores = []
    qual_len = 0
    prev_was_blank = False
    for chunk in fh:
        chunk = chunk.strip()
        if chunk:
            if chunk.startswith("@") and qual_len == seq_len:
                return phred_scores, chunk
            else:
                if prev_was_blank:
                    raise FASTQFormatError("Found blank line within FASTQ "
                                           "record.")
                qual_len += len(chunk)

                if qual_len > seq_len:
                    raise FASTQFormatError(

After Change

    phred_scores = []
    qual_len = 0
    prev = "+"
    for chunk, line_number in _line_generator(fh):
        if chunk:
            if chunk.startswith("@") and qual_len == seq_len:
                return phred_scores, chunk

Instances