Aligned BAM was converted with pysam, using .get_forward_sequence() and .get_forward_qualities() functions. The later returns array dtype instead of string and could lead to malformatted fq if not converted to string. Running seqtk subseq on malformatted file will not throw any error.
seqtk will fail silently with malformatted fq.
Aligned BAM was converted with pysam, using .get_forward_sequence() and .get_forward_qualities() functions. The later returns array dtype instead of string and could lead to malformatted fq if not converted to string. Running seqtk subseq on malformatted file will not throw any error.
Example FQ entry:
@SRR.ABC.123 AGGGCAATGTACTTCGTTCA..... +SRR.ABC.123 array('B', [3, 3, 3, 3, 2,....])