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single-cell-genetics / cellSNP

Pileup biallelic SNPs from single-cell and bulk RNA-seq data
Apache License 2.0
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Fix using qqual and query_alignment_sequence #11

Closed hxj5 closed 4 years ago

hxj5 commented 4 years ago

Using qqual and query_alignment_sequence in pileup_bases() and fetch_bases() could cause error when CIGAR string includes the 'I' (Insertion) op.

With help of Cython, this pull request fixes the bug above by replacing qqual and query_alignment_sequence with two new functions called get_query_qualities and get_query_bases.