bioa.io.sam.reads_from_sam_quick
Utilities
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Parse aligned reads from SAM/BAM file.
sam_file : pysam.SamFile
The SAM/BAM file object.
reference : Bio.Seq
The reference sequence used for alignment.
align_start, align_stop, reads, ref : (int, int, list, Bio.Seq)
The alignment start, alignment stop, list of reads (str, int), and extended reference. Each (str, int) pair represents the read and its starting position.